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Selective silencing of euchromatic L1s revealed by genome-wide screens for L1 regulators

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Abstract

Transposable elements (TEs) are now recognized not only as parasitic DNA, whose spread in the genome must be controlled by the host, but also as major players in genome evolution and regulation1–6. Long INterspersed Element-1 (LINE-1 or L1), the only currently autonomous mobile transposon in humans, occupies 17% of the genome and continues to generate inter- and intra-individual genetic variation, in some cases resulting in disease1–7. Nonetheless, how L1 activity is controlled and what function L1s play in host gene regulation remain incompletely understood. Here, we use CRISPR/Cas9 screening strategies in two distinct human cell lines to provide the first genome-wide survey of genes involved in L1 retrotransposition control. We identified functionally diverse genes that either promote or restrict L1 retrotransposition. These genes, often associated with human diseases, control the L1 lifecycle at transcriptional or post-transcriptional levels and in a manner that can depend on the endogenous L1 sequence, underscoring the complexity of L1 regulation. We further investigated L1 restriction by MORC2 and human silencing hub (HUSH) complex subunits MPP8 and TASOR8. HUSH/MORC2 selectively bind evolutionarily young, full-length L1s located within transcriptionally permissive euchromatic environment, and promote H3K9me3 deposition for transcriptional silencing. Interestingly, these silencing events often occur within introns of transcriptionally active genes and lead to down-regulation of host gene expression in a HUSH/MORC2-dependent manner. Together, we provide a rich resource for studies of L1 retrotransposition, elucidate a novel L1 restriction pathway, and illustrate how epigenetic silencing of TEs rewires host gene expression programs.

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Author information

Author notes

    • Edward Grow

    Present address: Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 841125550, USA.

    • Nian Liu
    •  & Cameron H. Lee

    Co-first author

Affiliations

  1. Department of Chemical and Systems Biology, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA

    • Nian Liu
    • , Tomek Swigut
    • , Bo Gu
    •  & Joanna Wysocka
  2. Department of Genetics, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA

    • Cameron H. Lee
    • , Edward Grow
    •  & Michael Bassik
  3. Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA

    • Michael Bassik
  4. Institute of Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA

    • Joanna Wysocka
  5. Department of Developmental Biology, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA

    • Joanna Wysocka
  6. Howard Hughes Medical Institute, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA

    • Joanna Wysocka

Authors

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Corresponding authors

Correspondence to Michael Bassik or Joanna Wysocka.

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    This file contains the uncropped scans with size marker indications.

  2. 2.

    Life Sciences Reporting Summary

Excel files

  1. 1.

    Supplementary Table 1

    This table contains genome-wide screen results in K562 cells and HeLa cells.

  2. 2.

    Supplementary Table 2

    This table contains the secondary screen results in K562 cells and HeLa cells.

  3. 3.

    Supplementary Table 3

    The sequence of sgRNAs in this study.

  4. 4.

    Supplementary Table 4

    This table contains the sequences of oligonucleotides used in this work.

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