More than half of the human genome is made of transposable elements whose ongoing mobilization is a driving force in genetic diversity; however, little is known about how the host regulates their activity. Here, we show that the Microprocessor (Drosha-DGCR8), which is required for microRNA biogenesis, also recognizes and binds RNAs derived from human long interspersed element 1 (LINE-1), Alu and SVA retrotransposons. Expression analyses demonstrate that cells lacking a functional Microprocessor accumulate LINE-1 mRNA and encoded proteins. Furthermore, we show that structured regions of the LINE-1 mRNA can be cleaved in vitro by Drosha. Additionally, we used a cell culture–based assay to show that the Microprocessor negatively regulates LINE-1 and Alu retrotransposition in vivo. Altogether, these data reveal a new role for the Microprocessor as a post-transcriptional repressor of mammalian retrotransposons and a defender of human genome integrity.
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Beck, C.R., Garcia-Perez, J.L., Badge, R.M. & Moran, J.V. LINE-1 elements in structural variation and disease. Annu. Rev. Genomics Hum. Genet. 12, 187–215 (2011).
Brouha, B. et al. Hot L1s account for the bulk of retrotransposition in the human population. Proc. Natl. Acad. Sci. USA 100, 5280–5285 (2003).
Dewannieux, M., Esnault, C. & Heidmann, T. LINE-mediated retrotransposition of marked Alu sequences. Nat. Genet. 35, 41–48 (2003).
Hancks, D.C., Goodier, J.L., Mandal, P.K., Cheung, L.E. & Kazazian, H.H. Retrotransposition of marked SVA elements by human L1s in cultured cells. Hum. Mol. Genet. 20, 3386–3400 (2011).
Raiz, J. et al. The non-autonomous retrotransposon SVA is trans-mobilized by the human LINE-1 protein machinery. Nucleic Acids Res. 40, 1666–1683 (2012).
Esnault, C., Maestre, J. & Heidmann, T. Human LINE retrotransposons generate processed pseudogenes. Nat. Genet. 24, 363–367 (2000).
Wei, W. et al. Human L1 retrotransposition: cis preference versus trans complementation. Mol. Cell. Biol. 21, 1429–1439 (2001).
Garcia-Perez, J.L., Doucet, A.J., Bucheton, A., Moran, J.V. & Gilbert, N. Distinct mechanisms for trans-mediated mobilization of cellular RNAs by the LINE-1 reverse transcriptase. Genome Res. 17, 602–611 (2007).
Iskow, R.C. et al. Natural mutagenesis of human genomes by endogenous retrotransposons. Cell 141, 1253–1261 (2010).
Kidd, J.M. et al. A human genome structural variation sequencing resource reveals insights into mutational mechanisms. Cell 143, 837–847 (2010).
Baillie, J.K. et al. Somatic retrotransposition alters the genetic landscape of the human brain. Nature 479, 534–537 (2011).
Boissinot, S., Entezam, A., Young, L., Munson, P.J. & Furano, A.V. The insertional history of an active family of L1 retrotransposons in humans. Genome Res. 14, 1221–1231 (2004).
Martin, S.L. Ribonucleoprotein particles with LINE-1 RNA in mouse embryonal carcinoma cells. Mol. Cell. Biol. 11, 4804–4807 (1991).
Moran, J.V. et al. High frequency retrotransposition in cultured mammalian cells. Cell 87, 917–927 (1996).
Batzer, M.A. & Deininger, P.L. Alu repeats and human genomic diversity. Nat. Rev. Genet. 3, 370–379 (2002).
Bennett, E.A. et al. Active Alu retrotransposons in the human genome. Genome Res. 18, 1875–1883 (2008).
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).
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).
Bushati, N. & Cohen, S.M. microRNA functions. Annu. Rev. Cell Dev. Biol. 23, 175–205 (2007).
Denli, A.M., Tops, B.B.J., Plasterk, R.H.A., Ketting, R.F. & Hannon, G.J. Processing of primary microRNAs by the Microprocessor complex. Nature 432, 231–235 (2004).
Gregory, R.I. et al. The Microprocessor complex mediates the genesis of microRNAs. Nature 432, 235–240 (2004).
Han, J. et al. The Drosha-DGCR8 complex in primary microRNA processing. Genes Dev. 18, 3016–3027 (2004).
Kim, V.N., Han, J. & Siomi, M.C. Biogenesis of small RNAs in animals. Nat. Rev. Mol. Cell Biol. 10, 126–139 (2009).
Macias, S. et al. DGCR8 HITS-CLIP reveals novel functions for the Microprocessor. Nat. Struct. Mol. Biol. 19, 760–766 (2012).
Faulkner, G.J. et al. The regulated retrotransposon transcriptome of mammalian cells. Nat. Genet. 41, 563–571 (2009).
Macia, A. et al. Epigenetic control of retrotransposon expression in human embryonic stem cells. Mol. Cell. Biol. 31, 300–316 (2011).
Deininger, P. Alu elements: know the SINEs. Genome Biol. 12, 236 (2011).
Speek, M. Antisense promoter of human L1 retrotransposon drives transcription of adjacent cellular genes. Mol. Cell. Biol. 21, 1973–1985 (2001).
Carninci, P. et al. The transcriptional landscape of the mammalian genome. Science 309, 1559–1563 (2005).
Garcia-Perez, J.L. et al. Epigenetic silencing of engineered L1 retrotransposition events in human embryonic carcinoma cells. Nature 466, 769–773 (2010).
Yeom, K.-H., Lee, Y., Han, J., Suh, M.R. & Kim, V.N. Characterization of DGCR8/Pasha, the essential cofactor for Drosha in primary miRNA processing. Nucleic Acids Res. 34, 4622–4629 (2006).
Perepelitsa-Belancio, V. & Deininger, P. RNA truncation by premature polyadenylation attenuates human mobile element activity. Nat. Genet. 35, 363–366 (2003).
Belancio, V.P., Hedges, D.J. & Deininger, P. LINE-1 RNA splicing and influences on mammalian gene expression. Nucleic Acids Res. 34, 1512–1521 (2006).
Wissing, S. et al. Reprogramming somatic cells into iPS cells activates LINE-1 retroelement mobility. Hum. Mol. Genet. 21, 208–218 (2012).
Han, J. et al. Posttranscriptional crossregulation between Drosha and DGCR8. Cell 136, 75–84 (2009).
Bourc'his, D. & Bestor, T.H. Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature 431, 96–99 (2004).
Coufal, N.G. et al. L1 retrotransposition in human neural progenitor cells. Nature 460, 1127–1131 (2009).
Wang, Y., Medvid, R., Melton, C., Jaenisch, R. & Blelloch, R. DGCR8 is essential for microRNA biogenesis and silencing of embryonic stem cell self-renewal. Nat. Genet. 39, 380–385 (2007).
Naas, T.P. et al. An actively retrotransposing, novel subfamily of mouse L1 elements. EMBO J. 17, 590–597 (1998).
DeBerardinis, R.J., Goodier, J.L., Ostertag, E.M. & Kazazian, H.H. Rapid amplification of a retrotransposon subfamily is evolving the mouse genome. Nat. Genet. 20, 288–290 (1998).
Goodier, J.L., Ostertag, E.M., Du, K. & Kazazian, H.H. A novel active L1 retrotransposon subfamily in the mouse. Genome Res. 11, 1677–1685 (2001).
Dombroski, B.A., Scott, A.F. & Kazazian, H.H. Two additional potential retrotransposons isolated from a human L1 subfamily that contains an active retrotransposable element. Proc. Natl. Acad. Sci. USA 90, 6513–6517 (1993).
Morrish, T.A. et al. DNA repair mediated by endonuclease-independent LINE-1 retrotransposition. Nat. Genet. 31, 159–165 (2002).
Bogerd, H.P. et al. Cellular inhibitors of long interspersed element 1 and Alu retrotransposition. Proc. Natl. Acad. Sci. USA 103, 8780–8785 (2006).
Wagstaff, B.J., Barnerssoi, M. & Roy-Engel, A.M. Evolutionary conservation of the functional modularity of primate and murine LINE-1 elements. PLoS ONE 6, e19672 (2011).
Han, J.S. & Boeke, J.D. A highly active synthetic mammalian retrotransposon. Nature 429, 314–318 (2004).
Borchert, G.M., Lanier, W. & Davidson, B.L. RNA polymerase III transcribes human microRNAs. Nat. Struct. Mol. Biol. 13, 1097–1101 (2006).
Guil, S. & Cáceres, J.F. The multifunctional RNA-binding protein hnRNP A1 is required for processing of miR-18a. Nat. Struct. Mol. Biol. 14, 591–596 (2007).
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).
He, L. & Hannon, G.J. MicroRNAs: small RNAs with a big role in gene regulation. Nat. Rev. Genet. 5, 522–531 (2004).
Garcia-Perez, J.L. et al. LINE-1 retrotransposition in human embryonic stem cells. Hum. Mol. Genet. 16, 1569–1577 (2007).
Kano, H. et al. L1 retrotransposition occurs mainly in embryogenesis and creates somatic mosaicism. Genes Dev. 23, 1303–1312 (2009).
Muotri, A.R. et al. Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition. Nature 435, 903–910 (2005).
Lee, E. et al. Landscape of somatic retrotransposition in human cancers. Science 337, 967–971 (2012).
Evrony, G.D. et al. Single-neuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain. Cell 151, 483–496 (2012).
Solyom, S. et al. Extensive somatic L1 retrotransposition in colorectal tumors. Genome Res. 22, 2328–2338 (2012).
Goodier, J.L., Cheung, L.E. & Kazazian, H.H. Mapping the LINE1 ORF1 protein interactome reveals associated inhibitors of human retrotransposition. Nucleic Acids Res. doi:10.1093/nar/gkt512 (2013).
Stetson, D.B., Ko, J.S., Heidmann, T. & Medzhitov, R. Trex1 prevents cell-intrinsic initiation of autoimmunity. Cell 134, 587–598 (2008).
Arjan-Odedra, S., Swanson, C.M., Sherer, N.M., Wolinsky, S.M. & Malim, M.H. Endogenous MOV10 inhibits the retrotransposition of endogenous retroelements but not the replication of exogenous retroviruses. Retrovirology 9, 53 (2012).
Goodier, J.L., Cheung, L.E. & Kazazian, H.H. MOV10 RNA helicase is a potent inhibitor of retrotransposition in cells. PLoS Genet. 8, e1002941 (2012).
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
Fujita, P.A. et al. The UCSC Genome Browser database: update 2011. Nucleic Acids Res. 39, D876–D882 (2011).
Jurka, J. et al. Repbase update: a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 110, 462–467 (2005).
Richardson, J.E. fjoin: simple and efficient computation of feature overlaps. J. Comput. Biol. 13, 1457–1464 (2006).
Slater, G.S.C. & Birney, E. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6, 31 (2005).
Zisoulis, D.G. et al. Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans. Nat. Struct. Mol. Biol. 17, 173–179 (2010).
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).
Goodier, J.L., Zhang, L., Vetter, M.R. & Kazazian, H.H. LINE-1 ORF1 protein localizes in stress granules with other RNA-binding proteins, including components of RNA interference RNA-induced silencing complex. Mol. Cell. Biol. 27, 6469–6483 (2007).
Wei, W., Morrish, T.A., Alisch, R.S. & Moran, J.V. A transient assay reveals that cultured human cells can accommodate multiple LINE-1 retrotransposition events. Anal. Biochem. 284, 435–438 (2000).
Beck, C.R. et al. LINE-1 retrotransposition activity in human genomes. Cell 141, 1159–1170 (2010).
Mathews, D.H., Sabina, J., Zuker, M. & Turner, D.H. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288, 911–940 (1999).
We thank N. Hastie and J.V. Moran for comments and critical reading of the manuscript. We also are grateful to M. Madej, J. Reddington and R. Meehan for advice on DNA methylation assays and to I. Adams for discussions. We thank R. Blelloch (University of California San Francisco, San Francisco, California, USA), V.N. Kim (Seoul National University, Seoul, Korea), S.L. Martin (University of Colorado School of Medicine, Aurora, Colorado, USA), A. Roy-Engel (Tulane Cancer Center, New Orleans, LA USA), T. Heidmann (Institut Gustave Roussy, Villejuif, France and Université Paris-Sud, Orsay, France) and J.V. Moran (Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, Michigan, USA) for their generous gifts of reagents. S.M. was supported by a long-term European Molecular Biology Organization postdoctoral fellowship. S.R.H. was supported by a Marie Curie Intra-European Fellowship and a Marie Curie CIG-Grant (PCIG10-GA-2011-303812). M.P. and E.E. were supported by the Spanish Ministry of Science (BIO2011-23920) and by the Sandra Ibarra Foundation (CSD2009-00080). M.P. is supported by the Novo Nordisk Foundation. J.L.G.-P. is supported by FP7-PEOPLE-2007-4-3-IRG, CICE-FEDER-P09-CTS-4980, PeS-FEDER-PI-002, FIS-FEDER-PI11/01489 and the Howard Hughes Medical Institute (IECS-55007420). J.F.C. was supported by Core funding from the Medical Research Council and by the Wellcome Trust (grant 095518/B/11/Z).
The authors declare no competing financial interests.
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Heras, S., Macias, S., Plass, M. et al. The Microprocessor controls the activity of mammalian retrotransposons. Nat Struct Mol Biol 20, 1173–1181 (2013). https://doi.org/10.1038/nsmb.2658
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