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

Abstract

Summary 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 regulation1,2,3,4,5,6. 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 disease1,2,3,4,5,6,7. 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.

KAP 1 regulates endogenous retroviruses in adult human cells and contributes to innate immune control

“…All error bars show SD. Venn diagram showing H3K9me3‐enriched sites (18,271) as those identified in both ChIP replicates in the human cell line K562 (left) using data from Ref. . Right: % of ISGs or random genes intersecting a H3K9me3 or KAP1 ChIP‐seq peak.…”

Initiation of homologous recombination at DNA nicks

“…The resolution of LINE-1 retrotransposition, following second strand synthesis, is not well characterized but may require a second nick. Intriguingly, LINE-1 retrotransposition is inhibited by homologous recombination factors including RAD51 and BRCA2 (47). This could reflect stabilization of the nick in a fully annealed configuration by RAD51, as has been proposed for HDR at nicks supported by ssDNA donors [(10); and see below] and would inhibit mRNA annealing to the 3′-TTTT; or alternatively, RAD51 may promote competition for repair of the targeted nick by HDR with the sister chromatid or homologous chomosome.…”

Genomic Accumulation of Retrotransposons Was Facilitated by Repressive RNA‐Binding Proteins: A Hypothesis

“…Finally, nucleolin and SAFB proteins are co‐factors of L1, and depletion of either protein reduces retrotransposition . At the same time, they also act on nuclear scaffold RNAs derived from or rich in L1 sequence .…”