Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

A guide to the biogenesis and functions of endogenous small non-coding RNAs in animals

Subjects

Abstract

Small non-coding RNAs can be categorized into two main classes: structural RNAs and regulatory RNAs. Structural RNAs, which are abundant and ubiquitously expressed, have essential roles in the maturation of pre-mRNAs, modification of rRNAs and the translation of coding transcripts. By contrast, regulatory RNAs are often expressed in a developmental-specific, tissue-specific or cell-type-specific manner and exert precise control over gene expression. Reductions in cost and improvements in the accuracy of high-throughput RNA sequencing have led to the identification of many new small RNA species. In this Review, we provide a broad discussion of the genomic origins, biogenesis and functions of structural small RNAs, including tRNAs, small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNAs), vault RNAs (vtRNAs) and Y RNAs as well as their derived RNA fragments, and of regulatory small RNAs, such as microRNAs (miRNAs), endogenous small interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs), in animals.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Biogenesis and functions of tRNAs and tRNA-derived fragments.
Fig. 2: Biogenesis and functions of snRNAs and snRNA-derived fragments.
Fig. 3: Biogenesis and functions of snoRNAs and sdRNAs.
Fig. 4: Biogenesis and functions of vtRNAs and Y RNAs.
Fig. 5: Biogenesis and functions of miRNAs and endo-siRNAs.
Fig. 6: Biogenesis and functions of piRNAs.

Similar content being viewed by others

References

  1. Cech, T. R. & Steitz, J. A. The noncoding RNA revolution-trashing old rules to forge new ones. Cell 157, 77–94 (2014).

    Article  CAS  PubMed  Google Scholar 

  2. Lambert, M., Benmoussa, A. & Provost, P. Small non-coding RNAs derived from eukaryotic ribosomal RNA. Noncoding RNA 5, 16 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  3. Krishna, S. et al. Dynamic expression of tRNA-derived small RNAs define cellular states. EMBO Rep. 20, e47789 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  4. Taft, R. J. et al. Small RNAs derived from snoRNAs. RNA 15, 1233–1240 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Nicolas, F. E., Hall, A. E., Csorba, T., Turnbull, C. & Dalmay, T. Biogenesis of Y RNA-derived small RNAs is independent of the microRNA pathway. FEBS Lett. 586, 1226–1230 (2012).

    Article  CAS  PubMed  Google Scholar 

  6. Persson, H. et al. The non-coding RNA of the multidrug resistance-linked vault particle encodes multiple regulatory small RNAs. Nat. Cell Biol. 11, 1268–1271 (2009).

    Article  CAS  PubMed  Google Scholar 

  7. Kuscu, C. et al. tRNA fragments (tRFs) guide Ago to regulate gene expression post-transcriptionally in a Dicer-independent manner. RNA 24, 1093–1105 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Chen, Q. et al. Sperm tsRNAs contribute to intergenerational inheritance of an acquired metabolic disorder. Science 351, 397–400 (2016).

    Article  CAS  PubMed  Google Scholar 

  9. Kim, H. K. et al. A transfer-RNA-derived small RNA regulates ribosome biogenesis. Nature 552, 57–62 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Ender, C. et al. A human snoRNA with microRNA-like functions. Mol. Cell 32, 519–528 (2008).

    Article  CAS  PubMed  Google Scholar 

  11. Chakrabortty, S. K., Prakash, A., Nechooshtan, G., Hearn, S. & Gingeras, T. R. Extracellular vesicle-mediated transfer of processed and functional RNY5 RNA. RNA 21, 1966–1979 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Wilson, D. N. & Cate, J. H. D. The structure and function of the eukaryotic ribosome. Cold Spring Harb. Perspect. Biol. 4, a011536 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  13. Collins, L. & Penny, D. Complex spliceosomal organization ancestral to extant eukaryotes. Mol. Biol. Evol. 22, 1053–1066 (2005).

    Article  CAS  PubMed  Google Scholar 

  14. Hoeppner, M. P. & Poole, A. M. Comparative genomics of eukaryotic small nucleolar RNAs reveals deep evolutionary ancestry amidst ongoing intragenomic mobility. BMC Evol. Biol. 12, 183 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Shi, J. et al. PANDORA-seq expands the repertoire of regulatory small RNAs by overcoming RNA modifications. Nat. Cell Biol. 23, 424–436 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Mleczko, A. M. et al. Levels of sdRNAs in cytoplasm and their association with ribosomes are dependent upon stress conditions but independent from snoRNA expression. Sci. Rep. 9, 18397 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Suzuki, T. The expanding world of tRNA modifications and their disease relevance. Nat. Rev. Mol. Cell Biol. 22, 375–392 (2021).

    Article  CAS  PubMed  Google Scholar 

  18. Korostelev, A. A. The structural dynamics of translation. Annu. Rev. Biochem. 91, 245–267 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Weinmann, R. & Roeder, R. G. Role of DNA-dependent RNA polymerase 3 in the transcription of the tRNA and 5S RNA genes. Proc. Natl Acad. Sci. USA 71, 1790–1794 (1974).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Robertson, H. D., Altman, S. & Smith, J. D. Purification and properties of a specific Escherichia coli ribonuclease which cleaves a tyrosine transfer ribonucleic acid presursor. J. Biol. Chem. 247, 5243–5251 (1972).

    Article  CAS  PubMed  Google Scholar 

  21. Guerrier-Takada, C., Gardiner, K., Marsh, T., Pace, N. & Altman, S. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35, 849–857 (1983).

    Article  CAS  PubMed  Google Scholar 

  22. Garber, R. L. & Altman, S. In vitro processing of B. mori transfer RNA precursor molecules. Cell 17, 389–397 (1979).

    Article  CAS  PubMed  Google Scholar 

  23. Hagenbüchle, O., Larson, D., Hall, G. I. & Sprague, K. U. The primary transcription product of a silkworm alanine tRNA gene: identification of in vitro sites of initiation, termination and processing. Cell 18, 1217–1229 (1979).

    Article  PubMed  Google Scholar 

  24. Castaño, J. G., Tobian, J. A. & Zasloff, M. Purification and characterization of an endonuclease from Xenopus laevis ovaries which accurately processes the 3’ terminus of human pre-tRNA-Met(i) (3’ pre-tRNase). J. Biol. Chem. 260, 9002–9008 (1985).

    Article  PubMed  Google Scholar 

  25. Frendewey, D., Dingermann, T., Cooley, L. & Söll, D. Processing of precursor tRNAs in Drosophila. Processing of the 3’ end involves an endonucleolytic cleavage and occurs after 5’ end maturation. J. Biol. Chem. 260, 449–454 (1985).

    Article  CAS  PubMed  Google Scholar 

  26. Stefano, J. E. Purified lupus antigen La recognizes an oligouridylate stretch common to the 3’ termini of RNA polymerase III transcripts. Cell 36, 145–154 (1984).

    Article  CAS  PubMed  Google Scholar 

  27. Rinke, J. & Steitz, J. A. Precursor molecules of both human 5S ribosomal RNA and transfer RNAs are bound by a cellular protein reactive with anti-La lupus antibodies. Cell 29, 149–159 (1982).

    Article  CAS  PubMed  Google Scholar 

  28. Mathews, M. B. & Francoeur, A. M. La antigen recognizes and binds to the 3’-oligouridylate tail of a small RNA. Mol. Cell Biol. 4, 1134–1140 (1984).

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Yoo, C. J. & Wolin, S. L. The yeast La protein is required for the 3’ endonucleolytic cleavage that matures tRNA precursors. Cell 89, 393–402 (1997).

    Article  CAS  PubMed  Google Scholar 

  30. Chakshusmathi, G., Kim, S. D., Rubinson, D. A. & Wolin, S. L. A La protein requirement for efficient pre-tRNA folding. EMBO J. 22, 6562–6572 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Deutscher, M. P. Synthesis and functions of the -C-C-A terminus of transfer RNA. Prog. Nucleic Acid. Res. Mol. Biol. 13, 51–92 (1973).

    Article  CAS  PubMed  Google Scholar 

  32. Trotta, C. R. et al. The yeast tRNA splicing endonuclease: a tetrameric enzyme with two active site subunits homologous to the archaeal tRNA endonucleases. Cell 89, 849–858 (1997).

    Article  CAS  PubMed  Google Scholar 

  33. Paushkin, S. V., Patel, M., Furia, B. S., Peltz, S. W. & Trotta, C. R. Identification of a human endonuclease complex reveals a link between tRNA splicing and pre-mRNA 3’ end formation. Cell 117, 311–321 (2004).

    Article  CAS  PubMed  Google Scholar 

  34. Hayne, C. K. et al. Structural basis for pre-tRNA recognition and processing by the human tRNA splicing endonuclease complex. Nat. Struct. Mol. Biol. 30, 824–833 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Popow, J. et al. HSPC117 is the essential subunit of a human tRNA splicing ligase complex. Science 331, 760–764 (2011).

    Article  CAS  PubMed  Google Scholar 

  36. Holley, R. W. et al. Structure of a ribonucleic acid. Science 147, 1462–1465 (1965).

    Article  CAS  PubMed  Google Scholar 

  37. Kim, S. H. et al. Three-dimensional tertiary structure of yeast phenylalanine transfer RNA. Science 185, 435–440 (1974).

    Article  CAS  PubMed  Google Scholar 

  38. Phizicky, E. M. & Alfonzo, J. D. Do all modifications benefit all tRNAs. FEBS Lett. 584, 265–271 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Roundtree, I. A., Evans, M. E., Pan, T. & He, C. Dynamic RNA modifications in gene expression regulation. Cell 169, 1187–1200 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Yamasaki, S., Ivanov, P., Hu, G. F. & Anderson, P. Angiogenin cleaves tRNA and promotes stress-induced translational repression. J. Cell Biol. 185, 35–42 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Emara, M. M. et al. Angiogenin-induced tRNA-derived stress-induced RNAs promote stress-induced stress granule assembly. J. Biol. Chem. 285, 10959–10968 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Ivanov, P., Emara, M. M., Villen, J., Gygi, S. P. & Anderson, P. Angiogenin-induced tRNA fragments inhibit translation initiation. Mol. Cell 43, 613–623 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Sharma, U. et al. Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals. Science 351, 391–396 (2016).

    Article  CAS  PubMed  Google Scholar 

  44. Zhang, Y. et al. Angiogenin mediates paternal inflammation-induced metabolic disorders in offspring through sperm tsRNAs. Nat. Commun. 12, 6673 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Saxena, S. K., Rybak, S. M., Davey, R. T., Youle, R. J. & Ackerman, E. J. Angiogenin is a cytotoxic, tRNA-specific ribonuclease in the RNase A superfamily. J. Biol. Chem. 267, 21982–21986 (1992).

    Article  CAS  PubMed  Google Scholar 

  46. Saikia, M. et al. Genome-wide identification and quantitative analysis of cleaved tRNA fragments induced by cellular stress. J. Biol. Chem. 287, 42708–42725 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Czech, A., Wende, S., Mörl, M., Pan, T. & Ignatova, Z. Reversible and rapid transfer-RNA deactivation as a mechanism of translational repression in stress. PLoS Genet. 9, e1003767 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Shapiro, R., Riordan, J. F. & Vallee, B. L. Characteristic ribonucleolytic activity of human angiogenin. Biochemistry 25, 3527–3532 (1986).

    Article  CAS  PubMed  Google Scholar 

  49. Loveland, A. B., Koh, C. S., Ganesan, R., Jacobson, A. & Korostelev, A. A. Structural mechanism of angiogenin activation by the ribosome. Nature 630, 769–776 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Donovan, J., Rath, S., Kolet-Mandrikov, D. & Korennykh, A. Rapid RNase L-driven arrest of protein synthesis in the dsRNA response without degradation of translation machinery. RNA 23, 1660–1671 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Su, Z., Kuscu, C., Malik, A., Shibata, E. & Dutta, A. Angiogenin generates specific stress-induced tRNA halves and is not involved in tRF-3-mediated gene silencing. J. Biol. Chem. 294, 16930–16941 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Nechooshtan, G., Yunusov, D., Chang, K. & Gingeras, T. R. Processing by RNase 1 forms tRNA halves and distinct Y RNA fragments in the extracellular environment. Nucleic Acids Res. 48, 8035–8049 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Saikia, M. et al. Angiogenin-cleaved tRNA halves interact with cytochrome c, protecting cells from apoptosis during osmotic stress. Mol. Cell Biol. 34, 2450–2463 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  54. Durdevic, Z., Mobin, M. B., Hanna, K., Lyko, F. & Schaefer, M. The RNA methyltransferase Dnmt2 is required for efficient Dicer-2-dependent siRNA pathway activity in Drosophila. Cell Rep. 4, 931–937 (2013).

    Article  CAS  PubMed  Google Scholar 

  55. Haussecker, D. et al. Human tRNA-derived small RNAs in the global regulation of RNA silencing. RNA 16, 673–695 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Lee, Y. S., Shibata, Y., Malhotra, A. & Dutta, A. A novel class of small RNAs: tRNA-derived RNA fragments (tRFs). Genes Dev. 23, 2639–2649 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Liao, J. Y. et al. Deep sequencing of human nuclear and cytoplasmic small RNAs reveals an unexpectedly complex subcellular distribution of miRNAs and tRNA 3’ trailers. PLoS One 5, e10563 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  58. Kumar, P., Anaya, J., Mudunuri, S. B. & Dutta, A. Meta-analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets. BMC Biol. 12, 78 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  59. Goodarzi, H. et al. Endogenous tRNA-derived fragments suppress breast cancer progression via YBX1 displacement. Cell 161, 790–802 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Telonis, A. G. et al. Dissecting tRNA-derived fragment complexities using personalized transcriptomes reveals novel fragment classes and unexpected dependencies. Oncotarget 6, 24797–24822 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  61. Cole, C. et al. Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. RNA 15, 2147–2160 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Di Fazio, A., Schlackow, M., Pong, S. K., Alagia, A. & Gullerova, M. Dicer dependent tRNA derived small RNAs promote nascent RNA silencing. Nucleic Acids Res. 50, 1734–1752 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Babiarz, J. E., Ruby, J. G., Wang, Y., Bartel, D. P. & Blelloch, R. Mouse ES cells express endogenous shRNAs, siRNAs, and other microprocessor-independent, Dicer-dependent small RNAs. Genes Dev. 22, 2773–2785 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Li, Z. et al. Extensive terminal and asymmetric processing of small RNAs from rRNAs, snoRNAs, snRNAs, and tRNAs. Nucleic Acids Res. 40, 6787–6799 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Maute, R. L. et al. tRNA-derived microRNA modulates proliferation and the DNA damage response and is down-regulated in B cell lymphoma. Proc. Natl Acad. Sci. USA 110, 1404–1409 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Martinez, G., Choudury, S. G. & Slotkin, R. K. tRNA-derived small RNAs target transposable element transcripts. Nucleic Acids Res. 45, 5142–5152 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Schorn, A. J., Gutbrod, M. J., LeBlanc, C. & Martienssen, R. LTR-retrotransposon control by tRNA-derived small RNAs. Cell 170, 61–71.e11 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Guzzi, N. et al. Pseudouridylation of tRNA-derived fragments steers translational control in stem cells. Cell 173, 1204–1216.e26 (2018).

    Article  CAS  PubMed  Google Scholar 

  69. Luo, S. et al. Drosophila tsRNAs preferentially suppress general translation machinery via antisense pairing and participate in cellular starvation response. Nucleic Acids Res. 46, 5250–5268 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  70. Boskovic, A., Bing, X. Y., Kaymak, E. & Rando, O. J. Control of noncoding RNA production and histone levels by a 5’ tRNA fragment. Genes Dev. 34, 118–131 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Busch, H., Reddy, R., Rothblum, L. & Choi, Y. C. SnRNAs, SnRNPs, and RNA processing. Annu. Rev. Biochem. 51, 617–654 (1982).

    Article  CAS  PubMed  Google Scholar 

  72. Chen, W. & Moore, M. J. Spliceosomes. Curr. Biol. 25, R181–R183 (2015).

    Article  CAS  PubMed  Google Scholar 

  73. Yan, C., Wan, R. & Shi, Y. Molecular mechanisms of pre-mRNA splicing through structural biology of the spliceosome. Cold Spring Harb. Perspect. Biol. 11, a032409 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Jackson, L. J. A reappraisal of non-consensus mRNA splice sites. Nucleic Acids Res. 19, 3795–3798 (1991).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Hall, S. L. & Padgett, R. A. Conserved sequences in a class of rare eukaryotic nuclear introns with non-consensus splice sites. J. Mol. Biol. 239, 357–365 (1994).

    Article  CAS  PubMed  Google Scholar 

  76. Breathnach, R., Benoist, C., O’Hare, K., Gannon, F. & Chambon, P. Ovalbumin gene: evidence for a leader sequence in mRNA and DNA sequences at the exon-intron boundaries. Proc. Natl Acad. Sci. 75, 4853–4857 (1978).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Mount, S. M. A catalogue of splice junction sequences. Nucleic Acids Res. 10, 459–472 (1982).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Mowry, K. L. & Steitz, J. A. Identification of the human U7 snRNP as one of several factors involved in the 3′ end maturation of histone premessenger RNA’s. Science 238, 1682–1687 (1987).

    Article  CAS  PubMed  Google Scholar 

  79. Müller, B. & Schümperli, D. The U7 snRNP and the hairpin binding protein: key players in histone mRNA metabolism. Semin. Cell Dev. Biol. 8, 567–576 (1997).

    Article  PubMed  Google Scholar 

  80. Ideue, T. et al. U7 small nuclear ribonucleoprotein represses histone gene transcription in cell cycle-arrested cells. Proc. Natl Acad. Sci. USA 109, 5693–5698 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Dominski, Z. & Marzluff, W. F. Formation of the 3’ end of histone mRNA: getting closer to the end. Gene 396, 373–390 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Romeo, V. & Schümperli, D. Cycling in the nucleus: regulation of RNA 3’ processing and nuclear organization of replication-dependent histone genes. Curr. Opin. Cell Biol. 40, 23–31 (2016).

    Article  CAS  PubMed  Google Scholar 

  83. Kaida, D. et al. U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation. Nature 468, 664–668 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Berg, M. G. et al. U1 snRNP determines mRNA length and regulates isoform expression. Cell 150, 53–64 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Venters, C. C., Oh, J. M., Di, C., So, B. R. & Dreyfuss, G. U1 snRNP telescripting: suppression of premature transcription termination in introns as a new layer of gene regulation. Cold Spring Harb. Perspect. Biol. 11, a032235 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. O’Reilly, D. et al. Differentially expressed, variant U1 snRNAs regulate gene expression in human cells. Genome Res. 23, 281–291 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  87. Lindgren, V., Ares, M., Weiner, A. M. & Francke, U. Human genes for U2 small nuclear RNA map to a major adenovirus 12 modification site on chromosome 17. Nature 314, 115–116 (1985).

    Article  CAS  PubMed  Google Scholar 

  88. Tarn, W. Y., Yario, T. A. & Steitz, J. A. U12 snRNA in vertebrates: evolutionary conservation of 5’ sequences implicated in splicing of pre-mRNAs containing a minor class of introns. RNA 1, 644–656 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  89. Marz, M., Kirsten, T. & Stadler, P. F. Evolution of spliceosomal snRNA genes in metazoan animals. J. Mol. Evol. 67, 594–607 (2008).

    Article  CAS  PubMed  Google Scholar 

  90. Kunkel, G. R., Maser, R. L., Calvet, J. P. & Pederson, T. U6 small nuclear RNA is transcribed by RNA polymerase III. Proc. Natl Acad. Sci. USA 83, 8575–8579 (1986).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Henry, R. W., Mittal, V., Ma, B., Kobayashi, R. & Hernandez, N. SNAP19 mediates the assembly of a functional core promoter complex (SNAPc) shared by RNA polymerases II and III. Genes Dev. 12, 2664–2672 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Hung, K. H. & Stumph, W. E. Regulation of snRNA gene expression by the Drosophila melanogaster small nuclear RNA activating protein complex (DmSNAPc). Crit. Rev. Biochem. Mol. Biol. 46, 11–26 (2011).

    Article  CAS  PubMed  Google Scholar 

  93. Hernandez, N. & Weiner, A. M. Formation of the 3’ end of U1 snRNA requires compatible snRNA promoter elements. Cell 47, 249–258 (1986).

    Article  CAS  PubMed  Google Scholar 

  94. de Vegvar, H. E., Lund, E. & Dahlberg, J. E. 3’ end formation of U1 snRNA precursors is coupled to transcription from snRNA promoters. Cell 47, 259–266 (1986).

    Article  PubMed  Google Scholar 

  95. Cuello, P., Boyd, D. C., Dye, M. J., Proudfoot, N. J. & Murphy, S. Transcription of the human U2 snRNA genes continues beyond the 3’ box in vivo. EMBO J. 18, 2867–2877 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Baillat, D. et al. Integrator, a multiprotein mediator of small nuclear RNA processing, associates with the C-terminal repeat of RNA polymerase II. Cell 123, 265–276 (2005).

    Article  CAS  PubMed  Google Scholar 

  97. Lardelli, R. M. & Lykke-Andersen, J. Competition between maturation and degradation drives human snRNA 3′ end quality control. Genes Dev. 34, 989–1001 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Vidovic, I., Nottrott, S., Hartmuth, K., Lührmann, R. & Ficner, R. Crystal structure of the spliceosomal 15.5kD protein bound to a U4 snRNA fragment. Mol. Cell 6, 1331–1342 (2000).

    Article  CAS  PubMed  Google Scholar 

  99. Kondo, Y., Oubridge, C., van Roon, A.-M. M. & Nagai, K. Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5′ splice site recognition. eLife 4, e04986 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  100. Zhang, Z. et al. Molecular architecture of the human 17S U2 snRNP. Nature 583, 310–313 (2020).

    Article  CAS  PubMed  Google Scholar 

  101. Hallais, M. et al. CBC-ARS2 stimulates 3’-end maturation of multiple RNA families and favors cap-proximal processing. Nat. Struct. Mol. Biol. 20, 1358–1366 (2013).

    Article  CAS  PubMed  Google Scholar 

  102. Izumi, H., McCloskey, A., Shinmyozu, K. & Ohno, M. p54nrb/NonO and PSF promote U snRNA nuclear export by accelerating its export complex assembly. Nucleic Acids Res. 42, 3998–4007 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Ohno, M., Segref, A., Bachi, A., Wilm, M. & Mattaj, I. W. PHAX, a mediator of U snRNA nuclear export whose activity is regulated by phosphorylation. Cell 101, 187–198 (2000).

    Article  CAS  PubMed  Google Scholar 

  104. Fischer, U., Liu, Q. & Dreyfuss, G. The SMN-SIP1 complex has an essential role in spliceosomal snRNP biogenesis. Cell 90, 1023–1029 (1997).

    Article  CAS  PubMed  Google Scholar 

  105. Liu, Q., Fischer, U., Wang, F. & Dreyfuss, G. The spinal muscular atrophy disease gene product, SMN, and its associated protein SIP1 are in a complex with spliceosomal snRNP proteins. Cell 90, 1013–1021 (1997).

    Article  CAS  PubMed  Google Scholar 

  106. Charroux, B. et al. Gemin3: a novel DEAD box protein that interacts with SMN, the spinal muscular atrophy gene product, and is a component of gems. J. Cell Biol. 147, 1181–1194 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Charroux, B. et al. Gemin4. A novel component of the SMN complex that is found in both gems and nucleoli. J. Cell Biol. 148, 1177–1186 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Pellizzoni, L., Baccon, J., Rappsilber, J., Mann, M. & Dreyfuss, G. Purification of native survival of motor neurons complexes and identification of gemin6 as a novel component. J. Biol. Chem. 277, 7540–7545 (2002).

    Article  CAS  PubMed  Google Scholar 

  109. Baccon, J., Pellizzoni, L., Rappsilber, J., Mann, M. & Dreyfuss, G. Identification and characterization of gemin7, a novel component of the survival of motor neuron complex. J. Biol. Chem. 277, 31957–31962 (2002).

    Article  CAS  PubMed  Google Scholar 

  110. Gubitz, A. K. et al. Gemin5, a novel WD repeat protein component of the SMN complex that binds sm proteins. J. Biol. Chem. 277, 5631–5636 (2002).

    Article  CAS  PubMed  Google Scholar 

  111. Carissimi, C. et al. Unrip is a component of SMN complexes active in snRNP assembly. FEBS Lett. 579, 2348–2354 (2005).

    Article  CAS  PubMed  Google Scholar 

  112. Carissimi, C. et al. Gemin8 is a novel component of the survival motor neuron complex and functions in small nuclear ribonucleoprotein assembly. J. Biol. Chem. 281, 8126–8134 (2006).

    Article  CAS  PubMed  Google Scholar 

  113. Grimmler, M. et al. Unrip, a factor implicated in cap-independent translation, associates with the cytosolic SMN complex and influences its intracellular localization. Hum. Mol. Genet. 14, 3099–3111 (2005).

    Article  CAS  PubMed  Google Scholar 

  114. Pellizzoni, L., Yong, J. & Dreyfuss, G. Essential role for the SMN complex in the specificity of snRNP assembly. Science 298, 1775–1779 (2002).

    Article  CAS  PubMed  Google Scholar 

  115. Battle, D. J. et al. The gemin5 protein of the SMN complex identifies snRNAs. Mol. Cell 23, 273–279 (2006).

    Article  CAS  PubMed  Google Scholar 

  116. Golembe, T. J., Yong, J. & Dreyfuss, G. Specific sequence features, recognized by the SMN complex, identify snRNAs and determine their fate as snRNPs. Mol. Cell. Biol. 25, 10989–11004 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  117. Yong, J., Kasim, M., Bachorik, J. L., Wan, L. & Dreyfuss, G. Gemin5 delivers snRNA precursors to the SMN complex for snRNP biogenesis. Mol. Cell 38, 551–562 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. Yong, J. Sequence-specific interaction of U1 snRNA with the SMN complex. EMBO J. 21, 1188–1196 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Pánek, J. et al. The SMN complex drives structural changes in human snRNAs to enable snRNP assembly. Nat. Commun. 14, 6580 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  120. Fisher, D. E., Conner, G. E., Reeves, W. H., Wisniewolski, R. & Blobel, G. Small nuclear ribonucleoprotein particle assembly in vivo: demonstration of a 6S RNA-free core precursor and posttranslational modification. Cell 42, 751–758 (1985).

    Article  CAS  PubMed  Google Scholar 

  121. Chari, A. et al. An assembly chaperone collaborates with the SMN complex to generate spliceosomal SnRNPs. Cell 135, 497–509 (2008).

    Article  CAS  PubMed  Google Scholar 

  122. Zhang, R. et al. Structure of a key intermediate of the SMN complex reveals gemin2’s crucial function in snRNP assembly. Cell 146, 384–395 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  123. Grimm, C. et al. Structural basis of assembly chaperone-mediated snRNP formation. Mol. Cell 49, 692–703 (2013).

    Article  CAS  PubMed  Google Scholar 

  124. Brahms, H., Meheus, L., de Brabandere, V., Fischer, U. & Lührmann, R. Symmetrical dimethylation of arginine residues in spliceosomal Sm protein B/B′ and the Sm-like protein LSm4, and their interaction with the SMN protein. RNA 7, 1531–1542 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. Friesen, W. J., Massenet, S., Paushkin, S., Wyce, A. & Dreyfuss, G. SMN, the product of the spinal muscular atrophy gene, binds preferentially to dimethylarginine-containing protein targets. Mol. Cell 7, 1111–1117 (2001).

    Article  CAS  PubMed  Google Scholar 

  126. Friesen, W. J. et al. The methylosome, a 20S complex containing JBP1 and pICln, produces dimethylarginine-modified Sm proteins. Mol. Cell. Biol. 21, 8289–8300 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  127. Ogawa, C. et al. Role of survival motor neuron complex components in small nuclear ribonucleoprotein assembly. J. Biol. Chem. 284, 14609–14617 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. Mouaikel, J. et al. Interaction between the small‐nuclear‐RNA cap hypermethylase and the spinal muscular atrophy protein, survival of motor neuron. EMBO Rep. 4, 616–622 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. Ma, T., Xiong, E. S., Lardelli, R. M. & Lykke-Andersen, J. Sm complex assembly and 5′ cap trimethylation promote selective processing of snRNAs by the 3′ exonuclease TOE1. Proc. Natl Acad. Sci. USA 121, e2315259121 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  130. Palacios, I. Nuclear import of U snRNPs requires importin β. EMBO J. 16, 6783–6792 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  131. Huber, J. et al. Snurportin1, an m3G-cap-specific nuclear import receptor with a novel domain structure. EMBO J. 17, 4114–4126 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  132. Natalizio, A. H. & Matera, A. G. Identification and characterization of Drosophila Snurportin reveals a role for the import receptor Moleskin/importin-7 in snRNP biogenesis. Mol. Biol. Cell 24, 2932–2942 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  133. Darzacq, X. et al. Cajal body-specific small nuclear RNAs: a novel class of 2’-O-methylation and pseudouridylation guide RNAs. EMBO J. 21, 2746–2756 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  134. Jady, B. E. Modification of Sm small nuclear RNAs occurs in the nucleoplasmic Cajal body following import from the cytoplasm. EMBO J. 22, 1878–1888 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  135. Bizarro, J. et al. NUFIP and the HSP90/R2TP chaperone bind the SMN complex and facilitate assembly of U4-specific proteins. Nucleic Acids Res. 43, 8973–8989 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  136. Malinová, A. et al. Assembly of the U5 snRNP component PRPF8 is controlled by the HSP90/R2TP chaperones. J. Cell Biol. 216, 1579–1596 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  137. Cloutier, P. et al. R2TP/Prefoldin-like component RUVBL1/RUVBL2 directly interacts with ZNHIT2 to regulate assembly of U5 small nuclear ribonucleoprotein. Nat. Commun. 8, 15615 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  138. Yu, Y. T., Shu, M. D. & Steitz, J. A. Modifications of U2 snRNA are required for snRNP assembly and pre-mRNA splicing. EMBO J. 17, 5783–5795 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  139. Dönmez, G., Hartmuth, K. & Lührmann, R. Modified nucleotides at the 5’ end of human U2 snRNA are required for spliceosomal E-complex formation. RNA 10, 1925–1933 (2004).

    Article  PubMed  PubMed Central  Google Scholar 

  140. Newby, M. I. & Greenbaum, N. L. Sculpting of the spliceosomal branch site recognition motif by a conserved pseudouridine. Nat. Struct. Biol. 9, 958–965 (2002).

    Article  CAS  PubMed  Google Scholar 

  141. Jensen, E. G., Hellung-Larsen, P. & Frederiksen, S. Synthesis of low molecular weight RNA components A, C and D by polymerase II in α-amanitin-resistant hamster cells. Nucleic Acids Res. 6, 321–330 (1979).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  142. Roop, D. R., Kristo, P., Stumph, W. E., Tsai, M. J. & O’Malley, B. W. Structure and expression of a chicken gene coding for U1 RNA. Cell 23, 671–680 (1981).

    Article  CAS  PubMed  Google Scholar 

  143. Murphy, J. T., Burgess, R. R., Dahlberg, J. E. & Lund, E. Transcription of a gene for human U1 small nuclear RNA. Cell 29, 265–274 (1982).

    Article  CAS  PubMed  Google Scholar 

  144. Reddy, R., Henning, D., Das, G., Harless, M. & Wright, D. The capped U6 small nuclear RNA is transcribed by RNA polymerase III. J. Biol. Chem. 262, 75–81 (1987).

    Article  CAS  PubMed  Google Scholar 

  145. Krol, A., Carbon, P., Ebel, J.-P. & Appel, B. Xenopus tropicalis U6 snRNA genes transcribed by Pot III contain the upstream promoter elements used by pol II dependent U snRNA genes. Nucleic Acids Res. 15, 2463–2478 (1987).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  146. Das, G., Henning, D., Wright, D. & Reddy, R. Upstream regulatory elements are necessary and sufficient for transcription of a U6 RNA gene by RNA polymerase III. EMBO J. 7, 503–512 (1988).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  147. Kunkel, G. R. & Pederson, T. Upstream elements required for efficient transcription of a human U6 RNA gene resemble those of U1 and U2 genes even though a different polymerase is used. Genes Dev. 2, 196–204 (1988).

    Article  CAS  PubMed  Google Scholar 

  148. Tarn, W. Y. & Steitz, J. A. Highly diverged U4 and U6 small nuclear RNAs required for splicing rare AT-AC introns. Science 273, 1824–1832 (1996).

    Article  CAS  PubMed  Google Scholar 

  149. Rinke, J. & Steitz, J. A. Association of the lupus antigen La with a subset of U6 snRNA molecules. Nucleic Acids Res. 13, 2617–2629 (1985).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  150. Brow, D. A. & Guthrie, C. Spliceosomal RNA U6 is remarkably conserved from yeast to mammals. Nature 334, 213–218 (1988).

    Article  CAS  PubMed  Google Scholar 

  151. Karaduman, R., Fabrizio, P., Hartmuth, K., Urlaub, H. & Lührmann, R. RNA structure and RNA–protein interactions in purified yeast U6 snRNPs. J. Mol. Biol. 356, 1248–1262 (2006).

    Article  CAS  PubMed  Google Scholar 

  152. Bhattacharya, R., Perumal, K., Sinha, K., Maraia, R. & Reddy, R. Methylphosphate cap structure in small RNAs reduces the affinity of RNAs to La protein. Gene Expr. 10, 243–253 (2002).

    Article  CAS  PubMed  Google Scholar 

  153. Dong, G., Chakshusmathi, G., Wolin, S. L. & Reinisch, K. M. Structure of the La motif: a winged helix domain mediates RNA binding via a conserved aromatic patch. EMBO J. 23, 1000–1007 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  154. Singh, R. & Reddy, R. Gamma-monomethyl phosphate: a cap structure in spliceosomal U6 small nuclear RNA. Proc. Natl Acad. Sci. USA 86, 8280–8283 (1989).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  155. Mroczek, S. & Dziembowski, A. U6 RNA biogenesis and disease association. Wiley Interdiscip. Rev. RNA 4, 581–592 (2013).

    Article  CAS  PubMed  Google Scholar 

  156. Trippe, R. A highly specific terminal uridylyl transferase modifies the 3’-end of U6 small nuclear RNA. Nucleic Acids Res. 26, 3119–3126 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  157. Yamashita, S. & Tomita, K. Mechanism of U6 snRNA oligouridylation by human TUT1. Nat. Commun. 14, 4686 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  158. Mroczek, S. et al. C16orf57, a gene mutated in poikiloderma with neutropenia, encodes a putative phosphodiesterase responsible for the U6 snRNA 3′ end modification. Genes Dev. 26, 1911–1925 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  159. Hilcenko, C. et al. Aberrant 3′ oligoadenylation of spliceosomal U6 small nuclear RNA in poikiloderma with neutropenia. Blood 121, 1028–1038 (2013).

    Article  CAS  PubMed  Google Scholar 

  160. Licht, K., Medenbach, J., Lührmann, R., Kambach, C. & Bindereif, A. 3′-Cyclic phosphorylation of U6 snRNA leads to recruitment of recycling factor p110 through LSm proteins. RNA 14, 1532–1538 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  161. Achsel, T. A doughnut-shaped heteromer of human Sm-like proteins binds to the 3’-end of U6 snRNA, thereby facilitating U4/U6 duplex formation in vitro. EMBO J. 18, 5789–5802 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  162. Novotný, I. et al. Nuclear LSm8 affects number of cytoplasmic processing bodies via controlling cellular distribution of Like-Sm proteins. Mol. Biol. Cell 23, 3776–3785 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  163. Tycowski, K. T., You, Z.-H., Graham, P. J. & Steitz, J. A. Modification of U6 spliceosomal RNA is guided by other small RNAs. Mol. Cell 2, 629–638 (1998).

    Article  CAS  PubMed  Google Scholar 

  164. Ganot, P., Jády, B. E., Bortolin, M.-L., Darzacq, X. & Kiss, T. Nucleolar factors direct the 2′-O-ribose methylation and pseudouridylation of U6 spliceosomal RNA. Mol. Cell. Biol. 19, 6906–6917 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  165. Lange, T. S. & Gerbi, S. A. Transient nucleolar localization of U6 small nuclear RNA in Xenopus laevis oocytes. Mol. Biol. Cell 11, 2419–2428 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  166. Bell, M., Schreiner, S., Damianov, A., Reddy, R. & Bindereif, A. p110, a novel human U6 snRNP protein and U4/U6 snRNP recycling factor. EMBO J. 21, 2724–2735 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  167. Ghetti, A., Company, M. & Abelson, J. Specificity of Prp24 binding to RNA: a role for Prp24 in the dynamic interaction of U4 and U6 snRNAs. RNA 1, 132–145 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  168. Raghunathan, P. L. & Guthrie, C. A spliceosomal recycling factor that reanneals U4 and U6 small nuclear ribonucleoprotein particles. Science 279, 857–860 (1998).

    Article  CAS  PubMed  Google Scholar 

  169. Schaffert, N., Hossbach, M., Heintzmann, R., Achsel, T. & Lührmann, R. RNAi knockdown of hPrp31 leads to an accumulation of U4/U6 di-snRNPs in Cajal bodies. EMBO J. 23, 3000–3009 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  170. Makarova, O. V. Protein 61K, encoded by a gene (PRPF31) linked to autosomal dominant retinitis pigmentosa, is required for U4/U6middle dotU5 tri-snRNP formation and pre-mRNA splicing. EMBO J. 21, 1148–1157 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  171. Liu, S., Rauhut, R., Vornlocher, H.-P. & Lührmann, R. The network of protein–protein interactions within the human U4/U6.U5 tri-snRNP. RNA 12, 1418–1430 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  172. Will, C. L. & Luhrmann, R. Spliceosome structure and function. Cold Spring Harb. Perspect. Biol. 3, a003707 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  173. Liu, S. et al. A composite double-/single-stranded RNA-binding region in protein Prp3 supports tri-snRNP stability and splicing. eLife 4, e07320 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  174. Nguyen, T. H. D. et al. The architecture of the spliceosomal U4/U6.U5 tri-snRNP. Nature 523, 47–52 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  175. Agafonov, D. E. et al. Molecular architecture of the human U4/U6.U5 tri-snRNP. Science 351, 1416–1420 (2016).

    Article  CAS  PubMed  Google Scholar 

  176. Kawaji, H. et al. Hidden layers of human small RNAs. BMC Genomics 9, 157 (2008).

    Article  PubMed  PubMed Central  Google Scholar 

  177. Burroughs, A. M. et al. Deep-sequencing of human Argonaute-associated small RNAs provides insight into miRNA sorting and reveals Argonaute association with RNA fragments of diverse origin. RNA Biol. 8, 158–177 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  178. Chen, C. J. & Heard, E. Small RNAs derived from structural non-coding RNAs. Methods 63, 76–84 (2013).

    Article  CAS  PubMed  Google Scholar 

  179. Wang, H. et al. CPA-seq reveals small ncRNAs with methylated nucleosides and diverse termini. Cell Discov. 7, 25 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  180. Mesquita-Ribeiro, R. et al. Distinct small non-coding RNA landscape in the axons and released extracellular vesicles of developing primary cortical neurons and the axoplasm of adult nerves. RNA Biol. 18, 832–855 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  181. Yamakawa, N. et al. Novel functional small RNAs are selectively loaded onto mammalian Ago1. Nucleic Acids Res. 42, 5289–5301 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  182. Thomson, D. W. et al. Assessing the gene regulatory properties of Argonaute-bound small RNAs of diverse genomic origin. Nucleic Acids Res. 43, 470–481 (2015).

    Article  CAS  PubMed  Google Scholar 

  183. Tollervey, D. & Kiss, T. Function and synthesis of small nucleolar RNAs. Curr. Opin. Cell Biol. 9, 337–342 (1997).

    Article  CAS  PubMed  Google Scholar 

  184. Decatur, W. A. & Fournier, M. J. RNA-guided nucleotide modification of ribosomal and other RNAs. J. Biol. Chem. 278, 695–698 (2003).

    Article  CAS  PubMed  Google Scholar 

  185. Liang, X. H., Liu, Q. & Fournier, M. J. rRNA modifications in an intersubunit bridge of the ribosome strongly affect both ribosome biogenesis and activity. Mol. Cell 28, 965–977 (2007).

    Article  CAS  PubMed  Google Scholar 

  186. Liu, B., Liang, X. H., Piekna-Przybylska, D., Liu, Q. & Fournier, M. J. Mis-targeted methylation in rRNA can severely impair ribosome synthesis and activity. RNA Biol. 5, 249–254 (2008).

    Article  CAS  PubMed  Google Scholar 

  187. Esguerra, J., Warringer, J. & Blomberg, A. Functional importance of individual rRNA 2’-O-ribose methylations revealed by high-resolution phenotyping. RNA 14, 649–656 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  188. Liang, X. H., Liu, Q. & Fournier, M. J. Loss of rRNA modifications in the decoding center of the ribosome impairs translation and strongly delays pre-rRNA processing. RNA 15, 1716–1728 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  189. Karijolich, J. & Yu, Y. T. Spliceosomal snRNA modifications and their function. RNA Biol. 7, 192–204 (2010).

    Article  CAS  PubMed  Google Scholar 

  190. Jack, K. et al. rRNA pseudouridylation defects affect ribosomal ligand binding and translational fidelity from yeast to human cells. Mol. Cell 44, 660–666 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  191. Bratkovič, T., Božič, J. & Rogelj, B. Functional diversity of small nucleolar RNAs. Nucleic Acids Res. 48, 1627–1651 (2020).

    Article  PubMed  Google Scholar 

  192. Ikegami, K. & Lieb, J. D. Integral nuclear pore proteins bind to Pol III-transcribed genes and are required for Pol III transcript processing in C. elegans. Mol. Cell 51, 840–849 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  193. Tycowski, K. T., Shu, M. D. & Steitz, J. A. A small nucleolar RNA is processed from an intron of the human gene encoding ribosomal protein S3. Genes Dev. 7, 1176–1190 (1993).

    Article  CAS  PubMed  Google Scholar 

  194. Kiss, T. & Filipowicz, W. Small nucleolar RNAs encoded by introns of the human cell cycle regulatory gene RCC1. EMBO J. 12, 2913–2920 (1993).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  195. Kiss, T. & Filipowicz, W. Exonucleolytic processing of small nucleolar RNAs from pre-mRNA introns. Genes Dev. 9, 1411–1424 (1995).

    Article  CAS  PubMed  Google Scholar 

  196. Fragapane, P., Prislei, S., Michienzi, A., Caffarelli, E. & Bozzoni, I. A novel small nucleolar RNA (U16) is encoded inside a ribosomal protein intron and originates by processing of the pre-mRNA. EMBO J. 12, 2921–2928 (1993).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  197. Caffarelli, E. et al. Processing of the intron-encoded U16 and U18 snoRNAs: the conserved C and D boxes control both the processing reaction and the stability of the mature snoRNA. EMBO J. 15, 1121–1131 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  198. Watkins, N. J., Leverette, R. D., Xia, L., Andrews, M. T. & Maxwell, E. S. Elements essential for processing intronic U14 snoRNA are located at the termini of the mature snoRNA sequence and include conserved nucleotide boxes C and D. RNA 2, 118–133 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  199. Watkins, N. J., Newman, D. R., Kuhn, J. F. & Maxwell, E. S. In vitro assembly of the mouse U14 snoRNP core complex and identification of a 65-kDa box C/D-binding protein. RNA 4, 582–593 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  200. Lafontaine, D. L. & Tollervey, D. Nop58p is a common component of the box C+D snoRNPs that is required for snoRNA stability. RNA 5, 455–467 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  201. Xia, L., Watkins, N. J. & Maxwell, E. S. Identification of specific nucleotide sequences and structural elements required for intronic U14 snoRNA processing. RNA 3, 17–26 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  202. Samarsky, D. A., Fournier, M. J., Singer, R. H. & Bertrand, E. The snoRNA box C/D motif directs nucleolar targeting and also couples snoRNA synthesis and localization. EMBO J. 17, 3747–3757 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  203. Richard, P. et al. A common sequence motif determines the Cajal body-specific localization of box H/ACA scaRNAs. EMBO J. 22, 4283–4293 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  204. Tyc, K. & Steitz, J. A. U3, U8 and U13 comprise a new class of mammalian snRNPs localized in the cell nucleolus. EMBO J. 8, 3113–3119 (1989).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  205. Kiss-László, Z., Henry, Y., Bachellerie, J. P., Caizergues-Ferrer, M. & Kiss, T. Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs. Cell 85, 1077–1088 (1996).

    Article  PubMed  Google Scholar 

  206. Nicoloso, M., Qu, L. H., Michot, B. & Bachellerie, J. P. Intron-encoded, antisense small nucleolar RNAs: the characterization of nine novel species points to their direct role as guides for the 2’-O-ribose methylation of rRNAs. J. Mol. Biol. 260, 178–195 (1996).

    Article  CAS  PubMed  Google Scholar 

  207. Watkins, N. J. & Bohnsack, M. T. The box C/D and H/ACA snoRNPs: key players in the modification, processing and the dynamic folding of ribosomal RNA. Wiley Interdiscip. Rev. RNA 3, 397–414 (2012).

    Article  CAS  PubMed  Google Scholar 

  208. Watkins, N. J. et al. A common core RNP structure shared between the small nucleoar box C/D RNPs and the spliceosomal U4 snRNP. Cell 103, 457–466 (2000).

    Article  CAS  PubMed  Google Scholar 

  209. Watkins, N. J., Dickmanns, A. & Lührmann, R. Conserved stem II of the box C/D motif is essential for nucleolar localization and is required, along with the 15.5K protein, for the hierarchical assembly of the box C/D snoRNP. Mol. Cell. Biol. 22, 8342–8352 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  210. Szewczak, L. B., Gabrielsen, J. S., Degregorio, S. J., Strobel, S. A. & Steitz, J. A. Molecular basis for RNA kink-turn recognition by the h15.5K small RNP protein. RNA 11, 1407–1419 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  211. Tycowski, K. T., Smith, C. M., Shu, M. D. & Steitz, J. A. A small nucleolar RNA requirement for site-specific ribose methylation of rRNA in Xenopus. Proc. Natl Acad. Sci. USA 93, 14480–14485 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  212. Kiss-László, Z., Henry, Y. & Kiss, T. Sequence and structural elements of methylation guide snoRNAs essential for site-specific ribose methylation of pre-rRNA. EMBO J. 17, 797–807 (1998).

    Article  PubMed  PubMed Central  Google Scholar 

  213. Cahill, N. M. Site-specific cross-linking analyses reveal an asymmetric protein distribution for a box C/D snoRNP. EMBO J. 21, 3816–3828 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  214. Szewczak, L. B. W., DeGregorio, S. J., Strobel, S. A. & Steitz, J. A. Exclusive interaction of the 15.5 kD protein with the terminal box C/D motif of a methylation guide snoRNP. Chem. Biol. 9, 1095–1107 (2002).

    Article  CAS  PubMed  Google Scholar 

  215. Qu, G., van Nues, R. W., Watkins, N. J. & Maxwell, E. S. The spatial-functional coupling of box C/D and C′/D′ RNPs is an evolutionarily conserved feature of the eukaryotic box C/D snoRNP nucleotide modification complex. Mol. Cell. Biol. 31, 365–374 (2011).

    Article  CAS  PubMed  Google Scholar 

  216. Balakin, A. G., Smith, L. & Fournier, M. J. The RNA world of the nucleolus: two major families of small RNAs defined by different box elements with related functions. Cell 86, 823–834 (1996).

    Article  CAS  PubMed  Google Scholar 

  217. Kiss, T., Bortolin, M. L. & Filipowicz, W. Characterization of the intron-encoded U19 RNA, a new mammalian small nucleolar RNA that is not associated with fibrillarin. Mol. Cell Biol. 16, 1391–1400 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  218. Ganot, P., Caizergues-Ferrer, M. & Kiss, T. The family of box ACA small nucleolar RNAs is defined by an evolutionarily conserved secondary structure and ubiquitous sequence elements essential for RNA accumulation. Genes Dev. 11, 941–956 (1997).

    Article  CAS  PubMed  Google Scholar 

  219. Girard, J. P. et al. GAR1 is an essential small nucleolar RNP protein required for pre-rRNA processing in yeast. EMBO J. 11, 673–682 (1992).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  220. Bousquet-Antonelli, C. A small nucleolar RNP protein is required for pseudouridylation of eukaryotic ribosomal RNAs. EMBO J. 16, 4770–4776 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  221. Henras, A. et al. Nhp2p and Nop10p are essential for the function of H/ACA snoRNPs. EMBO J. 17, 7078–7090 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  222. Lafontaine, D. L. J., Bousquet-Antonelli, C., Henry, Y., Caizergues-Ferrer, M. & Tollervey, D. The box H+ACA snoRNAs carry Cbf5p, the putative rRNA pseudouridine synthase. Genes Dev. 12, 527–537 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  223. Watkins, N. J. et al. Cbf5p, a potential pseudouridine synthase, and Nhp2p, a putative RNA-binding protein, are present together with Gar1p in all H BOX/ACA-motif snoRNPs and constitute a common bipartite structure. RNA 4, 1549–1568 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  224. Meier, U. T. RNA modification in Cajal bodies. RNA Biol. 14, 693–700 (2017).

    Article  PubMed  Google Scholar 

  225. Hirose, T., Ninomiya, K., Nakagawa, S. & Yamazaki, T. A guide to membraneless organelles and their various roles in gene regulation. Nat. Rev. Mol. Cell Biol. 24, 288–304 (2023).

    Article  CAS  PubMed  Google Scholar 

  226. Reichow, S. L., Hamma, T., Ferré-D’Amaré, A. R. & Varani, G. The structure and function of small nucleolar ribonucleoproteins. Nucleic Acids Res. 35, 1452–1464 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  227. Ganot, P., Bortolin, M. L. & Kiss, T. Site-specific pseudouridine formation in preribosomal RNA is guided by small nucleolar RNAs. Cell 89, 799–809 (1997).

    Article  CAS  PubMed  Google Scholar 

  228. Bortolin, M. L., Ganot, P. & Kiss, T. Elements essential for accumulation and function of small nucleolar RNAs directing site-specific pseudouridylation of ribosomal RNAs. EMBO J. 18, 457–469 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  229. Matera, A. G., Terns, R. M. & Terns, M. P. Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs. Nat. Rev. Mol. Cell Biol. 8, 209–220 (2007).

    Article  CAS  PubMed  Google Scholar 

  230. Deryusheva, S. & Gall, J. G. scaRNAs and snoRNAs: are they limited to specific classes of substrate RNAs. RNA 25, 17–22 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  231. Kishore, S. & Stamm, S. The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C. Science 311, 230–232 (2006).

    Article  CAS  PubMed  Google Scholar 

  232. Huang, C. et al. A snoRNA modulates mRNA 3’ end processing and regulates the expression of a subset of mRNAs. Nucleic Acids Res. 45, 8647–8660 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  233. Falaleeva, M. et al. Dual function of C/D box small nucleolar RNAs in rRNA modification and alternative pre-mRNA splicing. Proc. Natl Acad. Sci. USA 113, E1625–E1634 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  234. Kass, S., Tyc, K., Steitz, J. A. & Sollner-Webb, B. The U3 small nucleolar ribonucleoprotein functions in the first step of preribosomal RNA processing. Cell 60, 897–908 (1990).

    Article  CAS  PubMed  Google Scholar 

  235. Hughes, J. M. & Ares, M. Depletion of U3 small nucleolar RNA inhibits cleavage in the 5′ external transcribed spacer of yeast pre-ribosomal RNA and impairs formation of 18S ribosomal RNA. EMBO J. 10, 4231–4239 (1991).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  236. Savino, R. & Gerbi, S. A. In vivo disruption of Xenopus U3 snRNA affects ribosomal RNA processing. EMBO J. 9, 2299–2308 (1990).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  237. Beltrame, M. & Tollervey, D. Base pairing between U3 and the pre-ribosomal RNA is required for 18S rRNA synthesis. EMBO J. 14, 4350–4356 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  238. Peculis, B. A. & Steitz, J. A. Disruption of U8 nucleolar snRNA inhibits 5.8S and 28S rRNA processing in the Xenopus oocyte. Cell 73, 1233–1245 (1993).

    Article  CAS  PubMed  Google Scholar 

  239. Peculis, B. A. & Steitz, J. A. Sequence and structural elements critical for U8 snRNP function in Xenopus oocytes are evolutionarily conserved. Genes Dev. 8, 2241–2255 (1994).

    Article  CAS  PubMed  Google Scholar 

  240. Srivastava, L., Lapik, Y. R., Wang, M. & Pestov, D. G. Mammalian DEAD box protein Ddx51 acts in 3′ end maturation of 28S rRNA by promoting the release of U8 snoRNA. Mol. Cell. Biol. 30, 2947–2956 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  241. Scott, M. S., Avolio, F., Ono, M., Lamond, A. I. & Barton, G. J. Human miRNA precursors with box H/ACA snoRNA features. PLoS Comput. Biol. 5, e1000507 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  242. Ono, M. et al. Identification of human miRNA precursors that resemble box C/D snoRNAs. Nucleic Acids Res. 39, 3879–3891 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  243. Brameier, M., Herwig, A., Reinhardt, R., Walter, L. & Gruber, J. Human box C/D snoRNAs with miRNA like functions: expanding the range of regulatory RNAs. Nucleic Acids Res. 39, 675–686 (2011).

    Article  CAS  PubMed  Google Scholar 

  244. Scott, M. S. et al. Human box C/D snoRNA processing conservation across multiple cell types. Nucleic Acids Res. 40, 3676–3688 (2012).

    Article  CAS  PubMed  Google Scholar 

  245. Macias, S. et al. DGCR8 HITS-CLIP reveals novel functions for the Microprocessor. Nat. Struct. Mol. Biol. 19, 760–766 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  246. Macias, S., Cordiner, R. A., Gautier, P., Plass, M. & Cáceres, J. F. DGCR8 acts as an adaptor for the exosome complex to degrade double-stranded structured RNAs. Mol. Cell 60, 873–885 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  247. Ono, M. et al. Analysis of human small nucleolar RNAs (snoRNA) and the development of snoRNA modulator of gene expression vectors. Mol. Biol. Cell 21, 1569–1584 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  248. Kishore, S. et al. The snoRNA MBII-52 (SNORD 115) is processed into smaller RNAs and regulates alternative splicing. Hum. Mol. Genet. 19, 1153–1164 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  249. Kedersha, N. L. & Rome, L. H. Isolation and characterization of a novel ribonucleoprotein particle: large structures contain a single species of small RNA. J. Cell Biol. 103, 699–709 (1986).

    Article  CAS  PubMed  Google Scholar 

  250. Berger, W., Steiner, E., Grusch, M., Elbling, L. & Micksche, M. Vaults and the major vault protein: novel roles in signal pathway regulation and immunity. Cell Mol. Life Sci. 66, 43–61 (2009).

    Article  CAS  PubMed  Google Scholar 

  251. Kedersha, N. L., Miquel, M. C., Bittner, D. & Rome, L. H. Vaults. II. Ribonucleoprotein structures are highly conserved among higher and lower eukaryotes. J. Cell Biol. 110, 895–901 (1990).

    Article  CAS  PubMed  Google Scholar 

  252. Rome, L., Kedersha, N. & Chugani, D. Unlocking vaults: organelles in search of a function. Trends Cell Biol. 1, 47–50 (1991).

    Article  CAS  PubMed  Google Scholar 

  253. Vasu, S. K., Kedersha, N. L. & Rome, L. H. cDNA cloning and disruption of the major vault protein α gene (mvpA) in Dictyostelium discoideum. J. Biol. Chem. 268, 15356–15360 (1993).

    Article  CAS  PubMed  Google Scholar 

  254. Herrmann, C., Zimmermann, H. & Volknandt, W. Analysis of a cDNA encoding the major vault protein from the electric ray Discopyge ommata. Gene 188, 85–90 (1997).

    Article  CAS  PubMed  Google Scholar 

  255. Mossink, M. et al. The genomic sequence of the murine major vault protein and its promoter. Gene 294, 225–232 (2002).

    Article  CAS  PubMed  Google Scholar 

  256. Suprenant, K. A., Bloom, N., Fang, J. & Lushington, G. The major vault protein is related to the toxic anion resistance protein (TelA) family. J. Exp. Biol. 210, 946–955 (2007).

    Article  CAS  PubMed  Google Scholar 

  257. Stadler, P. F. et al. Evolution of vault RNAs. Mol. Biol. Evol. 26, 1975–1991 (2009).

    Article  CAS  PubMed  Google Scholar 

  258. Hamill, D. R. & Suprenant, K. A. Characterization of the sea urchin major vault protein: a possible role for vault ribonucleoprotein particles in nucleocytoplasmic transport. Dev. Biol. 190, 117–128 (1997).

    Article  CAS  PubMed  Google Scholar 

  259. Kickhoefer, V. A. et al. Vaults are up-regulated in multidrug-resistant cancer cell lines. J. Biol. Chem. 273, 8971–8974 (1998).

    Article  CAS  PubMed  Google Scholar 

  260. Kim, E. et al. Crosstalk between Src and major vault protein in epidermal growth factor-dependent cell signalling. FEBS J. 273, 793–804 (2006).

    Article  CAS  PubMed  Google Scholar 

  261. van Zon, A., Mossink, M. H., Scheper, R. J., Sonneveld, P. & Wiemer, E. A. The vault complex. Cell Mol. Life Sci. 60, 1828–1837 (2003).

    Article  PubMed  PubMed Central  Google Scholar 

  262. Slesina, M. et al. Movement of vault particles visualized by GFP-tagged major vault protein. Cell Tissue Res. 324, 403–410 (2006).

    Article  CAS  PubMed  Google Scholar 

  263. Slesina, M., Inman, E. M., Rome, L. H. & Volknandt, W. Nuclear localization of the major vault protein in U373 cells. Cell Tissue Res. 321, 97–104 (2005).

    Article  CAS  PubMed  Google Scholar 

  264. van Zon, A. et al. Vault mobility depends in part on microtubules and vaults can be recruited to the nuclear envelope. Exp. Cell Res. 312, 245–255 (2006).

    PubMed  Google Scholar 

  265. van Zon, A. et al. The formation of vault-tubes: a dynamic interaction between vaults and vault PARP. J. Cell Sci. 116, 4391–4400 (2003).

    Article  PubMed  Google Scholar 

  266. Kitazono, M. et al. Multidrug resistance and the lung resistance-related protein in human colon carcinoma SW-620 cells. J. Natl Cancer Inst. 91, 1647–1653 (1999).

    Article  CAS  PubMed  Google Scholar 

  267. Herrmann, C., Golkaramnay, E., Inman, E., Rome, L. & Volknandt, W. Recombinant major vault protein is targeted to neuritic tips of PC12 cells. J. Cell Biol. 144, 1163–1172 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  268. Herrmann, C., Volknandt, W., Wittich, B., Kellner, R. & Zimmermann, H. The major vault protein (MVP100) is contained in cholinergic nerve terminals of electric ray electric organ. J. Biol. Chem. 271, 13908–13915 (1996).

    Article  CAS  PubMed  Google Scholar 

  269. Li, J. Y. et al. Axonal transport of ribonucleoprotein particles (vaults). Neuroscience 91, 1055–1065 (1999).

    Article  CAS  PubMed  Google Scholar 

  270. Abbondanza, C. et al. Interaction of vault particles with estrogen receptor in the MCF-7 breast cancer cell. J. Cell Biol. 141, 1301–1310 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  271. Chugani, D. C., Rome, L. H. & Kedersha, N. L. Evidence that vault ribonucleoprotein particles localize to the nuclear pore complex. J. Cell Sci. 106, 23–29 (1993).

    Article  CAS  PubMed  Google Scholar 

  272. Chung, J. H., Ginn-Pease, M. E. & Eng, C. Phosphatase and tensin homologue deleted on chromosome 10 (PTEN) has nuclear localization signal-like sequences for nuclear import mediated by major vault protein. Cancer Res. 65, 4108–4116 (2005).

    Article  CAS  PubMed  Google Scholar 

  273. Ryu, S. J. et al. On the role of major vault protein in the resistance of senescent human diploid fibroblasts to apoptosis. Cell Death Differ. 15, 1673–1680 (2008).

    Article  CAS  PubMed  Google Scholar 

  274. Shimamoto, Y. et al. Direct activation of the human major vault protein gene by DNA-damaging agents. Oncol. Rep. 15, 645–652 (2006).

    CAS  PubMed  Google Scholar 

  275. Kowalski, M. P. et al. Host resistance to lung infection mediated by major vault protein in epithelial cells. Science 317, 130–132 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  276. Rome, L. H. & Kickhoefer, V. A. Development of the vault particle as a platform technology. ACS Nano 7, 889–902 (2013).

    Article  CAS  PubMed  Google Scholar 

  277. Kong, L. B., Siva, A. C., Kickhoefer, V. A., Rome, L. H. & Stewart, P. L. RNA location and modeling of a WD40 repeat domain within the vault. RNA 6, 890–900 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  278. Kedersha, N. L., Heuser, J. E., Chugani, D. C. & Rome, L. H. Vaults. III. Vault ribonucleoprotein particles open into flower-like structures with octagonal symmetry. J. Cell Biol. 112, 225–235 (1991).

    Article  CAS  PubMed  Google Scholar 

  279. Nandy, C. et al. Epstein-Barr virus-induced expression of a novel human vault RNA. J. Mol. Biol. 388, 776–784 (2009).

    Article  CAS  PubMed  Google Scholar 

  280. Lee, K. et al. Precursor miR-886, a novel noncoding RNA repressed in cancer, associates with PKR and modulates its activity. RNA 17, 1076–1089 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  281. Amort, M. et al. Expression of the vault RNA protects cells from undergoing apoptosis. Nat. Commun. 6, 7030 (2015).

    Article  CAS  PubMed  Google Scholar 

  282. Li, F. et al. Robust expression of vault RNAs induced by influenza A virus plays a critical role in suppression of PKR-mediated innate immunity. Nucleic Acids Res. 43, 10321–10337 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  283. Horos, R. et al. The small non-coding vault RNA1-1 acts as a riboregulator of autophagy. Cell 176, 1054–1067.e12 (2019).

    Article  CAS  PubMed  Google Scholar 

  284. Kickhoefer, V. A. et al. Vault ribonucleoprotein particles from rat and bullfrog contain a related small RNA that is transcribed by RNA polymerase III. J. Biol. Chem. 268, 7868–7873 (1993).

    Article  CAS  PubMed  Google Scholar 

  285. Schramm, L. & Hernandez, N. Recruitment of RNA polymerase III to its target promoters. Genes Dev. 16, 2593–2620 (2002).

    Article  CAS  PubMed  Google Scholar 

  286. Kickhoefer, V. A., Poderycki, M. J., Chan, E. K. L. & Rome, L. H. The La RNA-binding protein interacts with the vault RNA and is a vault-associated protein. J. Biol. Chem. 277, 41282–41286 (2002).

    Article  CAS  PubMed  Google Scholar 

  287. van Zon, A. et al. Multiple human vault RNAs. Expression and association with the vault complex. J. Biol. Chem. 276, 37715–37721 (2001).

    Article  PubMed  Google Scholar 

  288. Mrázek, J., Kreutmayer, S. B., Grässer, F. A., Polacek, N. & Hüttenhofer, A. Subtractive hybridization identifies novel differentially expressed ncRNA species in EBV-infected human B cells. Nucleic Acids Res. 35, e73 (2007).

    Article  PubMed  PubMed Central  Google Scholar 

  289. Kickhoefer, V. A., Emre, N., Stephen, A. G., Poderycki, M. J. & Rome, L. H. Identification of conserved vault RNA expression elements and a non-expressed mouse vault RNA gene. Gene 309, 65–70 (2003).

    Article  CAS  PubMed  Google Scholar 

  290. Vilalta, A., Kickhoefer, V. A., Rome, L. H. & Johnson, D. L. The rat vault RNA gene contains a unique RNA polymerase III promoter composed of both external and internal elements that function synergistically. J. Biol. Chem. 269, 29752–29759 (1994).

    Article  CAS  PubMed  Google Scholar 

  291. Nolte-’t Hoen, E. N. et al. Deep sequencing of RNA from immune cell-derived vesicles uncovers the selective incorporation of small non-coding RNA biotypes with potential regulatory functions. Nucleic Acids Res. 40, 9272–9285 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  292. Miñones-Moyano, E. et al. Upregulation of a small vault RNA (svtRNA2-1a) is an early event in Parkinson disease and induces neuronal dysfunction. RNA Biol. 10, 1093–1106 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  293. Fort, R. S., Garat, B., Sotelo-Silveira, J. R. & Duhagon, M. A. vtRNA2-1/nc886 produces a small RNA that contributes to its tumor suppression action through the microRNA pathway in prostate cancer. Noncoding RNA 6, 7 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  294. Hussain, S. et al. NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs. Cell Rep. 4, 255–261 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  295. Sajini, A. A. et al. Loss of 5-methylcytosine alters the biogenesis of vault-derived small RNAs to coordinate epidermal differentiation. Nat. Commun. 10, 2550 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  296. Lerner, M. R., Boyle, J. A., Hardin, J. A. & Steitz, J. A. Two novel classes of small ribonucleoproteins detected by antibodies associated with lupus erythematosus. Science 211, 400–402 (1981).

    Article  CAS  PubMed  Google Scholar 

  297. Wolin, S. L. & Steitz, J. A. Genes for two small cytoplasmic Ro RNAs are adjacent and appear to be single-copy in the human genome. Cell 32, 735–744 (1983).

    Article  CAS  PubMed  Google Scholar 

  298. Maraia, R. J., Sasaki-Tozawa, N., Driscoll, C. T., Green, E. D. & Darlington, G. J. The human Y4 small cytoplasmic RNA gene is controlled by upstream elements and resides on chromosome 7 with all other hY scRNA genes. Nucleic Acids Res. 22, 3045–3052 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  299. Maraia, R., Sakulich, A. L., Brinkmann, E. & Green, E. D. Gene encoding human Ro-associated autoantigen Y5 RNA. Nucleic Acids Res. 24, 3552–3559 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  300. Hendrick, J. P., Wolin, S. L., Rinke, J., Lerner, M. R. & Steitz, J. A. Ro small cytoplasmic ribonucleoproteins are a subclass of La ribonucleoproteins: further characterization of the Ro and La small ribonucleoproteins from uninfected mammalian cells. Mol. Cell Biol. 1, 1138–1149 (1981).

    CAS  PubMed  PubMed Central  Google Scholar 

  301. Pruijn, G. J., Slobbe, R. L. & van Venrooij, W. J. Analysis of protein-RNA interactions within Ro ribonucleoprotein complexes. Nucleic Acids Res. 19, 5173–5180 (1991).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  302. Simons, F. H., Rutjes, S. A., van Venrooij, W. J. & Pruijn, G. J. The interactions with Ro60 and La differentially affect nuclear export of hY1 RNA. RNA 2, 264–273 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  303. Wolin, S. L. & Cedervall, T. The La protein. Annu. Rev. Biochem. 71, 375–403 (2002).

    Article  CAS  PubMed  Google Scholar 

  304. O’Brien, C. A., Margelot, K. & Wolin, S. L. Xenopus Ro ribonucleoproteins: members of an evolutionarily conserved class of cytoplasmic ribonucleoproteins. Proc. Natl Acad. Sci. USA 90, 7250–7254 (1993).

    Article  PubMed  PubMed Central  Google Scholar 

  305. Van Horn, D. J., Eisenberg, D., O’Brien, C. A. & Wolin, S. L. Caenorhabditis elegans embryos contain only one major species of Ro RNP. RNA 1, 293–303 (1995).

    PubMed  PubMed Central  Google Scholar 

  306. Mosig, A., Guofeng, M., Stadler, B. M. & Stadler, P. F. Evolution of the vertebrate Y RNA cluster. Theory Biosci. 126, 9–14 (2007).

    Article  CAS  PubMed  Google Scholar 

  307. Perreault, J., Perreault, J. P. & Boire, G. Ro-associated Y RNAs in metazoans: evolution and diversification. Mol. Biol. Evol. 24, 1678–1689 (2007).

    Article  CAS  PubMed  Google Scholar 

  308. Boria, I. et al. Nematode sbRNAs: homologs of vertebrate Y RNAs. J. Mol. Evol. 70, 346–358 (2010).

    Article  CAS  PubMed  Google Scholar 

  309. Duarte Junior, F. F. et al. Identification and molecular structure analysis of a new noncoding RNA, a sbRNA homolog, in the silkworm Bombyx mori genome. Mol. Biosyst. 11, 801–808 (2015).

    Article  CAS  PubMed  Google Scholar 

  310. Teunissen, S. W. et al. Conserved features of Y RNAs: a comparison of experimentally derived secondary structures. Nucleic Acids Res. 28, 610–619 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  311. Wolin, S. L. & Steitz, J. A. The Ro small cytoplasmic ribonucleoproteins: identification of the antigenic protein and its binding site on the Ro RNAs. Proc. Natl Acad. Sci. USA 81, 1996–2000 (1984).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  312. Green, C. D., Long, K. S., Shi, H. & Wolin, S. L. Binding of the 60-kDa Ro autoantigen to Y RNAs: evidence for recognition in the major groove of a conserved helix. RNA 4, 750–765 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  313. Rutjes, S. A. et al. Identification of a novel cis-acting RNA element involved in nuclear export of hY RNAs. RNA 7, 741–752 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  314. Sim, S. et al. The zipcode-binding protein ZBP1 influences the subcellular location of the Ro 60-kDa autoantigen and the noncoding Y3 RNA. RNA 18, 100–110 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  315. Gendron, M., Roberge, D. & Boire, G. Heterogeneity of human Ro ribonucleoproteins (RNPs): nuclear retention of Ro RNPS containing the human hY5 RNA in human and mouse cells. Clin. Exp. Immunol. 125, 162–168 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  316. O’Brien, C. A. & Wolin, S. L. A possible role for the 60-kD Ro autoantigen in a discard pathway for defective 5S rRNA precursors. Genes Dev. 8, 2891–2903 (1994).

    Article  PubMed  Google Scholar 

  317. Shi, H., O’Brien, C. A., Van Horn, D. J. & Wolin, S. L. A misfolded form of 5S rRNA is complexed with the Ro and La autoantigens. RNA 2, 769–784 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  318. Chen, X. et al. The Ro autoantigen binds misfolded U2 small nuclear RNAs and assists mammalian cell survival after UV irradiation. Curr. Biol. 13, 2206–2211 (2003).

    Article  CAS  PubMed  Google Scholar 

  319. Fuchs, G., Stein, A. J., Fu, C., Reinisch, K. M. & Wolin, S. L. Structural and biochemical basis for misfolded RNA recognition by the Ro autoantigen. Nat. Struct. Mol. Biol. 13, 1002–1009 (2006).

    Article  CAS  PubMed  Google Scholar 

  320. Stein, A. J., Fuchs, G., Fu, C., Wolin, S. L. & Reinisch, K. M. Structural insights into RNA quality control: the Ro autoantigen binds misfolded RNAs via its central cavity. Cell 121, 529–539 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  321. Christov, C. P., Gardiner, T. J., Szüts, D. & Krude, T. Functional requirement of noncoding Y RNAs for human chromosomal DNA replication. Mol. Cell Biol. 26, 6993–7004 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  322. Gardiner, T. J., Christov, C. P., Langley, A. R. & Krude, T. A conserved motif of vertebrate Y RNAs essential for chromosomal DNA replication. RNA 15, 1375–1385 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  323. Krude, T., Christov, C. P., Hyrien, O. & Marheineke, K. Y RNA functions at the initiation step of mammalian chromosomal DNA replication. J. Cell Sci. 122, 2836–2845 (2009).

    Article  CAS  PubMed  Google Scholar 

  324. Zhang, A. T. et al. Dynamic interaction of Y RNAs with chromatin and initiation proteins during human DNA replication. J. Cell Sci. 124, 2058–2069 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  325. Collart, C., Christov, C. P., Smith, J. C. & Krude, T. The midblastula transition defines the onset of Y RNA-dependent DNA replication in Xenopus laevis. Mol. Cell Biol. 31, 3857–3870 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  326. Kowalski, M. P., Baylis, H. A. & Krude, T. Non-coding stem-bulge RNAs are required for cell proliferation and embryonic development in C. elegans. J. Cell Sci. 128, 2118–2129 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  327. Köhn, M., Ihling, C., Sinz, A., Krohn, K. & Hüttelmaier, S. The Y3** ncRNA promotes the 3’ end processing of histone mRNAs. Genes Dev. 29, 1998–2003 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  328. Shi, Y. et al. Molecular architecture of the human pre-mRNA 3′ processing complex. Mol. Cell 33, 365–376 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  329. Sun, Y. et al. Structure of an active human histone pre-mRNA 3’-end processing machinery. Science 367, 700–703 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  330. Tebaldi, T. et al. HuD is a neural translation enhancer acting on mtorc1-responsive genes and counteracted by the Y3 small non-coding RNA. Mol. Cell 71, 256–270.e10 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  331. Rutjes, S. A., van der Heijden, A., Utz, P. J., van Venrooij, W. J. & Pruijn, G. J. Rapid nucleolytic degradation of the small cytoplasmic Y RNAs during apoptosis. J. Biol. Chem. 274, 24799–24807 (1999).

    Article  CAS  PubMed  Google Scholar 

  332. Meiri, E. et al. Discovery of microRNAs and other small RNAs in solid tumors. Nucleic Acids Res. 38, 6234–6246 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  333. Verhagen, A. P. & Pruijn, G. J. Are the Ro RNP-associated Y RNAs concealing microRNAs? Y RNA-derived miRNAs may be involved in autoimmunity. Bioessays 33, 674–682 (2011).

    Article  CAS  PubMed  Google Scholar 

  334. Dhahbi, J. M. et al. 5’-YRNA fragments derived by processing of transcripts from specific YRNA genes and pseudogenes are abundant in human serum and plasma. Physiol. Genomics 45, 990–998 (2013).

    Article  CAS  PubMed  Google Scholar 

  335. Dhahbi, J. M., Spindler, S. R., Atamna, H., Boffelli, D. & Martin, D. I. Deep sequencing of serum small RNAs identifies patterns of 5’ tRNA half and YRNA fragment expression associated with breast cancer. Biomark. Cancer 6, 37–47 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  336. Vojtech, L. et al. Exosomes in human semen carry a distinctive repertoire of small non-coding RNAs with potential regulatory functions. Nucleic Acids Res. 42, 7290–7304 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  337. Langenberger, D., Çakir, M. V., Hoffmann, S. & Stadler, P. F. Dicer-processed small RNAs: rules and exceptions. J. Exp. Zool. B Mol. Dev. Evol. 320, 35–46 (2013).

    Article  CAS  PubMed  Google Scholar 

  338. Billmeier, M. et al. Mechanistic insights into non-coding Y RNA processing. RNA Biol. 19, 468–480 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  339. Seroussi, U. et al. A comprehensive survey of C. elegans argonaute proteins reveals organism-wide gene regulatory networks and functions. eLife 12, e83853 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  340. Parker, J. S., Parizotto, E. A., Wang, M., Roe, S. M. & Barford, D. Enhancement of the seed-target recognition step in RNA silencing by a PIWI/MID domain protein. Mol. Cell 33, 204–214 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  341. Schirle, N. T. & MacRae, I. J. The crystal structure of human Argonaute2. Science 336, 1037–1040 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  342. Anzelon, T. A. et al. Structural basis for piRNA targeting. Nature 597, 285–289 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  343. Lee, Y. et al. MicroRNA genes are transcribed by RNA polymerase II. EMBO J. 23, 4051–4060 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  344. Cai, X., Hagedorn, C. H. & Cullen, B. R. Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA 10, 1957–1966 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  345. Han, J. et al. Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell 125, 887–901 (2006).

    Article  CAS  PubMed  Google Scholar 

  346. Nguyen, T. A. et al. Functional anatomy of the human microprocessor. Cell 161, 1374–1387 (2015).

    Article  CAS  PubMed  Google Scholar 

  347. Quick-Cleveland, J. et al. The DGCR8 RNA-binding heme domain recognizes primary microRNAs by clamping the hairpin. Cell Rep. 7, 1994–2005 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  348. Kwon, S. C. et al. Structure of human DROSHA. Cell 164, 81–90 (2016).

    Article  CAS  PubMed  Google Scholar 

  349. Partin, A. C. et al. Cryo-EM structures of human drosha and DGCR8 in complex with primary microRNA. Mol. Cell 78, 411–422.e4 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  350. Auyeung, V. C., Ulitsky, I., McGeary, S. E. & Bartel, D. P. Beyond secondary structure: primary-sequence determinants license pri-miRNA hairpins for processing. Cell 152, 844–858 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  351. Fernandez, N. et al. Genetic variation and RNA structure regulate microRNA biogenesis. Nat. Commun. 8, 15114 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  352. Nguyen, T. A., Park, J., Dang, T. L., Choi, Y. G. & Kim, V. N. Microprocessor depends on hemin to recognize the apical loop of primary microRNA. Nucleic Acids Res. 46, 5726–5736 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  353. Dang, T. L. et al. Select amino acids in DGCR8 are essential for the UGU-pri-miRNA interaction and processing. Commun. Biol. 3, 344 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  354. Kim, K., Nguyen, T. D., Li, S. & Nguyen, T. A. SRSF3 recruits DROSHA to the basal junction of primary microRNAs. RNA 24, 892–898 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  355. Fang, W. & Bartel, D. P. The menu of features that define primary microRNAs and enable de novo design of microRNA genes. Mol. Cell 60, 131–145 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  356. Roden, C. et al. Novel determinants of mammalian primary microRNA processing revealed by systematic evaluation of hairpin-containing transcripts and human genetic variation. Genome Res. 27, 374–384 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  357. Kwon, S. C. et al. Molecular basis for the single-nucleotide precision of primary microRNA processing. Mol. Cell 73, 505–518.e5 (2019).

    Article  CAS  PubMed  Google Scholar 

  358. Li, S., Nguyen, T. D., Nguyen, T. L. & Nguyen, T. A. Mismatched and wobble base pairs govern primary microRNA processing by human Microprocessor. Nat. Commun. 11, 1926 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  359. Rice, G. M., Shivashankar, V., Ma, E. J., Baryza, J. L. & Nutiu, R. Functional atlas of primary miRNA maturation by the microprocessor. Mol. Cell 80, 892–902.e4 (2020).

    Article  CAS  PubMed  Google Scholar 

  360. Jin, W., Wang, J., Liu, C. P., Wang, H. W. & Xu, R. M. Structural basis for pri-miRNA recognition by Drosha. Mol. Cell 78, 423–433.e5 (2020).

    Article  CAS  PubMed  Google Scholar 

  361. Li, S., Le, T. N., Nguyen, T. D., Trinh, T. A. & Nguyen, T. A. Bulges control pri-miRNA processing in a position and strand-dependent manner. RNA Biol. 18, 1716–1726 (2021).

    Article  CAS  PubMed  Google Scholar 

  362. Kim, K. et al. A quantitative map of human primary microRNA processing sites. Mol. Cell 81, 3422–3439.e11 (2021).

    Article  CAS  PubMed  Google Scholar 

  363. Kang, W. et al. MapToCleave: high-throughput profiling of microRNA biogenesis in living cells. Cell Rep. 37, 110015 (2021).

    Article  CAS  PubMed  Google Scholar 

  364. Nguyen, T. L., Nguyen, T. D., Ngo, M. K. & Nguyen, T. A. Dissection of the Caenorhabditis elegans Microprocessor. Nucleic Acids Res. 51, 1512–1527 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  365. Lee, Y. et al. The nuclear RNase III Drosha initiates microRNA processing. Nature 425, 415–419 (2003).

    Article  CAS  PubMed  Google Scholar 

  366. Denli, A. M., Tops, B. B., Plasterk, R. H., Ketting, R. F. & Hannon, G. J. Processing of primary microRNAs by the microprocessor complex. Nature 432, 231–235 (2004).

    Article  CAS  PubMed  Google Scholar 

  367. Gregory, R. I. et al. The Microprocessor complex mediates the genesis of microRNAs. Nature 432, 235–240 (2004).

    Article  CAS  PubMed  Google Scholar 

  368. Han, J. et al. The Drosha-DGCR8 complex in primary microRNA processing. Genes Dev. 18, 3016–3027 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  369. Lund, E., Güttinger, S., Calado, A., Dahlberg, J. E. & Kutay, U. Nuclear export of microRNA precursors. Science 303, 95–98 (2004).

    Article  CAS  PubMed  Google Scholar 

  370. Bohnsack, M. T., Czaplinski, K. & Gorlich, D. Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs. RNA 10, 185–191 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  371. Yi, R., Qin, Y., Macara, I. G. & Cullen, B. R. Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev. 17, 3011–3016 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  372. Büssing, I., Yang, J. S., Lai, E. C. & Grosshans, H. The nuclear export receptor XPO-1 supports primary miRNA processing in C. elegans and Drosophila. EMBO J. 29, 1830–1839 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  373. Grishok, A. et al. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 106, 23–34 (2001).

    Article  CAS  PubMed  Google Scholar 

  374. Hutvágner, G. et al. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293, 834–838 (2001).

    Article  PubMed  Google Scholar 

  375. Knight, S. W. & Bass, B. L. A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science 293, 2269–2271 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  376. Zhang, H., Kolb, F. A., Jaskiewicz, L., Westhof, E. & Filipowicz, W. Single processing center models for human Dicer and bacterial RNase III. Cell 118, 57–68 (2004).

    Article  CAS  PubMed  Google Scholar 

  377. Macrae, I. J. et al. Structural basis for double-stranded RNA processing by Dicer. Science 311, 195–198 (2006).

    Article  CAS  PubMed  Google Scholar 

  378. Vermeulen, A. et al. The contributions of dsRNA structure to Dicer specificity and efficiency. RNA 11, 674–682 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  379. Zhang, H., Kolb, F. A., Brondani, V., Billy, E. & Filipowicz, W. Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP. EMBO J. 21, 5875–5885 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  380. Tian, Y. et al. A phosphate-binding pocket within the platform-PAZ-connector helix cassette of human Dicer. Mol. Cell 53, 606–616 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  381. Tsutsumi, A., Kawamata, T., Izumi, N., Seitz, H. & Tomari, Y. Recognition of the pre-miRNA structure by Drosophila Dicer-1. Nat. Struct. Mol. Biol. 18, 1153–1158 (2011).

    Article  CAS  PubMed  Google Scholar 

  382. Gu, S. et al. The loop position of shRNAs and pre-miRNAs is critical for the accuracy of dicer processing in vivo. Cell 151, 900–911 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  383. Liu, Z. et al. Cryo-EM structure of human dicer and its complexes with a pre-miRNA substrate. Cell 173, 1191–1203.e12 (2018).

    Article  CAS  PubMed  Google Scholar 

  384. Luo, Q. J. et al. RNA structure probing reveals the structural basis of Dicer binding and cleavage. Nat. Commun. 12, 3397 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  385. Jouravleva, K. et al. Structural basis of microRNA biogenesis by Dicer-1 and its partner protein Loqs-PB. Mol. Cell 82, 4049–4063.e6 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  386. Nguyen, T. D., Trinh, T. A., Bao, S. & Nguyen, T. A. Secondary structure RNA elements control the cleavage activity of DICER. Nat. Commun. 13, 2138 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  387. Lee, Y. Y., Lee, H., Kim, H., Kim, V. N. & Roh, S. H. Structure of the human DICER-pre-miRNA complex in a dicing state. Nature 615, 331–338 (2023).

    Article  CAS  PubMed  Google Scholar 

  388. Lee, Y. Y., Kim, H. & Kim, V. N. Sequence determinant of small RNA production by DICER. Nature 615, 323–330 (2023).

    Article  CAS  PubMed  Google Scholar 

  389. Shang, R., Lee, S., Senavirathne, G. & Lai, E. C. microRNAs in action: biogenesis, function and regulation. Nat. Rev. Genet. 24, 816–833 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  390. Iwasaki, S. et al. Hsc70/Hsp90 chaperone machinery mediates ATP-dependent RISC loading of small RNA duplexes. Mol. Cell 39, 292–299 (2010).

    Article  CAS  PubMed  Google Scholar 

  391. Miyoshi, T., Takeuchi, A., Siomi, H. & Siomi, M. C. A direct role for Hsp90 in pre-RISC formation in Drosophila. Nat. Struct. Mol. Biol. 17, 1024–1026 (2010).

    Article  CAS  PubMed  Google Scholar 

  392. Tsuboyama, K., Tadakuma, H. & Tomari, Y. Conformational activation of argonaute by distinct yet coordinated actions of the Hsp70 and Hsp90 chaperone systems. Mol. Cell 70, 722–729.e4 (2018).

    Article  CAS  PubMed  Google Scholar 

  393. Naruse, K., Matsuura-Suzuki, E., Watanabe, M., Iwasaki, S. & Tomari, Y. In vitro reconstitution of chaperone-mediated human RISC assembly. RNA 24, 6–11 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  394. Khvorova, A., Reynolds, A. & Jayasena, S. D. Functional siRNAs and miRNAs exhibit strand bias. Cell 115, 209–216 (2003).

    Article  CAS  PubMed  Google Scholar 

  395. Schwarz, D. S. et al. Asymmetry in the assembly of the RNAi enzyme complex. Cell 115, 199–208 (2003).

    Article  CAS  PubMed  Google Scholar 

  396. Frank, F., Sonenberg, N. & Nagar, B. Structural basis for 5′-nucleotide base-specific recognition of guide RNA by human AGO2. Nature 465, 818–822 (2010).

    Article  CAS  PubMed  Google Scholar 

  397. Suzuki, H. I. et al. Small-RNA asymmetry is directly driven by mammalian Argonautes. Nat. Struct. Mol. Biol. 22, 512–521 (2015).

    Article  CAS  PubMed  Google Scholar 

  398. Lau, N. C., Lim, L. P., Weinstein, E. G. & Bartel, D. P. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294, 858–862 (2001).

    Article  CAS  PubMed  Google Scholar 

  399. Ghildiyal, M., Xu, J., Seitz, H., Weng, Z. & Zamore, P. D. Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway. RNA 16, 43–56 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  400. Hu, H. Y. et al. Sequence features associated with microRNA strand selection in humans and flies. BMC Genomics 10, 413 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  401. Ameres, S. L., Hung, J. H., Xu, J., Weng, Z. & Zamore, P. D. Target RNA-directed tailing and trimming purifies the sorting of endo-siRNAs between the two Drosophila Argonaute proteins. RNA 17, 54–63 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  402. Matranga, C., Tomari, Y., Shin, C., Bartel, D. P. & Zamore, P. D. Passenger-strand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes. Cell 123, 607–620 (2005).

    Article  CAS  PubMed  Google Scholar 

  403. Rand, T. A., Petersen, S., Du, F. & Wang, X. Argonaute2 cleaves the anti-guide strand of siRNA during RISC activation. Cell 123, 621–629 (2005).

    Article  CAS  PubMed  Google Scholar 

  404. Miyoshi, K., Tsukumo, H., Nagami, T., Siomi, H. & Siomi, M. C. Slicer function of Drosophila Argonautes and its involvement in RISC formation. Genes Dev. 19, 2837–2848 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  405. Shin, C. Cleavage of the star strand facilitates assembly of some microRNAs into Ago2-containing silencing complexes in mammals. Molecules Cell 26, 308–313 (2008).

    Article  CAS  Google Scholar 

  406. Bouasker, S. & Simard, M. J. The slicing activity of miRNA-specific Argonautes is essential for the miRNA pathway in C elegans. Nucleic Acids Res. 40, 10452–10462 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  407. Zinovyeva, A. Y., Veksler-Lublinsky, I., Vashisht, A. A., Wohlschlegel, J. A. & Ambros, V. R. Caenorhabditis elegans ALG-1 antimorphic mutations uncover functions for Argonaute in microRNA guide strand selection and passenger strand disposal. Proc. Natl Acad. Sci. USA 112, E5271–E5280 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  408. Kwak, P. B. & Tomari, Y. The N domain of Argonaute drives duplex unwinding during RISC assembly. Nat. Struct. Mol. Biol. 19, 145–151 (2012).

    Article  CAS  PubMed  Google Scholar 

  409. Park, J. H. & Shin, C. Slicer-independent mechanism drives small-RNA strand separation during human RISC assembly. Nucleic Acids Res. 43, 9418–9433 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  410. Tomari, Y., Du, T. & Zamore, P. D. Sorting of Drosophila small silencing RNAs. Cell 130, 299–308 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  411. Kawamata, T., Seitz, H. & Tomari, Y. Structural determinants of miRNAs for RISC loading and slicer-independent unwinding. Nat. Struct. Mol. Biol. 16, 953–960 (2009).

    Article  CAS  PubMed  Google Scholar 

  412. Yoda, M. et al. ATP-dependent human RISC assembly pathways. Nat. Struct. Mol. Biol. 17, 17–23 (2010).

    Article  CAS  PubMed  Google Scholar 

  413. Gu, S., Jin, L., Huang, Y., Zhang, F. & Kay, M. A. Slicing-independent RISC activation requires the argonaute PAZ domain. Curr. Biol. 22, 1536–1542 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  414. Moran, Y. et al. Cnidarian microRNAs frequently regulate targets by cleavage. Genome Res. 24, 651–663 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  415. Yekta, S., Shih, I. H. & Bartel, D. P. MicroRNA-directed cleavage of HOXB8 mRNA. Science 304, 594–596 (2004).

    Article  CAS  PubMed  Google Scholar 

  416. Davis, E. et al. RNAi-mediated allelic trans-interaction at the imprinted Rtl1/Peg11 locus. Curr. Biol. 15, 743–749 (2005).

    Article  CAS  PubMed  Google Scholar 

  417. Shin, C. et al. Expanding the microRNA targeting code: functional sites with centered pairing. Mol. Cell 38, 789–802 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  418. Karginov, F. V. et al. Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases. Mol. Cell 38, 781–788 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  419. Park, J. H. et al. Degradome sequencing reveals an endogenous microRNA target in C. elegans. FEBS Lett. 587, 964–969 (2013).

    Article  CAS  PubMed  Google Scholar 

  420. Lewis, B. P., Burge, C. B. & Bartel, D. P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15–20 (2005).

    Article  CAS  PubMed  Google Scholar 

  421. Ding, L., Spencer, A., Morita, K. & Han, M. The developmental timing regulator AIN-1 interacts with miRISCs and may target the argonaute protein ALG-1 to cytoplasmic P bodies in C. elegans. Mol. Cell 19, 437–447 (2005).

    Article  CAS  PubMed  Google Scholar 

  422. Rehwinkel, J., Behm-Ansmant, I., Gatfield, D. & Izaurralde, E. A crucial role for GW182 and the DCP1:DCP2 decapping complex in miRNA-mediated gene silencing. RNA 11, 1640–1647 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  423. Chen, C. Y., Zheng, D., Xia, Z. & Shyu, A. B. Ago-TNRC6 triggers microRNA-mediated decay by promoting two deadenylation steps. Nat. Struct. Mol. Biol. 16, 1160–1166 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  424. Fabian, M. R. et al. Mammalian miRNA RISC recruits CAF1 and PABP to affect PABP-dependent deadenylation. Mol. Cell 35, 868–880 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  425. Braun, J. E., Huntzinger, E., Fauser, M. & Izaurralde, E. GW182 proteins directly recruit cytoplasmic deadenylase complexes to miRNA targets. Mol. Cell 44, 120–133 (2011).

    Article  CAS  PubMed  Google Scholar 

  426. Chekulaeva, M. et al. miRNA repression involves GW182-mediated recruitment of CCR4-NOT through conserved W-containing motifs. Nat. Struct. Mol. Biol. 18, 1218–1226 (2011).

    Article  CAS  PubMed  Google Scholar 

  427. Fabian, M. R. et al. miRNA-mediated deadenylation is orchestrated by GW182 through two conserved motifs that interact with CCR4-NOT. Nat. Struct. Mol. Biol. 18, 1211–1217 (2011).

    Article  CAS  PubMed  Google Scholar 

  428. Mathys, H. et al. Structural and biochemical insights to the role of the CCR4-NOT complex and DDX6 ATPase in microRNA repression. Mol. Cell 54, 751–765 (2014).

    Article  CAS  PubMed  Google Scholar 

  429. Jonas, S. & Izaurralde, E. Towards a molecular understanding of microRNA-mediated gene silencing. Nat. Rev. Genet. 16, 421–433 (2015).

    Article  CAS  PubMed  Google Scholar 

  430. Bartel, D. P. Metazoan microRNAs. Cell 173, 20–51 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  431. Baek, D. et al. The impact of microRNAs on protein output. Nature 455, 64–71 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  432. Seitz, H. Redefining microRNA targets. Curr. Biol. 19, 870–873 (2009).

    Article  CAS  PubMed  Google Scholar 

  433. Friedman, R. C., Farh, K. K.-H., Burge, C. B. & Bartel, D. P. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 19, 92–105 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  434. Grimson, A. et al. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol. Cell 27, 91–105 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  435. Saetrom, P. et al. Distance constraints between microRNA target sites dictate efficacy and cooperativity. Nucleic Acids Res. 35, 2333–2342 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  436. Broderick, J. A., Salomon, W. E., Ryder, S. P., Aronin, N. & Zamore, P. D. Argonaute protein identity and pairing geometry determine cooperativity in mammalian RNA silencing. RNA 17, 1858–1869 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  437. Mukherji, S. et al. MicroRNAs can generate thresholds in target gene expression. Nat. Genet. 43, 854–859 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  438. Brennecke, J., Stark, A., Russell, R. B. & Cohen, S. M. Principles of microRNA-target recognition. PLoS Biol. 3, e85 (2005).

    Article  PubMed  PubMed Central  Google Scholar 

  439. Doench, J. G. & Sharp, P. A. Specificity of microRNA target selection in translational repression. Genes Dev. 18, 504–511 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  440. Vella, M. C., Choi, E. Y., Lin, S. Y., Reinert, K. & Slack, F. J. The C. elegans microRNA let-7 binds to imperfect let-7 complementary sites from the lin-41 3’UTR. Genes Dev. 18, 132–137 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  441. Wee, L. M., Flores-Jasso, C. F., Salomon, W. E. & Zamore, P. D. Argonaute divides its RNA guide into domains with distinct functions and RNA-binding properties. Cell 151, 1055–1067 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  442. Moore, M. J. et al. miRNA-target chimeras reveal miRNA 3’-end pairing as a major determinant of Argonaute target specificity. Nat. Commun. 6, 8864 (2015).

    Article  CAS  PubMed  Google Scholar 

  443. Salomon, W. E., Jolly, S. M., Moore, M. J., Zamore, P. D. & Serebrov, V. Single-molecule imaging reveals that argonaute reshapes the binding properties of its nucleic acid guides. Cell 162, 84–95 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  444. Broughton, J. P., Lovci, M. T., Huang, J. L., Yeo, G. W. & Pasquinelli, A. E. Pairing beyond the seed supports microRNA targeting specificity. Mol. Cell 64, 320–333 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  445. Sheu-Gruttadauria, J., Xiao, Y., Gebert, L. F. & MacRae, I. J. Beyond the seed: structural basis for supplementary microRNA targeting by human Argonaute2. EMBO J. 38, e101153 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  446. Becker, W. R. et al. High-throughput analysis reveals rules for target RNA binding and cleavage by AGO2. Mol. Cell 75, 741–755.e11 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  447. McGeary, S. E., Bisaria, N., Pham, T. M., Wang, P. Y. & Bartel, D. P. MicroRNA 3’-compensatory pairing occurs through two binding modes, with affinity shaped by nucleotide identity and position. eLife 11, e69803 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  448. Duan, Y., Veksler-Lublinsky, I. & Ambros, V. Critical contribution of 3’ non-seed base pairing to the in vivo function of the evolutionarily conserved let-7a microRNA. Cell Rep. 39, 110745 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  449. Pinzón, N. et al. microRNA target prediction programs predict many false positives. Genome Res. 27, 234–245 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  450. Seitz, H. Issues in current microRNA target identification methods. RNA Biol. 14, 831–834 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  451. Yang, N. & Kazazian, H. H. L1 retrotransposition is suppressed by endogenously encoded small interfering RNAs in human cultured cells. Nat. Struct. Mol. Biol. 13, 763–771 (2006).

    Article  CAS  PubMed  Google Scholar 

  452. Ghildiyal, M. et al. Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells. Science 320, 1077–1081 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  453. Czech, B. et al. An endogenous small interfering RNA pathway in Drosophila. Nature 453, 798–802 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  454. Okamura, K. et al. The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs. Nature 453, 803–806 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  455. Okamura, K., Balla, S., Martin, R., Liu, N. & Lai, E. C. Two distinct mechanisms generate endogenous siRNAs from bidirectional transcription in Drosophila melanogaster. Nat. Struct. Mol. Biol. 15, 581–590 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  456. Kawamura, Y. et al. Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells. Nature 453, 793–797 (2008).

    Article  CAS  PubMed  Google Scholar 

  457. Chung, W. J., Okamura, K., Martin, R. & Lai, E. C. Endogenous RNA interference provides a somatic defense against Drosophila transposons. Curr. Biol. 18, 795–802 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  458. Tam, O. H. et al. Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature 453, 534–538 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  459. Watanabe, T. et al. Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature 453, 539–543 (2008).

    Article  CAS  PubMed  Google Scholar 

  460. Ambros, V., Lee, R. C., Lavanway, A., Williams, P. T. & Jewell, D. MicroRNAs and other tiny endogenous RNAs in C. elegans. Curr. Biol. 13, 807–818 (2003).

    Article  CAS  PubMed  Google Scholar 

  461. Aravin, A. A. et al. The small RNA profile during Drosophila melanogaster development. Dev. Cell 5, 337–350 (2003).

    Article  CAS  PubMed  Google Scholar 

  462. Bernstein, E., Caudy, A. A., Hammond, S. M. & Hannon, G. J. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409, 363–366 (2001).

    Article  CAS  PubMed  Google Scholar 

  463. Lee, Y. S. et al. Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell 117, 69–81 (2004).

    Article  CAS  PubMed  Google Scholar 

  464. Pham, J. W., Pellino, J. L., Lee, Y. S., Carthew, R. W. & Sontheimer, E. J. A Dicer-2-dependent 80s complex cleaves targeted mRNAs during RNAi in Drosophila. Cell 117, 83–94 (2004).

    Article  CAS  PubMed  Google Scholar 

  465. Marques, J. T. et al. Loqs and R2D2 act sequentially in the siRNA pathway in Drosophila. Nat. Struct. Mol. Biol. 17, 24–30 (2010).

    Article  CAS  PubMed  Google Scholar 

  466. Fukunaga, R. et al. Dicer partner proteins tune the length of mature miRNAs in flies and mammals. Cell 151, 533–546 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  467. Mirkovic-Hösle, M. & Förstemann, K. Transposon defense by endo-siRNAs, piRNAs and somatic pilRNAs in Drosophila: contributions of Loqs-PD and R2D2. PLoS One 9, e84994 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  468. Cenik, E. S. et al. Phosphate and R2D2 restrict the substrate specificity of Dicer-2, an ATP-driven ribonuclease. Mol. Cell 42, 172–184 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  469. Fukunaga, R., Colpan, C., Han, B. W. & Zamore, P. D. Inorganic phosphate blocks binding of pre-miRNA to Dicer-2 via its PAZ domain. EMBO J. 33, 371–384 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  470. Naganuma, M., Tadakuma, H. & Tomari, Y. Single-molecule analysis of processive double-stranded RNA cleavage by Drosophila Dicer-2. Nat. Commun. 12, 4268 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  471. Su, S. et al. Structural insights into dsRNA processing by Drosophila Dicer-2-Loqs-PD. Nature 607, 399–406 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  472. Zamore, P. D., Tuschl, T., Sharp, P. A. & Bartel, D. P. RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 101, 25–33 (2000).

    Article  CAS  PubMed  Google Scholar 

  473. Welker, N. C. et al. Dicer’s helicase domain discriminates dsRNA termini to promote an altered reaction mode. Mol. Cell 41, 589–599 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  474. Nykänen, A., Haley, B. & Zamore, P. D. ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell 107, 309–321 (2001).

    Article  PubMed  Google Scholar 

  475. Liu, Q. et al. R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway. Science 301, 1921–1925 (2003).

    Article  CAS  PubMed  Google Scholar 

  476. Tomari, Y., Matranga, C., Haley, B., Martinez, N. & Zamore, P. D. A protein sensor for siRNA asymmetry. Science 306, 1377–1380 (2004).

    Article  CAS  PubMed  Google Scholar 

  477. Yamaguchi, S. et al. Structure of the Dicer-2-R2D2 heterodimer bound to a small RNA duplex. Nature 607, 393–398 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  478. Liu, Y. et al. C3PO, an endoribonuclease that promotes RNAi by facilitating RISC activation. Science 325, 750–753 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  479. Ye, X. et al. Structure of C3PO and mechanism of human RISC activation. Nat. Struct. Mol. Biol. 18, 650–657 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  480. Horwich, M. D. et al. The Drosophila RNA methyltransferase, DmHen1, modifies germline piRNAs and single-stranded siRNAs in RISC. Curr. Biol. 17, 1265–1272 (2007).

    Article  CAS  PubMed  Google Scholar 

  481. Pélisson, A., Sarot, E., Payen-Groschêne, G. & Bucheton, A. A novel repeat-associated small interfering RNA-mediated silencing pathway downregulates complementary sense gypsy transcripts in somatic cells of the Drosophila ovary. J. Virol. 81, 1951–1960 (2007).

    Article  PubMed  Google Scholar 

  482. Ameres, S. L. et al. Target RNA-directed trimming and tailing of small silencing RNAs. Science 328, 1534–1539 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  483. Ma, E., MacRae, I. J., Kirsch, J. F. & Doudna, J. A. Autoinhibition of human dicer by its internal helicase domain. J. Mol. Biol. 380, 237–243 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  484. Ma, E., Zhou, K., Kidwell, M. A. & Doudna, J. A. Coordinated activities of human dicer domains in regulatory RNA processing. J. Mol. Biol. 422, 466–476 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  485. Zapletal, D. et al. Structural and functional basis of mammalian microRNA biogenesis by Dicer. Mol. Cell 82, 4064–4079.e13 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  486. Schlee, M. & Hartmann, G. Discriminating self from non-self in nucleic acid sensing. Nat. Rev. Immunol. 16, 566–580 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  487. Chen, Y. G. & Hur, S. Cellular origins of dsRNA, their recognition and consequences. Nat. Rev. Mol. Cell Biol. 23, 286–301 (2022).

    Article  CAS  PubMed  Google Scholar 

  488. Stein, P., Zeng, F., Pan, H. & Schultz, R. M. Absence of non-specific effects of RNA interference triggered by long double-stranded RNA in mouse oocytes. Dev. Biol. 286, 464–471 (2005).

    Article  CAS  PubMed  Google Scholar 

  489. D’Angelo, W. et al. Development of antiviral innate immunity during in vitro differentiation of mouse embryonic stem cells. Stem Cell Dev. 25, 648–659 (2016).

    Article  Google Scholar 

  490. Wu, X. et al. Intrinsic immunity shapes viral resistance of stem cells. Cell 172, 423–438.e25 (2018).

    Article  CAS  PubMed  Google Scholar 

  491. Flemr, M. et al. A retrotransposon-driven dicer isoform directs endogenous small interfering RNA production in mouse oocytes. Cell 155, 807–816 (2013).

    Article  CAS  PubMed  Google Scholar 

  492. Calabrese, J. M., Seila, A. C., Yeo, G. W. & Sharp, P. A. RNA sequence analysis defines Dicer’s role in mouse embryonic stem cells. Proc. Natl Acad. Sci. USA 104, 18097–18102 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  493. Nejepinska, J. et al. dsRNA expression in the mouse elicits RNAi in oocytes and low adenosine deamination in somatic cells. Nucleic Acids Res. 40, 399–413 (2012).

    Article  CAS  PubMed  Google Scholar 

  494. Wianny, F. & Zernicka-Goetz, M. Specific interference with gene function by double-stranded RNA in early mouse development. Nat. Cell Biol. 2, 70–75 (2000).

    Article  CAS  PubMed  Google Scholar 

  495. Noland, C. L., Ma, E. & Doudna, J. A. siRNA repositioning for guide strand selection by human Dicer complexes. Mol. Cell 43, 110–121 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  496. Poirier, E. Z. et al. An isoform of Dicer protects mammalian stem cells against multiple RNA viruses. Science 373, 231–236 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  497. Duchaine, T. F. et al. Functional proteomics reveals the biochemical niche of C. elegans DCR-1 in multiple small-RNA-mediated pathways. Cell 124, 343–354 (2006).

    Article  CAS  PubMed  Google Scholar 

  498. Thivierge, C. et al. Tudor domain ERI-5 tethers an RNA-dependent RNA polymerase to DCR-1 to potentiate endo-RNAi. Nat. Struct. Mol. Biol. 19, 90–97 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  499. Pak, J. & Fire, A. Distinct populations of primary and secondary effectors during RNAi in C. elegans. Science 315, 241–244 (2007).

    Article  CAS  PubMed  Google Scholar 

  500. Aoki, K., Moriguchi, H., Yoshioka, T., Okawa, K. & Tabara, H. In vitro analyses of the production and activity of secondary small interfering RNAs in C. elegans. EMBO J. 26, 5007–5019 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  501. Blumenfeld, A. L. & Jose, A. M. Reproducible features of small RNAs in C. elegans reveal NU RNAs and provide insights into 22G RNAs and 26G RNAs. RNA 22, 184–192 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  502. Kao, C. C., Singh, P. & Ecker, D. J. De novo initiation of viral RNA-dependent RNA synthesis. Virology 287, 251–260 (2001).

    Article  CAS  PubMed  Google Scholar 

  503. Gu, W. et al. Distinct argonaute-mediated 22G-RNA pathways direct genome surveillance in the C. elegans germline. Mol. Cell 36, 231–244 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  504. Claycomb, J. M. et al. The Argonaute CSR-1 and its 22G-RNA cofactors are required for holocentric chromosome segregation. Cell 139, 123–134 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  505. Chaves, D. A. et al. The RNA phosphatase PIR-1 regulates endogenous small RNA pathways in C. elegans. Mol. Cell 81, 546–557.e5 (2021).

    Article  CAS  PubMed  Google Scholar 

  506. Ketting, R. F. et al. Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev. 15, 2654–2659 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  507. Han, T. et al. 26G endo-siRNAs regulate spermatogenic and zygotic gene expression in Caenorhabditis elegans. Proc. Natl Acad. Sci. USA 106, 18674–18679 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  508. Pavelec, D. M., Lachowiec, J., Duchaine, T. F., Smith, H. E. & Kennedy, S. Requirement for the ERI/DICER complex in endogenous RNA interference and sperm development in Caenorhabditis elegans. Genetics 183, 1283–1295 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  509. Conine, C. C. et al. Argonautes ALG-3 and ALG-4 are required for spermatogenesis-specific 26G-RNAs and thermotolerant sperm in Caenorhabditis elegans. Proc. Natl Acad. Sci. USA 107, 3588–3593 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  510. Vasale, J. J. et al. Sequential rounds of RNA-dependent RNA transcription drive endogenous small-RNA biogenesis in the ERGO-1/Argonaute pathway. Proc. Natl Acad. Sci. USA 107, 3582–3587 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  511. Gent, J. I. et al. Distinct phases of siRNA synthesis in an endogenous RNAi pathway in C. elegans soma. Mol. Cell 37, 679–689 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  512. Conine, C. C. et al. Argonautes promote male fertility and provide a paternal memory of germline gene expression in C. elegans. Cell 155, 1532–1544 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  513. Yigit, E. et al. Analysis of the C. elegans Argonaute family reveals that distinct Argonautes act sequentially during RNAi. Cell 127, 747–757 (2006).

    Article  CAS  PubMed  Google Scholar 

  514. Fischer, S. E. et al. The ERI-6/7 helicase acts at the first stage of an siRNA amplification pathway that targets recent gene duplications. PLoS Genet. 7, e1002369 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  515. Billi, A. C. et al. The Caenorhabditis elegans HEN1 ortholog, HENN-1, methylates and stabilizes select subclasses of germline small RNAs. PLoS Genet. 8, e1002617 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  516. Kamminga, L. M. et al. Differential impact of the HEN1 homolog HENN-1 on 21U and 26G RNAs in the germline of Caenorhabditis elegans. PLoS Genet. 8, e1002702 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  517. Montgomery, T. A. et al. PIWI associated siRNAs and piRNAs specifically require the Caenorhabditis elegans HEN1 ortholog henn-1. PLoS Genet. 8, e1002616 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  518. Haley, B. & Zamore, P. D. Kinetic analysis of the RNAi enzyme complex. Nat. Struct. Mol. Biol. 11, 599–606 (2004).

    Article  CAS  PubMed  Google Scholar 

  519. Ameres, S. L., Martinez, J. & Schroeder, R. Molecular basis for target RNA recognition and cleavage by human RISC. Cell 130, 101–112 (2007).

    Article  CAS  PubMed  Google Scholar 

  520. Ma, J. B. et al. Structural basis for 5’-end-specific recognition of guide RNA by the A. fulgidus Piwi protein. Nature 434, 666–670 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  521. Parker, J. S., Roe, S. M. & Barford, D. Structural insights into mRNA recognition from a PIWI domain-siRNA guide complex. Nature 434, 663–666 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  522. Sijen, T. & Plasterk, R. H. Transposon silencing in the Caenorhabditis elegans germ line by natural RNAi. Nature 426, 310–314 (2003).

    Article  CAS  PubMed  Google Scholar 

  523. Wen, J. et al. Adaptive regulation of testis gene expression and control of male fertility by the Drosophila hairpin RNA pathway. Mol. Cell 57, 165–178 (2015).

    Article  CAS  PubMed  Google Scholar 

  524. Lee, R. C., Hammell, C. M. & Ambros, V. Interacting endogenous and exogenous RNAi pathways in Caenorhabditis elegans. RNA 12, 589–597 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  525. Gerson-Gurwitz, A. et al. A small RNA-catalytic argonaute pathway tunes germline transcript levels to ensure embryonic divisions. Cell 165, 396–409 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  526. Stein, P. et al. Essential Role for endogenous siRNAs during meiosis in mouse oocytes. PLoS Genet. 11, e1005013 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  527. Lin, C. J. et al. The hpRNA/RNAi pathway is essential to resolve intragenomic conflict in the Drosophila male germline. Dev. Cell 46, 316–326.e5 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  528. Vedanayagam, J. et al. Essential and recurrent roles for hairpin RNAs in silencing de novo sex chromosome conflict in Drosophila simulans. PLoS Biol. 21, e3002136 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  529. Vedanayagam, J. et al. Regulatory logic of endogenous RNAi in silencing de novo genomic conflicts. PLoS Genet. 19, e1010787 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  530. Guang, S. et al. An argonaute transports siRNAs from the cytoplasm to the nucleus. Science 321, 537–541 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  531. Fagegaltier, D. et al. The endogenous siRNA pathway is involved in heterochromatin formation in Drosophila. Proc. Natl Acad. Sci. USA 106, 21258–21263 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  532. Juang, B. T. et al. Endogenous nuclear RNAi mediates behavioral adaptation to odor. Cell 154, 1010–1022 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  533. Cernilogar, F. M. et al. Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila. Nature 480, 391–395 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  534. Wedeles, C. J., Wu, M. Z. & Claycomb, J. M. Protection of germline gene expression by the C. elegans Argonaute CSR-1. Dev. Cell 27, 664–671 (2013).

    Article  CAS  PubMed  Google Scholar 

  535. Seth, M. et al. The C. elegans CSR-1 argonaute pathway counteracts epigenetic silencing to promote germline gene expression. Dev. Cell 27, 656–663 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  536. Houwing, S. et al. A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in Zebrafish. Cell 129, 69–82 (2007).

    Article  CAS  PubMed  Google Scholar 

  537. Vagin, V. V. et al. A distinct small RNA pathway silences selfish genetic elements in the germline. Science 313, 320–324 (2006).

    Article  CAS  PubMed  Google Scholar 

  538. Brennecke, J. et al. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 128, 1089–1103 (2007).

    Article  CAS  PubMed  Google Scholar 

  539. Mohn, F., Sienski, G., Handler, D. & Brennecke, J. The rhino-deadlock-cutoff complex licenses noncanonical transcription of dual-strand piRNA clusters in Drosophila. Cell 157, 1364–1379 (2014).

    Article  CAS  PubMed  Google Scholar 

  540. Goriaux, C., Desset, S., Renaud, Y., Vaury, C. & Brasset, E. Transcriptional properties and splicing of the flamenco piRNA cluster. EMBO Rep. 15, 411–418 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  541. Li, X. Z. et al. An ancient transcription factor initiates the burst of piRNA production during early meiosis in mouse testes. Mol. Cell 50, 67–81 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  542. Dennis, C., Brasset, E., Sarkar, A. & Vaury, C. Export of piRNA precursors by EJC triggers assembly of cytoplasmic Yb-body in Drosophila. Nat. Commun. 7, 13739 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  543. Prud’homme, N., Gans, M., Masson, M., Terzian, C. & Bucheton, A. Flamenco, a gene controlling the gypsy retrovirus of Drosophila melanogaster. Genetics 139, 697–711 (1995).

    Article  PubMed  PubMed Central  Google Scholar 

  544. Sarot, E., Payen-Groschêne, G., Bucheton, A. & Pélisson, A. Evidence for a piwi-dependent RNA silencing of the gypsy endogenous retrovirus by the Drosophila melanogaster flamenco gene. Genetics 166, 1313–1321 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  545. Li, Cet et al. Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies. Cell 137, 509–521 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  546. Malone, C. D. et al. Specialized piRNA pathways act in germline and somatic tissues of the Drosophila ovary. Cell 137, 522–535 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  547. Mével-Ninio, M., Pelisson, A., Kinder, J., Campos, A. R. & Bucheton, A. The flamenco locus controls the gypsy and ZAM retroviruses and is required for Drosophila oogenesis. Genetics 175, 1615–1624 (2007).

    Article  PubMed  PubMed Central  Google Scholar 

  548. Aravin, A. A., Sachidanandam, R., Girard, A., Fejes-Toth, K. & Hannon, G. J. Developmentally regulated piRNA clusters implicate MILI in transposon control. Science 316, 744–747 (2007).

    Article  CAS  PubMed  Google Scholar 

  549. Aravin, A. A. et al. A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice. Mol. Cell 31, 785–799 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  550. Aravin, A. A. et al. Cytoplasmic compartmentalization of the fetal piRNA pathway in mice. PLoS Genet. 5, e1000764 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  551. Watanabe, T. et al. MITOPLD is a mitochondrial protein essential for nuage formation and piRNA biogenesis in the mouse germline. Dev. Cell 20, 364–375 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  552. Reuter, M. et al. Miwi catalysis is required for piRNA amplification-independent LINE1 transposon silencing. Nature 480, 264–267 (2011).

    Article  CAS  PubMed  Google Scholar 

  553. Beyret, E., Liu, N. & Lin, H. piRNA biogenesis during adult spermatogenesis in mice is independent of the ping-pong mechanism. Cell Res. 22, 1429–1439 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  554. Vourekas, A. et al. Mili and Miwi target RNA repertoire reveals piRNA biogenesis and function of Miwi in spermiogenesis. Nat. Struct. Mol. Biol. 19, 773–781 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  555. Aravin, A. et al. A novel class of small RNAs bind to MILI protein in mouse testes. Nature 442, 203–207 (2006).

    Article  CAS  PubMed  Google Scholar 

  556. Girard, A., Sachidanandam, R., Hannon, G. J. & Carmell, M. A. A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 442, 199–202 (2006).

    Article  PubMed  Google Scholar 

  557. Lau, N. C. et al. Characterization of the piRNA complex from rat testes. Science 313, 363–367 (2006).

    Article  CAS  PubMed  Google Scholar 

  558. Özata, D. M. et al. Evolutionarily conserved pachytene piRNA loci are highly divergent among modern humans. Nat. Ecol. Evol. 4, 156–168 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  559. Klattenhoff, C. et al. The Drosophila HP1 homolog Rhino is required for transposon silencing and piRNA production by dual-strand clusters. Cell 138, 1137–1149 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  560. Fu, Y. et al. The genome of the Hi5 germ cell line from Trichoplusia ni, an agricultural pest and novel model for small RNA biology. eLife 7, e31628 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  561. Lim, A. K. & Kai, T. Unique germ-line organelle, nuage, functions to repress selfish genetic elements in Drosophila melanogaster. Proc. Natl Acad. Sci. 104, 6714–6719 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  562. Zhang, F. et al. UAP56 couples piRNA clusters to the perinuclear transposon silencing machinery. Cell 151, 871–884 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  563. Meikar, O. et al. An atlas of chromatoid body components. RNA 20, 483–495 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  564. Kneuss, E. et al. Specialization of the Drosophila nuclear export family protein Nxf3 for piRNA precursor export. Genes Dev. 33, 1208–1220 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  565. ElMaghraby, M. F. et al. A heterochromatin-specific RNA export pathway facilitates piRNA production. Cell 178, 964–979.e20 (2019).

    Article  CAS  PubMed  Google Scholar 

  566. Lin, Y., Suyama, R., Kawaguchi, S., Iki, T. & Kai, T. Tejas functions as a core component in nuage assembly and precursor processing in Drosophila piRNA biogenesis. J. Cell Biol. 222, e202303125 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  567. Fawcett, D. W., Eddy, E. M. & Phillips, D. M. Observations on the fine structure and relationships of the chromatoid body in mammalian spermatogenesis. Biol. Reprod. 2, 129–153 (1970).

    Article  CAS  PubMed  Google Scholar 

  568. Mahowald, A. P. Polar granules of Drosophila. 3. The continuity of polar granules during the life cycle of Drosophila. J. Exp. Zool. 176, 329–343 (1971).

    Article  CAS  PubMed  Google Scholar 

  569. Eddy, E. M. Fine structural observations on the form and distribution of nuage in germ cells of the rat. Anat. Rec. 178, 731–757 (1974).

    Article  CAS  PubMed  Google Scholar 

  570. Strome, S. & Wood, W. B. Immunofluorescence visualization of germ-line-specific cytoplasmic granules in embryos, larvae, and adults of Caenorhabditis elegans. Proc. Natl Acad. Sci. USA 79, 1558–1562 (1982).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  571. Wolf, N., Priess, J. & Hirsh, D. Segregation of germline granules in early embryos of Caenorhabditis elegans: an electron microscopic analysis. J. Embryol. Exp. Morphol. 73, 297–306 (1983).

    CAS  PubMed  Google Scholar 

  572. Braat, A. K., Zandbergen, T., van de Water, S., Goos, H. J. & Zivkovic, D. Characterization of zebrafish primordial germ cells: morphology and early distribution of vasa RNA. Dev. Dyn. 216, 153–167 (1999).

    Article  CAS  PubMed  Google Scholar 

  573. Szakmary, A., Reedy, M., Qi, H. & Lin, H. The Yb protein defines a novel organelle and regulates male germline stem cell self-renewal in Drosophila melanogaster. J. Cell Biol. 185, 613–627 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  574. Kawaoka, S., Izumi, N., Katsuma, S. & Tomari, Y. 3’ end formation of PIWI-interacting RNAs in vitro. Mol. Cell 43, 1015–1022 (2011).

    Article  CAS  PubMed  Google Scholar 

  575. Cora, E. et al. The MID-PIWI module of Piwi proteins specifies nucleotide- and strand-biases of piRNAs. RNA 20, 773–781 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  576. Wang, W. et al. The initial uridine of primary piRNAs does not create the tenth adenine that Is the hallmark of secondary piRNAs. Mol. Cell 56, 708–716 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  577. Matsumoto, N. et al. Crystal structure of silkworm PIWI-Clade Argonaute Siwi Bound to piRNA. Cell 167, 484–497.e9 (2016).

    Article  CAS  PubMed  Google Scholar 

  578. Mohn, F., Handler, D. & Brennecke, J. Noncoding RNA. piRNA-guided slicing specifies transcripts for Zucchini-dependent, phased piRNA biogenesis. Science 348, 812–817 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  579. Han, B. W., Wang, W., Li, C., Weng, Z. & Zamore, P. D. Noncoding RNA. piRNA-guided transposon cleavage initiates Zucchini-dependent, phased piRNA production. Science 348, 817–821 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  580. Wang, W. et al. Slicing and binding by Ago3 or Aub trigger piwi-bound piRNA production by distinct mechanisms. Mol. Cell 59, 819–830 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  581. Gainetdinov, I., Colpan, C., Arif, A., Cecchini, K. & Zamore, P. D. A single mechanism of biogenesis, initiated and directed by PIWI proteins, explains piRNA production in most animals. Mol. Cell 71, 775–790.e5 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  582. Gunawardane, L. S. et al. A slicer-mediated mechanism for repeat-associated siRNA 5’ end formation in Drosophila. Science 315, 1587–1590 (2007).

    Article  CAS  PubMed  Google Scholar 

  583. Brennecke, J. et al. An epigenetic role for maternally inherited piRNAs in transposon silencing. Science 322, 1387–1392 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  584. Haase, A. D. et al. Probing the initiation and effector phases of the somatic piRNA pathway in Drosophila. Genes Dev. 24, 2499–2504 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  585. Ipsaro, J. J., Haase, A. D., Knott, S. R., Joshua-Tor, L. & Hannon, G. J. The structural biochemistry of Zucchini implicates it as a nuclease in piRNA biogenesis. Nature 491, 279–283 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  586. Nishimasu, H. et al. Structure and function of Zucchini endoribonuclease in piRNA biogenesis. Nature 491, 284–287 (2012).

    Article  CAS  PubMed  Google Scholar 

  587. Homolka, D. et al. PIWI Slicing and RNA elements in precursors instruct directional primary piRNA biogenesis. Cell Rep. 12, 418–428 (2015).

    Article  CAS  PubMed  Google Scholar 

  588. Ge, D. T. et al. The RNA-binding ATPase, armitage, couples piRNA amplification in nuage to phased piRNA production on mitochondria. Mol. Cell 74, 982–995.e6 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  589. Izumi, N., Shoji, K., Suzuki, Y., Katsuma, S. & Tomari, Y. Zucchini consensus motifs determine the mechanism of pre-piRNA production. Nature 578, 311–316 (2020).

    Article  CAS  PubMed  Google Scholar 

  590. Ruby, J. G. et al. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127, 1193–1207 (2006).

    Article  CAS  PubMed  Google Scholar 

  591. Gu, W. et al. CapSeq and CIP-TAP identify Pol II start sites and reveal capped small RNAs as C. elegans piRNA precursors. Cell 151, 1488–1500 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  592. Cecere, G., Zheng, G. X., Mansisidor, A. R., Klymko, K. E. & Grishok, A. Promoters recognized by forkhead proteins exist for individual 21U-RNAs. Mol. Cell 47, 734–745 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  593. Kasper, D. M., Wang, G., Gardner, K. E., Johnstone, T. G. & Reinke, V. The C. elegans SNAPc component SNPC-4 coats piRNA domains and is globally required for piRNA abundance. Dev. Cell 31, 145–158 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  594. Weick, E.-M. et al. PRDE-1 is a nuclear factor essential for the biogenesis of Ruby motif-dependent piRNAs in C. elegans. Genes Dev. 28, 783–796 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  595. Weng, C. et al. The USTC co-opts an ancient machinery to drive piRNA transcription in C. elegans. Genes Dev. 33, 90–102 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  596. Cordeiro Rodrigues, R. J. et al. PETISCO is a novel protein complex required for 21U RNA biogenesis and embryonic viability. Genes Dev. 33, 857–870 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  597. Perez-Borrajero, C. et al. Structural basis of PETISCO complex assembly during piRNA biogenesis in C. elegans. Genes Dev. 35, 1304–1323 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  598. Wang, X. et al. Molecular basis for PICS-mediated piRNA biogenesis and cell division. Nat. Commun. 12, 5595 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  599. Zeng, C. et al. Functional proteomics identifies a PICS complex required for piRNA maturation and chromosome segregation. Cell Rep. 27, 3561–3572.e3 (2019).

    Article  CAS  PubMed  Google Scholar 

  600. Podvalnaya, N. et al. piRNA processing by a trimeric Schlafen-domain nuclease. Nature 622, 402–409 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  601. Batista, P. J. et al. PRG-1 and 21U-RNAs interact to form the piRNA complex required for fertility in C. elegans. Mol. Cell 31, 67–78 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  602. Bagijn, M. P. et al. Function, targets, and evolution of Caenorhabditis elegans piRNAs. Science 337, 574–578 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  603. Tang, W., Tu, S., Lee, H. C., Weng, Z. & Mello, C. C. The RNase PARN-1 trims piRNA 3’ ends to promote transcriptome surveillance in C. elegans. Cell 164, 974–984 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  604. Izumi, N. et al. Identification and functional analysis of the pre-piRNA 3’ trimmer in silkworms. Cell 164, 962–973 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  605. Saito, K. et al. Pimet, the Drosophila homolog of HEN1, mediates 2′-O-methylation of Piwi-interacting RNAs at their 3′ ends. Genes Dev. 21, 1603–1608 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  606. Lim, S. L. et al. HENMT1 and piRNA stability are required for adult male germ cell transposon repression and to define the spermatogenic program in the mouse. PLoS Genet. 11, e1005620 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  607. Kirino, Y. & Mourelatos, Z. Mouse Piwi-interacting RNAs are 2′-O-methylated at their 3′ termini. Nat. Struct. Mol. Biol. 14, 347–348 (2007).

    Article  CAS  PubMed  Google Scholar 

  608. Hayashi, R. et al. Genetic and mechanistic diversity of piRNA 3’-end formation. Nature 539, 588–592 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  609. Chary, S. & Hayashi, R. The absence of core piRNA biogenesis factors does not impact efficient transposon silencing in Drosophila. PLoS Biol. 21, e3002099 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  610. Aravin, A. A. et al. Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline. Curr. Biol. 11, 1017–1027 (2001).

    Article  CAS  PubMed  Google Scholar 

  611. De Fazio, S. et al. The endonuclease activity of Mili fuels piRNA amplification that silences LINE1 elements. Nature 480, 259–263 (2011).

    Article  PubMed  Google Scholar 

  612. Roovers, E. F. et al. Piwi proteins and piRNAs in mammalian oocytes and early embryos. Cell Rep. 10, 2069–2082 (2015).

    Article  CAS  PubMed  Google Scholar 

  613. Lewis, S. H. et al. Pan-arthropod analysis reveals somatic piRNAs as an ancestral defence against transposable elements. Nat. Ecol. Evol. 2, 174–181 (2018).

    Article  PubMed  Google Scholar 

  614. Jehn, J. et al. PIWI genes and piRNAs are ubiquitously expressed in mollusks and show patterns of lineage-specific adaptation. Commun. Biol. 1, 137 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  615. Yoshimura, T. et al. Mouse GTSF1 is an essential factor for secondary piRNA biogenesis. EMBO Rep. 19, e42054 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  616. Dönertas, D., Sienski, G. & Brennecke, J. Drosophila Gtsf1 is an essential component of the Piwi-mediated transcriptional silencing complex. Genes Dev. 27, 1693–1705 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  617. Muerdter, F. et al. A genome-wide RNAi screen draws a genetic framework for transposon control and primary piRNA biogenesis in Drosophila. Mol. Cell 50, 736–748 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  618. Arif, A. et al. GTSF1 accelerates target RNA cleavage by PIWI-clade Argonaute proteins. Nature 608, 618–625 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  619. Izumi, N., Shoji, K., Kiuchi, T., Katsuma, S. & Tomari, Y. The two Gtsf paralogs in silkworms orthogonally activate their partner PIWI proteins for target cleavage. RNA 29, 18–29 (2022).

    Article  PubMed  Google Scholar 

  620. Li, Z. et al. Mammalian PIWI-piRNA-target complexes reveal features for broad and efficient target silencing. Nat. Struct. Mol. Biol. 31, 1222–1231 (2024).

    Article  CAS  PubMed  Google Scholar 

  621. Gainetdinov, I. et al. Relaxed targeting rules help PIWI proteins silence transposons. Nature 619, 394–402 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  622. Dowling, M. et al. In vivo PIWI slicing in mouse testes deviates from rules established in vitro. RNA 29, 308–316 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  623. Sienski, G., Dönertas, D. & Brennecke, J. Transcriptional silencing of transposons by Piwi and maelstrom and its impact on chromatin state and gene expression. Cell 151, 964–980 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  624. Le Thomas, A. et al. Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state. Genes Dev. 27, 390–399 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  625. Pezic, D., Manakov, S. A., Sachidanandam, R. & Aravin, A. A. piRNA pathway targets active LINE1 elements to establish the repressive H3K9me3 mark in germ cells. Genes Dev. 28, 1410–1428 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  626. Kuramochi-Miyagawa, S. et al. DNA methylation of retrotransposon genes is regulated by Piwi family members MILI and MIWI2 in murine fetal testes. Genes Dev. 22, 908–917 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  627. Gou, L. T. et al. Pachytene piRNAs instruct massive mRNA elimination during late spermiogenesis. Cell Res. 24, 680–700 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  628. Goh, W. S. et al. piRNA-directed cleavage of meiotic transcripts regulates spermatogenesis. Genes Dev. 29, 1032–1044 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  629. Wu, P. H. et al. The evolutionarily conserved piRNA-producing locus pi6 is required for male mouse fertility. Nat. Genet. 52, 728–739 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  630. Rouget, C. et al. Maternal mRNA deadenylation and decay by the piRNA pathway in the early Drosophila embryo. Nature 467, 1128–1132 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  631. Barckmann, B. et al. Aubergine iCLIP reveals piRNA-dependent decay of mRNAs involved in germ cell development in the early embryo. Cell Rep. 12, 1205–1216 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  632. Kiuchi, T. et al. A single female-specific piRNA is the primary determiner of sex in the silkworm. Nature 509, 633–636 (2014).

    Article  CAS  PubMed  Google Scholar 

  633. Kotov, A. A. et al. piRNA silencing contributes to interspecies hybrid sterility and reproductive isolation in Drosophila melanogaster. Nucleic Acids Res. 47, 4255–4271 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  634. Morazzani, E. M., Wiley, M. R., Murreddu, M. G., Adelman, Z. N. & Myles, K. M. Production of virus-derived ping-pong-dependent piRNA-like small RNAs in the mosquito soma. PLoS Pathog. 8, e1002470 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  635. Miesen, P., Girardi, E. & van Rij, R. P. Distinct sets of PIWI proteins produce arbovirus and transposon-derived piRNAs in Aedes aegypti mosquito cells. Nucleic Acids Res. 43, 6545–6556 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  636. Fu, H. et al. Stress induces tRNA cleavage by angiogenin in mammalian cells. FEBS Lett. 583, 437–442 (2009).

    Article  CAS  PubMed  Google Scholar 

  637. Muthukumar, S., Li, C.-T., Liu, R.-J. & Bellodi, C. Roles and regulation of tRNA-derived small RNAs in animals. Nat. Rev. Mol. Cell Biol. 25, 359–378 (2024).

    Article  CAS  PubMed  Google Scholar 

  638. Narayanan, A., Speckmann, W., Terns, R. & Terns, M. P. Role of the box C/D motif in localization of small nucleolar RNAs to coiled bodies and nucleoli. Mol. Biol. Cell 10, 2131–2147 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  639. Boulon, S. et al. PHAX and CRM1 are required sequentially to transport U3 snoRNA to nucleoli. Mol. Cell 16, 777–787 (2004).

    Article  CAS  PubMed  Google Scholar 

  640. Zhang, Z. et al. The HP1 homolog rhino anchors a nuclear complex that suppresses piRNA precursor splicing. Cell 157, 1353–1363 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  641. Chen, Y. A. et al. Cutoff suppresses RNA polymerase II termination to ensure expression of piRNA precursors. Mol. Cell 63, 97–109 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  642. Andersen, P. R., Tirian, L., Vunjak, M. & Brennecke, J. A heterochromatin-dependent transcription machinery drives piRNA expression. Nature 549, 54–59 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  643. Hur, J. K. et al. Splicing-independent loading of TREX on nascent RNA is required for efficient expression of dual-strand piRNA clusters in Drosophila. Genes Dev. 30, 840–855 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  644. Zhang, G. et al. Co-dependent assembly of Drosophila piRNA precursor complexes and piRNA cluster heterochromatin. Cell Rep. 24, 3413–3422.e4 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  645. Le Thomas, A. et al. Transgenerationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing. Genes Dev. 28, 1667–1680 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  646. Akkouche, A. et al. Piwi is required during Drosophila embryogenesis to license dual-strand piRNA clusters for transposon repression in adult ovaries. Mol. Cell 66, 411–419.e4 (2017).

    Article  CAS  PubMed  Google Scholar 

  647. Volpe, A. M., Horowitz, H., Grafer, C. M., Jackson, S. M. & Berg, C. A. Drosophila rhino encodes a female-specific chromo-domain protein that affects chromosome structure and egg polarity. Genetics 159, 1117–1134 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  648. Vermaak, D. & Malik, H. S. Multiple roles for heterochromatin protein 1 genes in Drosophila. Annu. Rev. Genet. 43, 467–492 (2009).

    Article  CAS  PubMed  Google Scholar 

  649. Baumgartner, L. et al. The Drosophila ZAD zinc finger protein Kipferl guides Rhino to piRNA clusters. eLife 11, e80067 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  650. Pane, A., Jiang, P., Zhao, D. Y., Singh, M. & Schüpbach, T. The cutoff protein regulates piRNA cluster expression and piRNA production in the Drosophila germline. EMBO J. 30, 4601–4615 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  651. Chen, P., Luo, Y. & Aravin, A. A. RDC complex executes a dynamic piRNA program during Drosophila spermatogenesis to safeguard male fertility. PLoS Genet. 17, e1009591 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  652. Parhad, S. S., Tu, S., Weng, Z. & Theurkauf, W. E. Adaptive evolution leads to cross-species incompatibility in the piRNA transposon silencing machinery. Dev. Cell 43, 60–70.e5 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Contributions

The authors contributed equally to all aspects of the article.

Corresponding authors

Correspondence to Karina Jouravleva or Phillip D. Zamore.

Ethics declarations

Competing interests

The authors declare no competing interests.

Peer review

Peer review information

Nature Reviews Molecular Cell Biology thanks Martin Simard, Petr Svoboda and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Jouravleva, K., Zamore, P.D. A guide to the biogenesis and functions of endogenous small non-coding RNAs in animals. Nat Rev Mol Cell Biol 26, 347–370 (2025). https://doi.org/10.1038/s41580-024-00818-9

Download citation

  • Accepted:

  • Published:

  • Issue date:

  • DOI: https://doi.org/10.1038/s41580-024-00818-9

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing