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Probing the dynamic RNA structurome and its functions

Nature Reviews Genetics volume 24, pages 178–196 (2023)Cite this article

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Abstract

RNA is a key regulator of almost every cellular process, and the structures adopted by RNA molecules are thought to be central to their functions. The recent fast-paced evolution of high-throughput sequencing-based RNA structure mapping methods has enabled the rapid in vivo structural interrogation of entire cellular transcriptomes. Collectively, these studies are shedding new light on the long underestimated complexity of the structural organization of the transcriptome — the RNA structurome. Moreover, recent analyses are challenging the view that the RNA structurome is a static entity by revealing how RNA molecules establish intricate networks of alternative intramolecular and intermolecular interactions and that these ensembles of RNA structures are dynamically regulated to finely tune RNA functions in living cells. This new understanding of how RNA can shape cell phenotypes has important implications for the development of RNA-targeted therapeutic strategies.

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Fig. 1: Chemical probes for interrogating RNA structures.
Fig. 2: Read out of high-throughput sequencing (HTS)-based RNA structure mapping experiments.
Fig. 3: Long-range intramolecular and intermolecular RNA–RNA interactions.
Fig. 4: Determinants of RNA structure heterogeneity in the cell.
Fig. 5: Experimental and computational methods for RNA ensemble deconvolution.
Fig. 6: RNA structure ensembles identified in high-throughput sequencing (HTS)-based structure probing studies.
Fig. 7: Challenges in high-throughput sequencing (HTS)-based RNA structure mapping studies.

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References

  1. Leppek, K., Das, R. & Barna, M. Functional 5′ UTR mRNA structures in eukaryotic translation regulation and how to find them. Nat. Rev. Mol. Cell Biol. 19, 158–174 (2018).

    Article  CAS  PubMed  Google Scholar 

  2. Mayr, C. Regulation by 3′-untranslated regions. Annu. Rev. Genet. 51, 171–194 (2017).

    Article  CAS  PubMed  Google Scholar 

  3. Frankish, A. et al. GENCODE 2021. Nucleic Acids Res. 49, D916–D923 (2021).

    Article  CAS  PubMed  Google Scholar 

  4. Fu, X.-D. Non-coding RNA: a new frontier in regulatory biology. Natl Sci. Rev. 1, 190–204 (2014).

    Article  CAS  PubMed  Google Scholar 

  5. Mustoe, A. M., Brooks, C. L. & Al-Hashimi, H. M. Hierarchy of RNA functional dynamics. Annu. Rev. Biochem. 83, 441–466 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Ganser, L. R., Kelly, M. L., Herschlag, D. & Al-Hashimi, H. M. The roles of structural dynamics in the cellular functions of RNAs. Nat. Rev. Mol. Cell Biol. 20, 474–489 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Kortmann, J. & Narberhaus, F. Bacterial RNA thermometers: molecular zippers and switches. Nat. Rev. Microbiol. 10, 255–265 (2012).

    Article  CAS  PubMed  Google Scholar 

  8. Serganov, A. & Nudler, E. A decade of riboswitches. Cell 152, 17–24 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Kubota, M., Tran, C. & Spitale, R. C. Progress and challenges for chemical probing of RNA structure inside living cells. Nat. Chem. Biol. 11, 933–941 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Strobel, E. J., Yu, A. M. & Lucks, J. B. High-throughput determination of RNA structures. Nat. Rev. Genet. 19, 615–634 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Kwok, C. K., Tang, Y., Assmann, S. M. & Bevilacqua, P. C. The RNA structurome: transcriptome-wide structure probing with next-generation sequencing. Trends Biochem. Sci. 40, 221–232 (2015).

    Article  CAS  PubMed  Google Scholar 

  12. Wells, S. E., Hughes, J. M., Igel, A. H. & Ares, M. Use of dimethyl sulfate to probe RNA structure in vivo. Methods Enzymol. 318, 479–493 (2000).

    Article  CAS  PubMed  Google Scholar 

  13. Mustoe, A. M., Lama, N. N., Irving, P. S., Olson, S. W. & Weeks, K. M. RNA base-pairing complexity in living cells visualized by correlated chemical probing. Proc. Natl Acad. Sci. USA 116, 24574–24582 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Mitchell, D. et al. Glyoxals as in vivo RNA structural probes of guanine base-pairing. RNA 24, 114–124 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Wang, P. Y., Sexton, A. N., Culligan, W. J. & Simon, M. D. Carbodiimide reagents for the chemical probing of RNA structure in cells. RNA 25, 135–146 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Mitchell, D. et al. In vivo RNA structural probing of uracil and guanine base-pairing by 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC). RNA 25, 147–157 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Merino, E. J., Wilkinson, K. A., Coughlan, J. L. & Weeks, K. M. RNA structure analysis at single nucleotide resolution by selective 2′-hydroxyl acylation and primer extension (SHAPE). J. Am. Chem. Soc. 127, 4223–4231 (2005).

    Article  CAS  PubMed  Google Scholar 

  18. McGinnis, J. L., Dunkle, J. A., Cate, J. H. D. & Weeks, K. M. The mechanisms of RNA SHAPE chemistry. J. Am. Chem. Soc. 134, 6617–6624 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Xiao, L., Fang, L. & Kool, E. T. Acylation probing of “generic” RNA libraries reveals critical influence of loop constraints on reactivity. Cell Chem. Biol. 29, 1341–1352.e8 (2022).

    Article  CAS  PubMed  Google Scholar 

  20. Steen, K.-A., Rice, G. M. & Weeks, K. M. Fingerprinting noncanonical and tertiary RNA structures by differential SHAPE reactivity. J. Am. Chem. Soc. 134, 13160–13163 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Mortimer, S. A. & Weeks, K. M. Time-resolved RNA SHAPE chemistry. J. Am. Chem. Soc. 130, 16178–16180 (2008).

    Article  CAS  PubMed  Google Scholar 

  22. Busan, S., Weidmann, C. A., Sengupta, A. & Weeks, K. M. Guidelines for SHAPE reagent choice and detection strategy for RNA structure probing studies. Biochemistry 58, 2655–2664 (2019).

    Article  CAS  PubMed  Google Scholar 

  23. Spitale, R. C. et al. RNA SHAPE analysis in living cells. Nat. Chem. Biol. 9, 18–20 (2013).

    Article  CAS  PubMed  Google Scholar 

  24. Spitale, R. C. et al. Structural imprints in vivo decode RNA regulatory mechanisms. Nature 519, 486–490 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Marinus, T., Fessler, A. B., Ogle, C. A. & Incarnato, D. A novel SHAPE reagent enables the analysis of RNA structure in living cells with unprecedented accuracy. Nucleic Acids Res. 49, e34 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Ingle, S., Azad, R. N., Jain, S. S. & Tullius, T. D. Chemical probing of RNA with the hydroxyl radical at single-atom resolution. Nucleic Acids Res. 42, 12758–12767 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Kielpinski, L. J. & Vinther, J. Massive parallel-sequencing-based hydroxyl radical probing of RNA accessibility. Nucleic Acids Res. 42, e70 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Feng, C. et al. Light-activated chemical probing of nucleobase solvent accessibility inside cells. Nat. Chem. Biol. 14, 276–283 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Zinshteyn, B. et al. Assaying RNA structure with LASER-Seq. Nucleic Acids Res. 47, 43–55 (2019).

    Article  CAS  PubMed  Google Scholar 

  30. Homan, P. J. et al. Single-molecule correlated chemical probing of RNA. Proc. Natl Acad. Sci. USA 111, 13858–13863 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Siegfried, N. A., Busan, S., Rice, G. M., Nelson, J. A. E. & Weeks, K. M. RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP). Nat. Methods 11, 959–965 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Zubradt, M. et al. DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo. Nat. Methods 14, 75–82 (2017).

    Article  CAS  PubMed  Google Scholar 

  33. Guo, L.-T. et al. Sequencing and structure probing of long RNAs using MarathonRT: a next-generation reverse transcriptase. J. Mol. Biol. 432, 3338–3352 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Cimino, G. D., Gamper, H. B., Isaacs, S. T. & Hearst, J. E. Psoralens as photoactive probes of nucleic acid structure and function: organic chemistry, photochemistry, and biochemistry. Annu. Rev. Biochem. 54, 1151–1193 (1985).

    Article  CAS  PubMed  Google Scholar 

  35. Nilsen, T. W. Detecting RNA-RNA interactions using psoralen derivatives. Cold Spring Harb. Protoc. 2014, 996–1000 (2014).

    Article  PubMed  Google Scholar 

  36. Ramani, V., Qiu, R. & Shendure, J. High-throughput determination of RNA structure by proximity ligation. Nat. Biotechnol. 33, 980–984 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Lu, Z. et al. RNA duplex map in living cells reveals higher order transcriptome structure. Cell 165, 1267–1279 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Aw, J. G. A. et al. In vivo mapping of eukaryotic RNA interactomes reveals principles of higher-order organization and regulation. Mol. Cell 62, 603–617 (2016).

    Article  CAS  PubMed  Google Scholar 

  39. Sharma, E., Sterne-Weiler, T., O’Hanlon, D. & Blencowe, B. J. Global mapping of human RNA–RNA interactions. Mol. Cell 62, 618–626 (2016).

    Article  CAS  PubMed  Google Scholar 

  40. Nguyen, T. C. et al. Mapping RNA–RNA interactome and RNA structure in vivo by MARIO. Nat. Commun. 7, 12023 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Ziv, O. et al. COMRADES determines in vivo RNA structures and interactions. Nat. Methods 15, 785–788 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Velema, W. A., Park, H. S., Kadina, A., Orbai, L. & Kool, E. T. Trapping transient RNA complexes by chemically reversible acylation. Angew. Chem. Int. Ed. Engl. 59, 22017–22022 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Van Damme, R. et al. Chemical reversible crosslinking enables measurement of RNA 3D distances and alternative conformations in cells. Nat. Commun. 13, 911 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  44. Christy, T. W. et al. Direct mapping of higher-order RNA interactions by SHAPE-JuMP. Biochemistry 60, 1971–1982 (2021).

    Article  CAS  PubMed  Google Scholar 

  45. Corley, M. et al. Footprinting SHAPE-eCLIP reveals transcriptome-wide hydrogen bonds at RNA–protein interfaces. Mol. Cell 80, 903–914.e8 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Chan, D. et al. Diverse functional elements in RNA predicted transcriptome-wide by orthogonal RNA structure probing. Nucleic Acids Res. 49, 11868–11882 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Weidmann, C. A., Mustoe, A. M., Jariwala, P. B., Calabrese, J. M. & Weeks, K. M. Analysis of RNA–protein networks with RNP-MaP defines functional hubs on RNA. Nat. Biotechnol. 39, 347–356 (2021).

    Article  CAS  PubMed  Google Scholar 

  48. Li, P. et al. Integrative analysis of Zika virus genome RNA structure reveals critical determinants of viral infectivity. Cell Host Microbe 24, 875–886.e5 (2018).

    Article  CAS  PubMed  Google Scholar 

  49. Huber, R. G. et al. Structure mapping of dengue and Zika viruses reveals functional long-range interactions. Nat. Commun. 10, 1408 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  50. Ziv, O. et al. The short- and long-range RNA–RNA interactome of SARS-CoV-2. Mol. Cell 80, 1067–1077.e5 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Yang, S. L. et al. Comprehensive mapping of SARS-CoV-2 interactions in vivo reveals functional virus–host interactions. Nat. Commun. 12, 5113 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Zhang, Y. et al. In vivo structure and dynamics of the SARS-CoV-2 RNA genome. Nat. Commun. 12, 5695 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Uroda, T. et al. Conserved pseudoknots in lncRNA MEG3 are essential for stimulation of the p53 pathway. Mol. Cell 75, 982–995.e9 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Mustoe, A. M. et al. Pervasive regulatory functions of mRNA structure revealed by high-resolution SHAPE probing. Cell 173, 181–195.e18 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Beaudoin, J.-D. et al. Analyses of mRNA structure dynamics identify embryonic gene regulatory programs. Nat. Struct. Mol. Biol. 25, 677–686 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Rouskin, S., Zubradt, M., Washietl, S., Kellis, M. & Weissman, J. S. Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo. Nature 505, 701–705 (2014).

    Article  CAS  PubMed  Google Scholar 

  57. Sanford, T. J., Mears, H. V., Fajardo, T., Locker, N. & Sweeney, T. R. Circularization of flavivirus genomic RNA inhibits de novo translation initiation. Nucleic Acids Res. 47, 9789–9802 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Gabryelska, M. M. et al. Global mapping of RNA homodimers in living cells. Genome Res. 32, 956–967 (2022).

    PubMed  PubMed Central  Google Scholar 

  59. Dethoff, E. A., Chugh, J., Mustoe, A. M. & Al-Hashimi, H. M. Functional complexity and regulation through RNA dynamics. Nature 482, 322–330 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Herschlag, D. RNA chaperones and the RNA folding problem. J. Biol. Chem. 270, 20871–20874 (1995).

    Article  CAS  PubMed  Google Scholar 

  61. Ding, Y. et al. In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features. Nature 505, 696–700 (2014).

    Article  CAS  PubMed  Google Scholar 

  62. Incarnato, D., Neri, F., Anselmi, F. & Oliviero, S. Genome-wide profiling of mouse RNA secondary structures reveals key features of the mammalian transcriptome. Genome Biol. 15, 491 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  63. Watters, K. E., Strobel, E. J., Yu, A. M., Lis, J. T. & Lucks, J. B. Cotranscriptional folding of a riboswitch at nucleotide resolution. Nat. Struct. Mol. Biol. 23, 1124–1131 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Incarnato, D. et al. In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding. Nucleic Acids Res. 45, 9716–9725 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Cheng, C. Y., Kladwang, W., Yesselman, J. D. & Das, R. RNA structure inference through chemical mapping after accidental or intentional mutations. Proc. Natl Acad. Sci. USA 114, 9876–9881 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Byeon, G. W. et al. Functional and structural basis of extreme conservation in vertebrate 5′ untranslated regions. Nat. Genet. 53, 729–741 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Cordero, P. & Das, R. Rich RNA structure landscapes revealed by mutate-and-map analysis. PLoS Comput. Biol. 11, e1004473 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  68. Aviran, S. & Incarnato, D. Computational approaches for RNA structure ensemble deconvolution from structure probing data. J. Mol. Biol. https://doi.org/10.1016/j.jmb.2022.167635 (2022).

    Article  PubMed  Google Scholar 

  69. Li, H. & Aviran, S. Statistical modeling of RNA structure profiling experiments enables parsimonious reconstruction of structure landscapes. Nat. Commun. 9, 606 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  70. Spasic, A., Assmann, S. M., Bevilacqua, P. C. & Mathews, D. H. Modeling RNA secondary structure folding ensembles using SHAPE mapping data. Nucleic Acids Res. 46, 314–323 (2018).

    Article  CAS  PubMed  Google Scholar 

  71. Zhou, J. et al. IRIS: a method for predicting in vivo RNA secondary structures using PARIS data. Quant. Biol. 8, 369–381 (2020).

    Article  CAS  Google Scholar 

  72. McCaskill, J. S. The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29, 1105–1119 (1990).

    Article  CAS  PubMed  Google Scholar 

  73. Tomezsko, P. J. et al. Determination of RNA structural diversity and its role in HIV-1 RNA splicing. Nature 582, 438–442 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Morandi, E. et al. Genome-scale deconvolution of RNA structure ensembles. Nat. Methods 18, 249–252 (2021).

    Article  CAS  PubMed  Google Scholar 

  75. Olson, S. W. et al. Discovery of a large-scale, cell-state-responsive allosteric switch in the 7SK RNA using DANCE-MaP. Mol. Cell 82, 1708–1723.e10 (2022).

    Article  CAS  PubMed  Google Scholar 

  76. Wu, M. T.-P. & D’Souza, V. Alternate RNA structures. Cold Spring Harb. Perspect. Biol. 12, a032425 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Sherpa, C., Rausch, J. W., Le Grice, S. F. J., Hammarskjold, M.-L. & Rekosh, D. The HIV-1 Rev response element (RRE) adopts alternative conformations that promote different rates of virus replication. Nucleic Acids Res. 43, 4676–4686 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Lan, T. C. T. et al. Secondary structural ensembles of the SARS-CoV-2 RNA genome in infected cells. Nat. Commun. 13, 1128 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Manfredonia, I. & Incarnato, D. Structure and regulation of coronavirus genomes: state-of-the-art and novel insights from SARS-CoV-2 studies. Biochemical Soc. Trans. 49, 341–352 (2020).

    Article  Google Scholar 

  80. Plant, E. P. et al. A three-stemmed mRNA pseudoknot in the SARS coronavirus frameshift signal. PLoS Biol. 3, e172 (2005).

    Article  PubMed  PubMed Central  Google Scholar 

  81. Rangan, R. et al. De novo 3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures. Nucleic Acids Res. 49, 3092–3108 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Manfredonia, I. et al. Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements. Nucleic Acids Res. 48, 12436–12452 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Huston, N. C. et al. Comprehensive in vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms. Mol. Cell 81, 584–598.e5 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Schlick, T. et al. To knot or not to knot: multiple conformations of the SARS-CoV-2 frameshifting RNA element. J. Am. Chem. Soc. 143, 11404–11422 (2021).

    Article  CAS  PubMed  Google Scholar 

  85. Park, S.-J., Kim, Y.-G. & Park, H.-J. Identification of RNA pseudoknot-binding ligand that inhibits the –1 ribosomal frameshifting of SARS-coronavirus by structure-based virtual screening. J. Am. Chem. Soc. 133, 10094–10100 (2011).

    Article  CAS  PubMed  Google Scholar 

  86. Sun, Y. et al. Restriction of SARS-CoV-2 replication by targeting programmed −1 ribosomal frameshifting. Proc. Natl Acad. Sci. USA 118, e2023051118 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Fujinaga, K. P-TEFb as a promising therapeutic target. Molecules 25, E838 (2020).

    Article  Google Scholar 

  88. Hsue, B. & Masters, P. S. A bulged stem-loop structure in the 3’ untranslated region of the genome of the coronavirus mouse hepatitis virus is essential for replication. J. Virol. 71, 7567–7578 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Robertson, M. P. et al. The structure of a rigorously conserved RNA element within the SARS virus genome. PLOS Biol. 3, e5 (2004).

    Article  PubMed  PubMed Central  Google Scholar 

  90. Guo, A.-X., Cui, J.-J., Wang, L.-Y. & Yin, J.-Y. The role of CSDE1 in translational reprogramming and human diseases. Cell Commun. Signal. 18, 14 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Hajdin, C. E. et al. Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots. Proc. Natl Acad. Sci. USA 110, 5498–5503 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Batey, R. T. Riboswitches: still a lot of undiscovered country. RNA 21, 560–563 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Fazal, F. M. et al. Atlas of subcellular RNA localization revealed by APEX-seq. Cell 178, 473–490.e26 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Singha, M., Spitalny, L., Nguyen, K., Vandewalle, A. & Spitale, R. C. Chemical methods for measuring RNA expression with metabolic labeling. Wiley Interdiscip. Rev. RNA 12, e1650 (2021).

    Article  CAS  PubMed  Google Scholar 

  95. Yang, M. et al. In vivo single-molecule analysis reveals COOLAIR RNA structural diversity. Nature https://doi.org/10.1038/s41586-022-05135-9 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  96. Sengupta, A., Rice, G. M. & Weeks, K. M. Single-molecule correlated chemical probing reveals large-scale structural communication in the ribosome and the mechanism of the antibiotic spectinomycin in living cells. PLOS Biol. 17, e3000393 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Zeller, M. J. et al. SHAPE-enabled fragment-based ligand discovery for RNA. Proc. Natl Acad. Sci. USA 119, e2122660119 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Fang, L. et al. Pervasive transcriptome interactions of protein-targeted drugs. Preprint at https://doi.org/10.1101/2022.07.18.500496 (2022).

  99. Bushhouse, D. Z., Choi, E. K., Hertz, L. M. & Lucks, J. B. How does RNA fold dynamically? J. Mol. Biol. 167665 https://doi.org/10.1016/j.jmb.2022.167665 (2022).

  100. Strobel, E. J., Cheng, L., Berman, K. E., Carlson, P. D. & Lucks, J. B. A ligand-gated strand displacement mechanism for ZTP riboswitch transcription control. Nat. Chem. Biol. 15, 1067–1076 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Cheng, L. et al. Cotranscriptional RNA strand exchange underlies the gene regulation mechanism in a purine-sensing transcriptional riboswitch. Nucleic Acids Res. https://doi.org/10.1093/nar/gkac102 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  102. Saldi, T., Riemondy, K., Erickson, B. & Bentley, D. L. Alternative RNA structures formed during transcription depend on elongation rate and modify RNA processing. Mol. Cell 81, 1789–1801.e5 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Fu, Y., Dominissini, D., Rechavi, G. & He, C. Gene expression regulation mediated through reversible m6A RNA methylation. Nat. Rev. Genet. 15, 293–306 (2014).

    Article  CAS  PubMed  Google Scholar 

  104. Roost, C. et al. Structure and thermodynamics of N6-methyladenosine in RNA: a spring-loaded base modification. J. Am. Chem. Soc. 137, 2107–2115 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. Liu, N. et al. N6-Methyladenosine-dependent RNA structural switches regulate RNA–protein interactions. Nature 518, 560–564 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Aw, J. G. A. et al. Determination of isoform-specific RNA structure with nanopore long reads. Nat. Biotechnol. 39, 336–346 (2021).

    Article  CAS  PubMed  Google Scholar 

  107. Sun, L. et al. RNA structure maps across mammalian cellular compartments. Nat. Struct. Mol. Biol. 26, 322–330 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Liu, Z. et al. In vivo nuclear RNA structurome reveals RNA-structure regulation of mRNA processing in plants. Genome Biol. 22, 11 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Ray, P. S. et al. A stress-responsive RNA switch regulates VEGF expression. Nature 457, 915–919 (2009).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

This work was supported by funding from the Groningen Biomolecular Sciences and Biotechnology Institute (GBB, University of Groningen) to D.I.

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  1. Department of Pharmaceutical Sciences, University of California, Irvine, CA, USA

    Robert C. Spitale

  2. Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands

    Danny Incarnato

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  2. Danny Incarnato
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Glossary

Boltzmann distribution

A probability distribution describing the probability that a system will be in a certain state (in this case, a certain RNA conformation) as a function of the state’s energy and of the system’s temperature.

Covariation

In an RNA multiple sequence alignment, two covarying positions are those for which the sequence changes but their ability to base-pair is preserved.

Hydrogen abstraction

Removal of an atom or group from a molecule by a radical.

Pseudoknot

A non-nested structural RNA motif formed upon base-pairing between the loop of a secondary structure element (such as a stem-loop (SL)) and any complementary region along the RNA.

RNA structurome

The full range of RNA structures formed by the transcriptome of an organism.

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Spitale, R.C., Incarnato, D. Probing the dynamic RNA structurome and its functions. Nat Rev Genet 24, 178–196 (2023). https://doi.org/10.1038/s41576-022-00546-w

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