Morc3 silences endogenous retroviruses by enabling Daxx-mediated histone H3.3 incorporation

Sophia Groh,Lisa Katherina Marinelli,Anna Viktoria Milton,Cara V Sickinger,Gunnar Schotta,Angela Russo,Heike Bollig,Gustavo Pereira De Almeida,Axel Imhof,Andreas Schmidt,Ignasi Forné

doi:10.1038/s41467-021-26288-7

Abstract

Endogenous retroviruses (ERVs) comprise a significant portion of mammalian genomes. Although specific ERV loci feature regulatory roles for host gene expression, most ERV integrations are transcriptionally repressed by Setdb1-mediated H3K9me3 and DNA methylation. However, the protein network which regulates the deposition of these chromatin modifications is still incompletely understood. Here, we perform a genome-wide single guide RNA (sgRNA) screen for genes involved in ERV silencing and identify the GHKL ATPase protein Morc3 as a top-scoring hit. Morc3 knock-out (ko) cells display de-repression, reduced H3K9me3, and increased chromatin accessibility of distinct ERV families. We find that the Morc3 ATPase cycle and Morc3 SUMOylation are important for ERV chromatin regulation. Proteomic analyses reveal that Morc3 mutant proteins fail to interact with the histone H3.3 chaperone Daxx. This interaction depends on Morc3 SUMOylation and Daxx SUMO binding. Notably, in Morc3 ko cells, we observe strongly reduced histone H3.3 on Morc3 binding sites. Thus, our data demonstrate Morc3 as a critical regulator of Daxx-mediated histone H3.3 incorporation to ERV regions.

Highlights

Endogenous retroviruses (ERVs) comprise a significant portion of mammalian genomes
Using a genome-wide single-guide RNA screen for genes involved in SHIN silencing we identified Morc[3] as a player in ERV silencing
Top enriched single guide RNA (sgRNA) targeted the major known ERV silencing factors, such as Dnmt[1], Uhrf[1], Setdb[1], Trim[28], and Atrx/Daxx (Fig. 1b). Another top hit was Morc[3], a protein not previously implicated in ERV silencing

Summary

Introduction

Endogenous retroviruses (ERVs) comprise a significant portion of mammalian genomes. specific ERV loci feature regulatory roles for host gene expression, most ERV integrations are transcriptionally repressed by Setdb1-mediated H3K9me[3] and DNA methylation. Histone H3.3 deposition is necessary to replace evicted nucleosomes and ensure low chromatin accessibility[24] It is not clear how histone H3.3 turnover is regulated and coordinated with other chromatin-modifying activities to restrict chromatin accessibility and to mediate heterochromatin spreading on ERVs. We have previously identified a small heterochromatin inducing sequence (SHIN) in Intracisternal A Type particle (IAP) elements[20]. We demonstrate that Morc[3] binds ERV sequences and that loss of Morc[3] results in increased chromatin accessibility, reduced H3K9me[3], and de-repression of ERVs. We detect an interaction of Morc[3] with the histone H3.3 chaperone Daxx, which depends on the Morc3-ATPase cycle and SUMOylation. Our data indicate Morc[3] as a regulator of Daxx-mediated histone H3.3 incorporation

Methods

Results

Conclusion