Histone H3.3 is required for endogenous retroviral element silencing and genome stability [ChIP-Seq]. Mus musculus

Endogenous retroviruses (ERVs) have provided an evolutionary advantage in the diversification of transcript regulation and are thought to be involved in the establishment of extraembryonic tissues during development. However, silencing of these elements remains critical for the maintenance of genome stability. Here, we define a new chromatin state that is uniquely characterized by the combination of the histone variant H3.3 and H3K9me3, two chromatin ‘marks’ that have previously been considered to belong to fundamentally opposing chromatin states. H3.3/H3K9me3 heterochromatin is fundamentally distinct from ‘canonical’ H3K9me3 heterochromatin that has been under study for decades and this unique functional interplay of a histone variant and a repressive histone mark is crucial for silencing ERVs in ESCs. Our study solidifies the emerging notion that H3.3 is not a histone variant associated exclusively with “active” chromatin and further suggests that its incorporation at unique heterochromatic regions may be central to its function during development and the maintenance of genome stability. Overall design: Native ChIP analysis of H3K9me3 in two mouse embryonic stem cell lines (Control and H3.3KD1). Inputs with GSE42155. Crosslinking ChIP analysis of H3.3, and H3.1/2 in two ESC lines (Control and H3.3KD1). Inputs sequenced. Crosslinking ChIP analysis of H3K9me3, DAXX, and KAP1 in three ESC lines (WT, H3.3KO1, H3.3KO2). Native ChIP of H3-HA addback in H3.3KD1 and H3.3KO1 ESC. Native ChIP of H3.3-HA and H3K9me3 in WT and DAXX null ESC. Inputs sequenced. Native H3.3-HA and H3K9me3 ChIP in WT and ATRX null ESC. Inputs sequenced. Crosslinking ChIP of H3.3 in two WT and ATRX null ESC. Inputs sequenced. Crosslinking H3.3 ChIP in KAP1 WT and null ESC. Inputs sequenced. Crosslinking H3.3 and H3.3-H3K9me3 sequential (Re)-ChIP in ESET WT and null ESC. Inputs sequenced.