Systematic Identification of Factors for Provirus Silencing in Embryonic Stem Cells

Abstract

SUMMARY Embryonic stem cells (ESCs) repress the expression of exogenous proviruses and endogenous retroviruses (ERVs). Here, we systematically dissected the cellular factors involved in provirus repression in embryonic carcinomas (ECs) and ESCs by a genome-wide siRNA screen. Histone chaperones (Chaf1a/b), sumoylation factors (Sumo2/Ube2i/Sae1/Uba2/Senp6), and chromatin modifiers (Trim28/Eset/At-f7ip) are key determinants that establish provirus silencing. RNA-seq analysis uncovered the roles of Chaf1a/b and sumoylation modifiers in the repression of ERVs. ChIP-seq analysis demonstrates direct recruitment of Chaf1a and Sumo2 to ERVs. Chaf1a reinforces transcriptional repression via its interaction with members of the NuRD complex (Kdm1a, Hdac1/2) and Eset, while Sumo2 orchestrates the provirus repressive function of the canonical Zfp809/Trim28/Eset machinery by sumoylation of Trim28. Our study reports a genome-wide atlas of functional nodes that mediate proviral silencing in ESCs and illuminates the comprehensive, interconnected, and multi-layered genetic and epigenetic mechanisms by which ESCs repress retroviruses within the genome.

Histone chaperone CAF-1 mediates repressive histone modifications to protect preimplantation mouse embryos from endogenous retrotransposons

“…In ES cells, silencing of IAP was dependent on ESET, but silencing of LINE-1 was dependent on the other methyltransferase Suv39h1/2 (22,24). Intriguingly, CAF-1 knockdown in ES cells resulted in efficient induction of the twocell-like state and up-regulation of MERVL, but not non-LTR retrotransposons (25,26). A genome-wide siRNA analysis revealed that CAF-1 is the major or the sole repressor of MERVL (26).…”

“…Intriguingly, CAF-1 knockdown in ES cells resulted in efficient induction of the twocell-like state and up-regulation of MERVL, but not non-LTR retrotransposons (25,26). A genome-wide siRNA analysis revealed that CAF-1 is the major or the sole repressor of MERVL (26). Thus, it is likely that CAF-1 differentially represses retrotransposons in ES cells and preimplantation embryos.…”

Heterochromatin and the molecular mechanisms of ‘parent-of-origin’ effects in animals

“…The HP1 CD binds to H3K9me3. (3) The PHD domain of KAP1 is an E3 ligase that co-operates with UBE2i to sumoylate the KAP1 bromodomain (Ivanov et al 2007;Yang et al 2015). (4) The sumoylated bromodomain is bound by the NuRD complex that deacetylates acetylated histones (green circle) in preparation for histone methylation (Schultz et al 2001).…”

“…Sumoylation is mediated intra-molecularly. The KAP1 PHD domain is an E3 ligase that cooperates with UBE2i (also known as UBC9) to transfer SUMO2 (Yang et al 2015) to the KAP1 bromodomain ( Figure 3).…”

Provirus Silencing in Stem Cells: The Forbidden Regulators of Cell Fate

“…37 Apart from methylation, it has been recently shown that events of deacetylation and sumoylation are crucial in silencing the ERVs in embryonic stem (ES) cells. 39 Yang et al 39 through a genome wide screen of mouse ES cells have shown the role of histone chaperons Chaf1a and Chaf1b and sumoylation factors like Sumo2, Ubei 2 and few others in Trim-28-mediated proviral silencing (Fig. 4).…”