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The Microprocessor controls the activity of mammalian retrotransposons

Nature Structural & Molecular Biology volume 20, pages 1173–1181 (2013)Cite this article

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Abstract

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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Figure 1: DGCR8 binds a constellation of transcripts from repetitive elements.
Figure 2: The Microprocessor regulates the abundance of L1 mRNA and L1-encoded ORF1 protein.
Figure 3: The 5′ UTR of L1 mRNA is cleaved by immunopurified Drosha in vitro.
Figure 4: The Microprocessor negatively regulates L1 retrotransposition in vivo.
Figure 5: Alu is processed in vitro, and its retrotransposition is regulated by the Microprocessor.
Figure 6: LINE-1 regulation by the Microprocessor is Dicer and miRNA independent.
Figure 7: Model for the control of LINE-1 and Alu retrotransposition by the Microprocessor.

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Acknowledgements

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).

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  1. Sara R Heras and Sara Macias: These authors contributed equally to this work.

Authors and Affiliations

  1. Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK

    Sara R Heras, Sara Macias, Noemí Fernandez & Javier F Cáceres

  2. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government (GENYO), Granada, Spain

    Sara R Heras, David Cano & José L Garcia-Perez

  3. Computational Genomics Group, Universitat Pompeu Fabra, Barcelona, Spain

    Mireya Plass & Eduardo Eyras

  4. Department of Biology, Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark

    Mireya Plass

  5. Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain

    Eduardo Eyras

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Contributions

S.R.H., S.M., J.L.G.-P. and J.F.C. conceived of, designed and interpreted the experiments. S.R.H., S.M., D.C. and N.F. performed the experiments and data analysis. M.P. and E.E. provided all the bioinformatics analysis, including mapping of the CLIP tags to the genome and statistical analysis. J.L.G.-P. and J.F.C. supervised the whole project. The manuscript was written by all authors.

Corresponding authors

Correspondence to José L Garcia-Perez or Javier F Cáceres.

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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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