TASOR is a pseudo-PARP that directs HUSH complex assembly and epigenetic transposon control

Abstract

stability; histone H3 lysine 9 methylation (H3K9me3); transposable element (TE); long interspersed nuclear element-1 (LINE-1); poly-ADP ribose polymerase (PARP); RNA-binding protein; RNA-induced transcriptional silencing; CUT&RUN; CUT&Tag; genome profiling SummaryThe Human Silencing Hub (HUSH) complex epigenetically represses retroviruses, transposons and genes in vertebrates. HUSH therefore maintains genome integrity and is central in the interplay between intrinsic immunity, transposable elements and transcriptional regulation. Comprising three subunits -TASOR, MPP8 and Periphilin -HUSH regulates SETDB1-dependent deposition of the transcriptionally repressive epigenetic mark H3K9me3 and recruits MORC2 to modify local chromatin structure. However the mechanistic roles of each HUSH subunit remain undetermined. Here we show that TASOR lies at the heart of HUSH, providing a platform for assembling the other subunits. Targeted epigenomic profiling supports the model that TASOR binds and regulates H3K9me3 specifically over LINE-1 repeats and other repetitive exons in transcribed genes. We find TASOR associates with several components of the nuclear RNA processing machinery and its modular domain architecture bears striking similarities to that of Chp1, the central component of the yeast RNA-induced transcriptional silencing (RITS) complex. Together these observations suggest that an RNA intermediate may be important for HUSH activity. We identify the TASOR domains necessary for HUSH assembly and transgene repression. Structural and genomic analyses reveal that TASOR contains a poly-ADP ribose polymerase (PARP) domain dispensable for assembly and chromatin localization, but critical for epigenetic regulation of target elements. This domain contains a degenerated and obstructed active site and has hence lost catalytic activity. Together our data demonstrate that TASOR is a pseudo-PARP critical for HUSH complex assembly and H3K9me3 deposition over its genomic targets.

Periphilin self-association underpins epigenetic silencing by the HUSH complex

“…CUT&RUN experiments to assess H3K9me3 regulation by Periphilin variants were done in two independent replicate experiments. Peaks defined as HUSH-regulated were reported elsewhere ( 17 ). Normalized bigwig files were generated (UCSC), displayed in IGV (Broad Institute) and heatmaps plotted with computeMatrix and plotHeatmap commands (deepTools).…”

“…Vpr and Vpx proteins from lentiviruses including HIV target HUSH for proteasomal degradation, demonstrating the importance of HUSH-dependent silencing in controlling lentiviral infection ( 13–15 ). HUSH also silences hundreds of transcriptionally-active or recently-integrated genomic sequences, with a degree of selectivity for full-length LINE-1s located in euchromatic environments, often within introns of actively transcribed genes ( 16 , 17 ). In the current model of HUSH-dependent repression HUSH spreads histone H3 lysine 9 trimethylation (H3K9me3), a transcriptionally repressive mark, by recruiting the H3K9 methyltransferase SETDB1 and its stabilizing factor ATF7IP to existing H3K9me3 marks via MPP8, which binds both H3K9me3 and ATF7IP ( 11 , 18 ).…”

“…Overexpression of Periphilin transcriptionally represses certain proteins causing cell cycle arrest ( 23 , 24 ). Isoform 2 of Periphilin, one of at least 8 isoforms, was identified in a gene-trap mutagenesis screen as a component of the HUSH complex that binds TASOR but not MPP8 ( 11 , 17 ). Curiously, some of the isoform diversity is driven by TE insertion into Periphilin coding sequences ( 25 ).…”

Host Gene Regulation by Transposable Elements: The New, the Old and the Ugly

“…Genes repressed by the HUSH complex include KZFPs [ 58 ], which regulate TEs themselves. New data suggest that the HUSH complex targets RNA, revealing how it could be recruited to and exert epigenetic repression on transcriptionally active L1 elements [ 87 ].…”

A novel predicted ADP-ribosyltransferase family conserved in eukaryotic evolution

“…The full catalogue of ADP-ribosylation enzymes is likely far from completion, as one may expect from recent discoveries of novel ART domains in effectors from pathogenic bacteria that perform non-canonical ubiquitination [5,47,48], novel ART/macro pairs in bacterial toxin/antitoxin systems [49] and novel human macro domains [50]. Other examples of the novel ADPribosylation players are provided by the viral macro domains, present in many dangerous viruses, including the SARS and SARS-CoV-2 coronaviruses [51], and by the recently characterized novel ART-like domain (DUF3715) in the human TASOR protein involved in gene silencing [52,53].…”