TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells

Abstract

TRIM28 is critical for the silencing of endogenous retroviruses (ERVs) in embryonic stem (ES) cells. Here, we reveal that an essential impact of this process is the protection of cellular gene expression in early embryos from perturbation by cis-acting activators contained within these retroelements. In TRIM28-depleted ES cells, repressive chromatin marks at ERVs are replaced by histone modifications typical of active enhancers, stimulating transcription of nearby cellular genes, notably those harboring bivalent promoters. Correspondingly, ERV-derived sequences can repress or enhance expression from an adjacent promoter in transgenic embryos depending on their TRIM28 sensitivity in ES cells. TRIM28-mediated control of ERVs is therefore crucial not just to prevent retrotransposition, but more broadly to safeguard the transcriptional dynamics of early embryos.

KRAB zinc finger proteins

“…Despite their abundance, the functions of KRABZFPs have long remained ill-defined, although cumulated data have implicated some of them in processes as diverse as imprinting, cell differentiation, metabolic control and sexual dimorphism (reviewed by Lupo et al, 2013). This picture changed when the KRABbinding co-factor KAP1 was demonstrated to be essential for the early embryonic repression of TEs in both mouse and human, and when a few individual KRAB-ZFPs could be linked to this function as well Goff, 2007, 2009;Wolf et al, 2015b;Rowe et al, 2010Rowe et al, , 2013Jacobs et al, 2014). It was then suspected that the primary role of KRAB-ZFPs was to silence TEs, and that their evolutionary selection represented the host component of an arms race against these genetic invaders (Jacobs et al, 2014;Castro-Diaz et al, 2014;Thomas and Schneider, 2011).…”

Interplay of TRIM28 and DNA methylation in controlling human endogenous retroelements

“…Chromatin was prepared from 10 7 H1 cells or primary CD4 + T-cells isolated from two donors as previously described (Rowe et al 2013b), and ChIP performed with rabbit anti-TRIM28 (SY 3267-68, 60 µL per IP, Tronolab) or Abcam anti-TRIM28 (for the hES-2 ChIPseq, ab10483, 5 µL per IP), anti-H3K9me3 (pAb-056-050, 1 µg/µL, 10 µL per IP, Diagenode), anti-SETDB1 (a kind gift from F. Rauscher, 5 µL per IP), and anti-H3K4me1 (pAb-037-050, 5 µL per IP, Diagenode) antibodies. All qPCRs were performed in triplicate with SYBR Green mix (Applied Biosystems) on IPed material and Total input (Ti) using primers listed in the Supplemental Material.…”

“…TRIM28 is also essential for the silencing of endogenous and some exogenous retroviruses in murine embryonic cells Goff 2007, 2009;Matsui et al 2010;Rowe et al 2010), where its KRAB-ZFP-mediated docking triggers the formation of heterochromatin, notably through the recruitment of SETDB1, the histone methyltransferase responsible for depositing the H3K9me3 repressive mark (Schultz et al 2002;Ivanov et al 2007;Frietze et al 2010), and of DNA methyltransferases, the action of which extends to adjacent CpG islands (Quenneville et al 2011(Quenneville et al , 2012Zuo et al 2012). A major consequence of the TRIM28-mediated repression of ERVs is the preservation of the transcription dynamics of murine ES cells, as repressive chromatin marks at murine ERVs are replaced upon Trim28 knockout by histone modifications typically found on active enhancers, which results in inducing the expression of nearby cellular genes, notably those harboring bivalent promoters (Rowe et al 2013b). …”

A KRAB/KAP1-miRNA Cascade Regulates Erythropoiesis Through Stage-Specific Control of Mitophagy

“…KAP1, also known as TRIM28 (tripartite motif protein 28), TIF1β (transcription intermediary factor 1 beta) or KRIP-1 (KRAB-interacting protein 1), acts as a scaffold for a multimolecular complex that silences transcription through the formation of heterochromatin (8)(9)(10)(11). The KRAB/KAP1 system probably evolved initially to minimize retroelement-induced genome perturbations (12)(13)(14), but recent data indicate that it also regulates multiple aspects of mammalian physiology (15)(16)(17)(18)(19)(20)(21)(22)(23)(24). The present study was undertaken to explore its role in hematopoiesis.…”