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Production of functional oocytes requires maternally expressed PIWI genes and piRNAs in golden hamsters

Abstract

Many animals have a conserved adaptive genome defence system known as the Piwi-interacting RNA (piRNA) pathway, which is essential for germ cell development and function. Disruption of individual mouse Piwi genes results in male but not female sterility, leading to the assumption that PIWI genes play little or no role in mammalian oocytes. Here, we report the generation of PIWI-defective golden hamsters, which have defects in the production of functional oocytes. The mechanisms involved vary among the hamster PIWI genes, whereby the lack of PIWIL1 has a major impact on gene expression, including hamster-specific young transposon de-silencing, whereas PIWIL3 deficiency has little impact on gene expression in oocytes, although DNA methylation was reduced to some extent in PIWIL3-deficient oocytes. Our findings serve as the foundation for developing useful models to study the piRNA pathway in mammalian oocytes, including humans.

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Fig. 1: Characterization of male phenotypes and piRNAs in the testes of PIWIL1-deficient golden hamsters.
Fig. 2: Female fertility phenotypes of PIWIL1-deficient and PIWIL3-deficient golden hamsters.
Fig. 3: Characterization of small RNAs in oocytes of PIWIL1-deficient and PIWIL3-deficient golden hamsters.
Fig. 4: Silencing of a number of genes and TEs requires PIWIL1, but not PIWIL3, in golden hamster MII oocytes.
Fig. 5: PIWIL1 and PIWIL1–piRNAs have an impact on TE silencing in MII oocytes.
Fig. 6: Loss of PIWIL3 leads to changes in DNA methylation in GV oocytes of golden hamsters.
Fig. 7: CG methylation levels of PIWIL3–piRNA clusters and targets.

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Data availability

The raw sequence data generated during this study are available from the Gene Expression Omnibus repository under accession number GSE164356. Requests for materials should be addressed to H. Siomi. Source data are provided with this paper. All data presented in this study are available in the main text or the supplementary materials.

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Acknowledgements

We thank all members of the Siomi Laboratory, especially H. Ishizu and K. Murano, for discussions and comments on this work, I. Ishimatsu for preparing paraffin sections, and H. Nishihara (Tokyo Institute of Technology) for his comments on hamster TEs. We also thank J. Oishi of the Sasaki Laboratory and T. Akinaga (Laboratory for Research Support, Medical Institute of Bioregulation, Kyushu University) for their help with whole-genome bisulfite sequencing. We are grateful to P. Svoboda (IMG, Czech Academy of Sciences), J. Li (Model Animal Research Center, Nanjing Medical University) and L. Wu (Shanghai Institute of Biochemistry and cell Biology, CAS) for sharing unpublished data. We are also grateful to M. Okabe and M. Ikawa (Osaka University) for their comments on the manuscript. Funding included support from a Grant-in-Aid for the Japan Society for the Promotion of Science (JSPS) KAKENHI grant no. 20H03175 (to H.H.), the Takeda Science Foundation (to H.H.), a JSPS Fellows (18J22025) (to K.I.), from JSPS KAKENHI grant nos 19H05268 and 18H02421, and from JST PRESTO grant no. JPMJPR20E2 (to Y.W.I.), for Scientific Research (S) (25221003) and the Program of totipotency (19H05753) (to H. Siomi). H. Siomi is also a recipient of funding for the project for elucidating and controlling mechanisms of ageing and longevity (1005442) from the Japan Agency for Medical Research and Development (AMED). This work was also supported by JSPS KAKENHI grant no. JP18H05214 (H. Sasaki).

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Authors

Contributions

H. Siomi and H.H. designed the experiments. H.H. generated the PIWIL1-deficient and PIWIL3-deficient hamsters (with the help of H.M.). K.I. and Y.W.I. conducted small RNA-seq and RNA-seq and analysed the obtained data. W.K.A.Y. and H. Sasaki conducted whole-genome bisulfite sequencing and analysed the obtained data. H. Siomi, H.H., Y.W.I. and H. Sasaki wrote the paper.

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Correspondence to Haruhiko Siomi.

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The authors declare no competing interests.

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Peer review information Nature Cell Biology thanks René Ketting, Jeremy Wang and the other, anonymous, reviewers for their contribution to the peer review of this work. Peer reviewer reports are available.

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Extended data

Extended Data Fig. 1 Strategy for the production of PIWIL1-deficient golden hamsters by CRISPR/Cas9.

a, Structure of the golden hamster PIWIL1 gene and target locus for sgRNA. b, The guide RNA sequence for the golden hamster PIWIL1 gene. c, Production of PIWIL1-deficient golden hamster lines. d, The PIWIL1 nucleic acid and amino acid sequences of the targeted site in wild-type hamsters. Upper case underlined denotes the exon sequence, bold with a red box denotes the target sequence, and red denotes the deleted sequence in the 15Adel4 line. e, The PIWIL1 nucleic acid and amino acid sequence of the targeted site in the mutant line (15 A del4). The amino acid sequences in red indicate sequences changed by deletion.

Extended Data Fig. 2 Strategy for the production of PIWIL3-deficient golden hamster by CRISPR/Cas9.

a, Structure of the golden hamster PIWIL3 gene and target loci for sgRNAs. b, The guide RNA sequences for the golden hamster PIWIL3 gene. c, Production of PIWIL3-deficient golden hamster lines. d, The PIWIL3 nucleic acid and amino acid sequence of targeted site in wild-type hamsters. Upper case underlined denotes the exon sequences, bold with a red box denotes the target sequences, and red denotes the deleted sequence in the 26Adel192 line. e, The PIWIL1 nucleic acid and amino acid sequence of targeted site in the mutant line (26 A del192). The amino acid sequences in red indicate sequences changed by deletion.

Extended Data Fig. 3 Defects in spermatogenesis in PIWIL1-deficient male golden hamsters.

a, Testis and cauda epididymis of 1-week-old (1w), 4-week-old (4w) and 10-week-old (10w) from wild-type and PIWIL1-deficient golden hamsters. Scale bars = 10 mm. b, Sperm from the 10w wild-type and PIWIL1-deficient cauda epididymis. Scale bars = 50 µm. c, d, Hematoxylin and eosin-stained 4w (c) and 15w (d) testis sections of wild-type and PIWIL1m/m hamsters, respectively. Scale bars = 100 µm. e, anti-PIWIL1 antibody staining of testis sections of 15-w wild-type and PIWIL1m/m hamsters. Scale bars = 100 µm.

Extended Data Fig. 4 Lack of PIWI proteins in oocytes of PIWIL1- or PIWIL3-deficient golden hamsters.

a, Total lysates of 20 MII oocytes each from heterozygous mutant (w/m) and homozygous mutant (m/m) golden hamsters were subjected to western blotting. TUBB was used as the loading control. Spectra™ Multicolor Broad Range Protein Ladder (Thermo Fisher Scientific) was used as size marker. b, Immunological staining of PIWIL1- and PIWIL3-deficient ovaries with an antiPIWIL1 and PIWIL3 antibodies. The arrowheads in the mutants indicate the ovarian follicles. The zona pellucida fixed with paraformaldehyde showed autofluorescence. In particular, PIWIL1, which requires a long exposure time, has strong ring-shaped fluorescence both in the wild type and PIWIL1m/m. Scale bars = 50 µm. c, Ovarian sections from 8‐week‐old wild-type and PIWIL1- and PIWIL3-deficient golden hamsters. Hematoxylin and eosinstained ovarian sections of wild-type, PIWIL1- and PIWIL3-deficient golden hamsters. Scale bars = 200 µm. Note: By fixing PIWIs, the antigenicity is weakened. PIWIL1 antigenicity is particularly weak even after antigen retrieval treatment: therefore, the exposure time is long and the background of the zona pellucida becomes visible.

Source data

Extended Data Fig. 5 Changes in the expression levels of each unique small RNA sequence in PIWI-deficient mutants.

An MA plot showing the expression level of each unique small RNA sequence. To calculate log2 fold change and expression levels, 1 was added to each value to calculate the levels of small RNA sequences with 0 in either sample.

Extended Data Fig. 6 Gene ontology analysis of MII oocytes in PIWIL1-deficient golden hamsters.

a, b, Enriched gene ontology (biological process) terms using DEGs obtained in PIWIL1-deficient MII oocyte transcriptome analysis. Upregulated genes in the PIWIL1-deficient MII oocytes (a). Downregulated genes in the PIWIL1-deficient MII oocytes (b). Terms with p-values lower than 0.001 are listed.

Source data

Extended Data Fig. 7 Nucleolus abnormalities in 2 C embryos derived from PIWIL1-deficient oocytes.

a, Pro-nucleus morphology of the zygotes. There were no pro-nucleus morphology differences in maternally PIWIL1- and PIWIL3-deficient zygotes. b, Nucleus morphology of the 2 C embryos. PIWIL1m/m showed a single large nucleolus, while PIWIL1w/m and PIWIL3m/m formed multiple small nucleoli. Enlarged view of box showed nucleus and arrows indicate the nucleolus. Scale bars = 50 µm.

Extended Data Fig. 8 DNA methylation in PIWIL1- and PIWIL3-deficient GV oocyte.

a, b, 5mC staining of PIWIL1-deficient (a) and PIWIL3-deficient GV oocytes (b). The amounts of 5mC were determined by measuring the fluorescence intensity using image J software (right). n indicates the number of independent GV oocytes collected from three females and used for analysis (Extended Data Fig. 9), and error bars indicate ± s.d. (***P=4.01e-8 by 2-sided t-test) Scale bars = 50 µm.

Source data

Extended Data Fig. 9 Representative GV oocytes stained with anti-5mC antibody.

GV oocytes were stained with a 5mC antibody (33D3) and the fluorescence GV nuclei were imaged. The fluorescence was analyzed by ImageJ and used to be described in Extended Data Fig. 8. Scale bars = 25 µm.

Extended Data Fig. 10 Meiosis and MII spindle formation in ovulated oocytes of PIWIL3-deficient golden hamsters.

a, PIWIL3w/m and PIWIL3m/m oocytes were collected, and the stages of meiosis at 7 and 10 am in the morning were analyzed following TUBA and DAPI staining. b, MII oocytes at 10 am in the morning were stained with anti-TUBA antibody (green) and DAPI (blue). Scale bars = 5 µm. c, The size of the MII spindles (A and B in Extended Data Fig. 10b) was measured and compared between PIWL3w/m and PIWL3m/m. n indicates the number of independent MII oocytes collected from three females and used for analysis, error bars indicate ± s.d. (A: ***P=0.000417, B: *P=0.0377 by 2-sided t-test).

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Supplementary Table 1: Sequencing and mapping summary of whole-genome bisulfate sequencing. Supplementary Table 2: Primers and gRNA.

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Hasuwa, H., Iwasaki, Y.W., Au Yeung, W.K. et al. Production of functional oocytes requires maternally expressed PIWI genes and piRNAs in golden hamsters. Nat Cell Biol 23, 1002–1012 (2021). https://doi.org/10.1038/s41556-021-00745-3

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