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.

  • Article
  • Published:

Loss of the Mili-interacting Tudor domain–containing protein-1 activates transposons and alters the Mili-associated small RNA profile

Nature Structural & Molecular Biology volume 16, pages 639–646 (2009)Cite this article

Abstract

Piwi proteins and their associated Piwi-interacting RNAs (piRNAs) are implicated in transposon silencing in the mouse germ line. There is currently little information on additional proteins in the murine Piwi complex and how they might regulate the entry of transcripts that accumulate as piRNAs in the Piwi ribonucleoprotein (piRNP). We isolated Mili-containing complexes from adult mouse testes and identified Tudor domain–containing protein-1 (Tdrd1) as a factor specifically associated with the Mili piRNP throughout spermatogenesis. Complex formation is promoted by the recognition of symmetrically dimethylated arginines at the N terminus of Mili by the tudor domains of Tdrd1. Similar to a Mili mutant, mice lacking Tdrd1 show derepression of L1 transposons accompanied by a loss of DNA methylation at their regulatory elements and delocalization of Miwi2 from the nucleus to the cytoplasm. Finally, we show that Mili piRNPs devoid of Tdrd1 accept the entry of abundant cellular transcripts into the piRNA pathway and accumulate piRNAs with a profile that is drastically different from that of the wild type. Our data suggest that Tdrd1 ensures the entry of correct transcripts into the normal piRNA pool.

Access through your institution
Buy or subscribe

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

Access options

Access through your institution

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

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

Figure 1: Tdrd1 is a Mili-specific interacting factor.
Figure 2: Tudor domains of Tdrd1 interact with the Mili N terminus, which carries symmetrical dimethyl modifications on RG dipeptides.
Figure 3: Tdrd1 associates with the Mili small RNAs throughout spermatogenesis.
Figure 4: Activation of L1 transposons in Tdrd1 mutant testes is coupled to loss of DNA methylation of the 5′ regulatory region of the L1 element.
Figure 5: Activation of L1 and mislocalization of Miwi2 in the fetal germ cells of Tdrd1 mutants.
Figure 6: Loss of Tdrd1 leads to overrepresentation of exonic reads in Mili.

Similar content being viewed by others

Accession codes

Accessions

Gene Expression Omnibus

References

  1. Filipowicz, W., Bhattacharyya, S.N. & Sonenberg, N. Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat. Rev. Genet. 9, 102–114 (2008).

    Article  CAS  Google Scholar 

  2. Aravin, A.A., Hannon, G.J. & Brennecke, J. The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science 318, 761–764 (2007).

    Article  CAS  Google Scholar 

  3. Seto, A.G., Kingston, R.E. & Lau, N.C. The coming of age for Piwi proteins. Mol. Cell 26, 603–609 (2007).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  5. Kuramochi-Miyagawa, S. et al. Mili, a mammalian member of piwi family gene, is essential for spermatogenesis. Development 131, 839–849 (2004).

    Article  CAS  Google Scholar 

  6. 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  Google Scholar 

  7. Deng, W. & Lin, H. miwi, a murine homolog of piwi, encodes a cytoplasmic protein essential for spermatogenesis. Dev. Cell 2, 819–830 (2002).

    Article  CAS  Google Scholar 

  8. 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  Google Scholar 

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

    Article  CAS  Google Scholar 

  10. 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  Google Scholar 

  11. Chuma, S. et al. Mouse tudor repeat-1 (MTR-1) is a novel component of chromatoid bodies/nuages in male germ cells and forms a complex with snRNPs. Mech. Dev. 120, 979–990 (2003).

    Article  CAS  Google Scholar 

  12. Liu, Y. et al. Structural basis for recognition of SMRT/N-CoR by the MYND domain and its contribution to AML1/ETO's activity. Cancer Cell 11, 483–497 (2007).

    Article  CAS  Google Scholar 

  13. 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  Google Scholar 

  14. Brahms, H. et al. The C-terminal RG dipeptide repeats of the spliceosomal Sm proteins D1 and D3 contain symmetrical dimethylarginines, which form a major B-cell epitope for anti-Sm autoantibodies. J. Biol. Chem. 275, 17122–17129 (2000).

    Article  CAS  Google Scholar 

  15. Hebert, M.D., Shpargel, K.B., Ospina, J.K., Tucker, K.E. & Matera, A.G. Coilin methylation regulates nuclear body formation. Dev. Cell 3, 329–337 (2002).

    Article  CAS  Google Scholar 

  16. Boisvert, F.M. et al. Symmetrical dimethylarginine methylation is required for the localization of SMN in Cajal bodies and pre-mRNA splicing. J. Cell Biol. 159, 957–969 (2002).

    Article  CAS  Google Scholar 

  17. Meister, G. & Fischer, U. Assisted RNP assembly: SMN and PRMT5 complexes cooperate in the formation of spliceosomal UsnRNPs. EMBO J. 21, 5853–5863 (2002).

    Article  CAS  Google Scholar 

  18. Gonsalvez, G.B. et al. Two distinct arginine methyltransferases are required for biogenesis of Sm-class ribonucleoproteins. J. Cell Biol. 178, 733–740 (2007).

    Article  CAS  Google Scholar 

  19. Chuma, S. et al. Tdrd1/Mtr-1, a tudor-related gene, is essential for male germ-cell differentiation and nuage/germinal granule formation in mice. Proc. Natl. Acad. Sci. USA 103, 15894–15899 (2006).

    Article  CAS  Google Scholar 

  20. Lane, N. et al. Resistance of IAPs to methylation reprogramming may provide a mechanism for epigenetic inheritance in the mouse. Genesis 35, 88–93 (2003).

    Article  CAS  Google Scholar 

  21. Martin, S.L. & Branciforte, D. Synchronous expression of LINE-1 RNA and protein in mouse embryonal carcinoma cells. Mol. Cell. Biol. 13, 5383–5392 (1993).

    Article  CAS  Google Scholar 

  22. Aravin, A.A. & Bourc'his, D. Small RNA guides for de novo DNA methylation in mammalian germ cells. Genes Dev. 22, 970–975 (2008).

    Article  CAS  Google Scholar 

  23. Carmell, M.A. et al. MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline. Dev. Cell 12, 503–514 (2007).

    Article  CAS  Google Scholar 

  24. Zhao, Q. et al. PRMT5-mediated methylation of histone H4R3 recruits DNMT3A, coupling histone and DNA methylation in gene silencing. Nat. Struct. Mol. Biol. 16, 304–311 (2009).

    Article  CAS  Google Scholar 

  25. Botuyan, M.V. et al. Structural basis for the methylation state-specific recognition of histone H4–K20 by 53BP1 and Crb2 in DNA repair. Cell 127, 1361–1373 (2006).

    Article  CAS  Google Scholar 

  26. Selenko, P. et al. SMN tudor domain structure and its interaction with the Sm proteins. Nat. Struct. Biol. 8, 27–31 (2001).

    Article  CAS  Google Scholar 

  27. Wang, J., Saxe, J.P., Tanaka, T., Chuma, S. & Lin, H. Mili interacts with tudor domain-containing protein 1 in regulating spermatogenesis. Curr. Biol. 19, 640–644 (2009).

    Article  CAS  Google Scholar 

  28. Kirino, Y. et al. Arginine methylation of Piwi proteins catalysed by dPRMT5 is required for Ago3 and Aub stability. Nat. Cell Biol. 11, 652–658 (2009).

    Article  CAS  Google Scholar 

  29. Anne, J., Ollo, R., Ephrussi, A. & Mechler, B.M. Arginine methyltransferase Capsuleen is essential for methylation of spliceosomal Sm proteins and germ cell formation in Drosophila . Development 134, 137–146 (2007).

    Article  CAS  Google Scholar 

  30. Gonsalvez, G.B., Rajendra, T.K., Tian, L. & Matera, A.G. The Sm-protein methyltransferase, dart5, is essential for germ-cell specification and maintenance. Curr. Biol. 16, 1077–1089 (2006).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  32. Pivot-Pajot, C. et al. Acetylation-dependent chromatin reorganization by BRDT, a testis-specific bromodomain-containing protein. Mol. Cell. Biol. 23, 5354–5365 (2003).

    Article  CAS  Google Scholar 

  33. Soper, S.F. et al. Mouse maelstrom, a component of nuage, is essential for spermatogenesis and transposon repression in meiosis. Dev. Cell 15, 285–297 (2008).

    Article  CAS  Google Scholar 

  34. Jurka, J. Repbase update: a database and an electronic journal of repetitive elements. Trends Genet. 16, 418–420 (2000).

    Article  CAS  Google Scholar 

  35. Kent, W.J. et al. The human genome browser at UCSC. Genome Res. 12, 996–1006 (2002).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank A. Aravin and G. Hannon (Cold Spring Harbour Laboratory), J. Martinez (Institute of Molecular Biotechnology, Vienna), S. Martin (University of Colorado School of Medicine), A. Bortvin (Carnegie Institution of Washington) and D. Schuemperli and M. Ruepp (University of Bern) for reagents. We thank the European Molecular Biology Laboratory (EMBL) Mononclonal Antibody Facility, Protein Expression and Gene Core facilities for antibody production and Solexa sequencing. We are grateful to D. O'Carroll, A. Verdel and W. Filipowicz and members of the Pillai group for excellent discussions and reading of the manuscript. Research in the Pillai group is supported by EMBL and a grant from Region Rhone Alp (CIBLE 2008).

Author information

Authors and Affiliations

  1. European Molecular Biology Laboratory, Grenoble Outstation, France

    Michael Reuter & Ramesh S Pillai

  2. Institute for Frontier Medical Sciences, Kyoto University, Japan

    Shinichiro Chuma & Takashi Tanaka

  3. European Molecular Biology Laboratory, Heidelberg, Germany

    Thomas Franz

  4. Institute of Molecular Pathology, Vienna, Austria

    Alexander Stark

Authors
  1. Michael Reuter
    View author publications

    You can also search for this author inPubMed Google Scholar

  2. Shinichiro Chuma
    View author publications

    You can also search for this author inPubMed Google Scholar

  3. Takashi Tanaka
    View author publications

    You can also search for this author inPubMed Google Scholar

  4. Thomas Franz
    View author publications

    You can also search for this author inPubMed Google Scholar

  5. Alexander Stark
    View author publications

    You can also search for this author inPubMed Google Scholar

  6. Ramesh S Pillai
    View author publications

    You can also search for this author inPubMed Google Scholar

Contributions

M.R. performed most of the experiments described in this study; S.C. provided immunostaining data and Tdrd1 mutant mice; T.T. purified germ cells by FACS; T.F. provided MS analysis; A.S. performed Solexa sequence analysis; R.S.P. designed the research and wrote the paper.

Corresponding author

Correspondence to Ramesh S Pillai.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–5 and Supplementary Tables 1–4 (PDF 1142 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Reuter, M., Chuma, S., Tanaka, T. et al. Loss of the Mili-interacting Tudor domain–containing protein-1 activates transposons and alters the Mili-associated small RNA profile. Nat Struct Mol Biol 16, 639–646 (2009). https://doi.org/10.1038/nsmb.1615

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsmb.1615

This article is cited by

Search

Advanced 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