The role of MORC3 in silencing transposable elements in mouse embryonic stem cells

Abstract

Background Microrchidia proteins (MORCs) are involved in epigenetic gene silencing in a variety of eukaryotic organisms. Deletion of MORCs result in several developmental abnormalities and their dysregulation has been implicated in developmental disease and multiple cancers. Specifically, mammalian MORC3 mutations are associated with immune system defects and human cancers such as bladder, uterine, stomach, lung, and diffuse large B cell lymphomas. While previous studies have shown that MORC3 binds to H3K4me3 in vitro and overlaps with H3K4me3 ChIP-seq peaks in mouse embryonic stem cells, the mechanism by which MORC3 regulates gene expression is unknown. Results In this study, we identified that mutation in Morc3 results in a suppressor of variegation phenotype in a Modifiers of murine metastable epialleles Dominant (MommeD) screen. We also find that MORC3 functions as an epigenetic silencer of transposable elements (TEs) in mouse embryonic stem cells (mESCs). Loss of Morc3 results in upregulation of TEs, specifically those belonging to the LTR class of retrotransposons also referred to as endogenous retroviruses (ERVs). Using ChIP-seq we found that MORC3, in addition to its known localization at H3K4me3 sites, also binds to ERVs, suggesting a direct role in regulating their expression. Previous studies have shown that these ERVs are marked by the repressive histone mark H3K9me3 which plays a key role in their silencing. However, we found that levels of H3K9me3 showed only minor losses in Morc3 mutant mES cells. Instead, we found that loss of Morc3 resulted in increased chromatin accessibility at ERVs as measured by ATAC-seq. Conclusions Our results reveal MORC3 as a novel regulator of ERV silencing in mouse embryonic stem cells. The relatively minor changes of H3K9me3 in the Morc3 mutant suggests that MORC3 acts mainly downstream of, or in a parallel pathway with, the TRIM28/SETDB1 complex that deposits H3K9me3 at these loci. The increased chromatin accessibility of ERVs in the Morc3 mutant suggests that MORC3 may act at the level of chromatin compaction to effect TE silencing.

MORC3 restricts human cytomegalovirus infection by suppressing the major immediate‐early promoter activity

“…12 MORC3 has been implicated in epigenetic regulation because the CW domain can read epigenetic marks of histone H3 lysine 4 (H3K4) dimethylation and trimethylation (H3K4me2 and H3K4me3). 16 MORC3 has been shown to mediate gene silencing via repressing promoter transcription in a SUMO-2-bound state, 19 function as an epigenetic silencer of transposable elements in mouse embryonic stem cells, 20 and silence endogenous retroviruses (ERVs) by enabling Daxx-mediated histone H3.3 incorporation. 21 Thus, PML-NBs likely recruit MORC3 to regulate target gene expression epigenetically.…”

MORC proteins regulate transcription factor binding by mediating chromatin compaction in active chromatin regions

“…In C. elegans , MORC-1 can compact DNA through a through topological entrapment [2], while in humans, MORC2 is recruited by the human silencing hub (HUSH) complex for H3K9me3 deposition, chromatin compaction, and gene silencing [3]. In mice, MORC1 is involved in germline transposon silencing [4], and MORC3 is essential for transposon silencing in embryonic stem cells [5].…”

MORC2 restriction factor silences HIV proviral expression

“…Recently, the ICP0 protein encoded by HSV-1 has been identified as a viral antagonist of MORC3, another member of the MORC family also involved in gene silencing and regulation of chromatin structure (55)(56)(57)(58), highlighting Herpesviridae antagonists as potential drivers of the evolution of MORCs.…”