Letter | Published:

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

Nature volume 553, pages 228232 (11 January 2018) | Download Citation


Transposable elements, also known as transposons, are now recognized not only as parasitic DNA, the spread of which in the genome must be controlled by the host, but also as major players in genome evolution and regulation1,2,3,4,5,6. Long interspersed element-1 (LINE-1, also known as L1), the only currently autonomous mobile transposon in humans, occupies 17% of the genome and generates inter- and intra-individual genetic variation, in some cases resulting in disease1,2,3,4,5,6,7. However, how L1 activity is controlled and the function of L1s in host gene regulation are not completely understood. Here we use CRISPR–Cas9 screening strategies in two distinct human cell lines to provide a genome-wide survey of genes involved in the control of L1 retrotransposition. We identify functionally diverse genes that either promote or restrict L1 retrotransposition. These genes, which are often associated with human diseases, control the L1 life cycle at the transcriptional or the post-transcriptional level in a manner that can depend on the endogenous L1 nucleotide sequence, underscoring the complexity of L1 regulation. We further investigate the restriction of L1 by the protein MORC2 and by the human silencing hub (HUSH) complex subunits MPP8 and TASOR8. HUSH and MORC2 can selectively bind evolutionarily young, full-length L1s located within transcriptionally permissive euchromatic environments, and promote deposition of histone H3 Lys9 trimethylation (H3K9me3) for transcriptional silencing. Notably, these silencing events often occur within introns of transcriptionally active genes, and lead to the downregulation of host gene expression in a HUSH-, MORC2-, and L1-dependent manner. Together, these results provide a rich resource for studies of L1 retrotransposition, elucidate a novel L1 restriction pathway and illustrate how epigenetic silencing of transposable elements rewires host gene expression programs.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from $8.99

All prices are NET prices.


Primary accessions


Gene Expression Omnibus

Sequence Read Archive


  1. 1.

    et al. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001)

  2. 2.

    & Dynamic interactions between transposable elements and their hosts. Nat. Rev. Genet. 12, 615–627 (2011)

  3. 3.

    , , & LINE-1 elements in structural variation and disease. Annu. Rev. Genomics Hum. Genet. 12, 187–215 (2011)

  4. 4.

    & How retrotransposons shape genome regulation. Curr. Opin. Genet. Dev. 37, 90–100 (2016)

  5. 5.

    Restricting retrotransposons: a review. Mob. DNA 7, 16 (2016)

  6. 6.

    , & Regulatory activities of transposable elements: from conflicts to benefits. Nat. Rev. Genet. 18, 71–86 (2017)

  7. 7.

    et al. Activation of individual L1 retrotransposon instances is restricted to cell-type dependent permissive loci. eLife 5, e13926 (2016)

  8. 8.

    et al. Epigenetic silencing by the HUSH complex mediates position–effect variegation in human cells. Science 348, 1481–1485 (2015)

  9. 9.

    et al. High frequency retrotransposition in cultured mammalian cells. Cell 87, 917–927 (1996)

  10. 10.

    et al. Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens. Nat. Commun. 8, 15178 (2017)

  11. 11.

    , , & Systematic comparison of CRISPR/Cas9 and RNAi screens for essential genes. Nat. Biotechnol. 34, 634–636 (2016)

  12. 12.

    et al. Genetic evidence that the non-homologous end-joining repair pathway is involved in LINE retrotransposition. PLoS Genet. 5, e1000461 (2009)

  13. 13.

    et al. Linkage of the gene for an autosomal dominant form of juvenile amyotrophic lateral sclerosis to chromosome 9q34. Am. J. Hum. Genet. 62, 633–640 (1998)

  14. 14.

    et al. Autosomal recessive cerebellar ataxia with oculomotor apraxia (ataxia-telangiectasia-like syndrome) is linked to chromosome 9q34. Am. J. Hum. Genet. 67, 1320–1326 (2000)

  15. 15.

    et al. MORC2 mutations cause axonal Charcot–Marie–Tooth disease with pyramidal signs. Ann. Neurol. 79, 419–427 (2016)

  16. 16.

    , , , & MORC2 mutation causes severe spinal muscular atrophy-phenotype, cerebellar atrophy, and diaphragmatic paralysis. Brain 139, 1–4 (2016)

  17. 17.

    et al. Upregulated LINE-1 activity in the Fanconi anemia cancer susceptibility syndrome leads to spontaneous pro-inflammatory cytokine production. EBioMedicine 8, 184–194 (2016)

  18. 18.

    , , , & Determination of L1 retrotransposition kinetics in cultured cells. Nucleic Acids Res. 28, 1418–1423 (2000)

  19. 19.

    & A highly active synthetic mammalian retrotransposon. Nature 429, 314–318 (2004)

  20. 20.

    , & Evolutionary conservation of the functional modularity of primate and murine LINE-1 elements. PLoS ONE 6, e19672 (2011)

  21. 21.

    et al. Hyperactivation of HUSH complex function by Charcot–Marie–Tooth disease mutation in MORC2. Nat. Genet. 49, 1035–1044 (2017)

  22. 22.

    et al. MORC family ATPases required for heterochromatin condensation and gene silencing. Science 336, 1448–1451 (2012)

  23. 23.

    et al. MORC1 represses transposable elements in the mouse male germline. Nat. Commun. 5, 5795 (2014)

  24. 24.

    et al. LINE-1 retrotransposition in human embryonic stem cells. Hum. Mol. Genet. 16, 1569–1577 (2007)

  25. 25.

    , & Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes. Nature 429, 268–274 (2004)

  26. 26.

    , , & Histone H3 lysine 9 trimethylation and HP1γ favor inclusion of alternative exons. Nat. Struct. Mol. Biol. 18, 337–344 (2011)

  27. 27.

    , & Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates. Genome Res. 16, 78–87 (2006)

  28. 28.

    et al. Reorganization of enhancer patterns in transition from naive to primed pluripotency. Cell Stem Cell 14, 838–853 (2014)

  29. 29.

    et al. Affinity proteomics reveals human host factors implicated in discrete stages of LINE-1 retrotransposition. Cell 155, 1034–1048 (2013)

  30. 30.

    et al. Evidence consistent with human L1 retrotransposition in maternal meiosis I. Am. J. Hum. Genet. 71, 327–336 (2002)

  31. 31.

    , & ERCC1/XPF limits L1 retrotransposition. DNA Repair (Amst.) 7, 983–989 (2008)

  32. 32.

    et al. Parallel shRNA and CRISPR–Cas9 screens enable antiviral drug target identification. Nat. Chem. Biol. 12, 361–366 (2016)

  33. 33.

    et al. A systematic mammalian genetic interaction map reveals pathways underlying ricin susceptibility. Cell 152, 909–922 (2013)

  34. 34.

    et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819–823 (2013)

  35. 35.

    et al. L1 retrotransposition in human neural progenitor cells. Nature 460, 1127–1131 (2009)

  36. 36.

    et al. Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma. Cell 153, 101–111 (2013)

  37. 37.

    et al. Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme. Mob. DNA 7, 21–34 (2016)

  38. 38.

    , , , & A 3′ poly(A) tract is required for LINE-1 retrotransposition. Mol. Cell 60, 728–741 (2015)

  39. 39.

    A threshold selection method from gray-level histograms. IEEE Trans. Syst. Man Cybern. 9, 62–66 (1979)

  40. 40.

    , & Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014)

  41. 41.

    et al. CHD7 cooperates with PBAF to control multipotent neural crest formation. Nature 463, 958–962 (2010)

  42. 42.

    et al. A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470, 279–283 (2011)

Download references


We thank J. Moran for the LRE-GFP plasmid and A. Engel for the codon-optimized L1 construct; D. Fuentes, A. Spencley, R. Srinivasan, J. Mohammed, V. Bajpai, K. Tsui, G. Hess, D. Morgens and G. Cornelis for assistance and discussions; K. Cimprich, A. Fire and A. Urban for comments on the manuscript; and L. Bruhn, S. Altschuler, B. Borgo, P. Sheffield and C. Carstens (Agilent) for discussions and oligonucleotide synthesis. This work was funded by grants from the Jane Coffin Childs Memorial Fund for Medical Research (N.L.), National Science Foundation DGE-114747 (C.H.L.), National Institutes of Health (NIH) R01HG008150, 1UM1HG009436-01 and NIH 1DP2HD084069-01 (M.C.B.), NIH R01 GM112720, Stinehart Reed Award and Howard Hughes Medical Institute (J.W.).

Author information

Author notes

    • Edward Grow

    Present address: Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112-5550, USA.

    • Nian Liu
    •  & Cameron H. Lee

    These authors contributed equally to this work.


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

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

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

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

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

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

    • Joanna Wysocka


  1. Search for Nian Liu in:

  2. Search for Cameron H. Lee in:

  3. Search for Tomek Swigut in:

  4. Search for Edward Grow in:

  5. Search for Bo Gu in:

  6. Search for Michael C. Bassik in:

  7. Search for Joanna Wysocka in:


N.L., C. H.L., T.S., J.W. and M.C.B. designed and performed experiments, analysed data and wrote the manuscript. E.G., C.H.L., J.W. and M.C.B. initiated the K562 genome-wide screen. B.G. analysed smFISH data. J.W. and M.C.B. supervised the study.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Michael C. Bassik or Joanna Wysocka.

Reviewer Information Nature thanks D. Bourc’his and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

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.

About this article

Publication history







By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.