The KRAB-ZFP/KAP1 System Contributes to the Early Embryonic Establishment of Site-Specific DNA Methylation Patterns Maintained during Development

Abstract

De novo DNA methylation is an essential aspect of the epigenetic reprogramming that takes place during early development, yet factors responsible for its instatement at particular genomic loci are poorly defined. Here, we demonstrate that the KRAB-ZFP-mediated recruitment of KAP1 to DNA in embryonic stem cells (ESCs) induces cytosine methylation. This process is preceded by H3K9 trimethylation, and genome-wide analyses reveal that it spreads over short distances from KAP1-binding sites so as to involve nearby CpG islands. In sharp contrast, in differentiated cells, KRAB/KAP1-induced heterochromatin formation does not lead to DNA methylation. Correspondingly, the methylation status of CpG islands in the adult mouse liver correlates with their proximity to KAP1-binding sites in ESCs, not in hepatocytes. Therefore, KRAB-ZFPs and their cofactor KAP1 are in part responsible for the establishment during early embryogenesis of site-specific DNA methylation patterns that are maintained through development.

Towards Sustained Silencing of HER2/neu in Cancer By Epigenetic Editing

“…A role of SKD in epigenetic remodeling has been suggested but it is controversial, and even upregulation of expression by targeting SKD has been reported (42). With respect to repression, it has been shown in embryonic stem cells that KRAB (as part of SKD) can indirectly induce de novo DNA methylation via recruiting its cofactor, KAP1 (43). In addition, KRAB/KAP1 can spread H3K9me3-containing heterochromatin in adult and embryonic stem cells (44).…”

Interplay of TRIM28 and DNA methylation in controlling human endogenous retroelements

“…3B). Reminiscent of a recent observation on murine retroelements (Quenneville et al 2012), CpG islands located within a few kb of a TRIM28-bound SVA or Class I HERV had a significantly greater chance of being heavily methylated (>80% met CpG) than islands situated farther away from these elements or elsewhere in the genome. However, surprisingly, we noted the inverse for TRIM28-bound HERV Class II-close CpG islands, of which 80% were <20% methylated, while the methylation status of CpG islands located near TRIM28-poor Class III HERVs was identical to that of CpG islands genome-wide.…”

“…We thus reasoned that TRIM28 recruitment to SVAs in human ES cells might be methylation-dependent, analogous to the ZFP57-mediated tethering of the co-repressor to imprinting control regions (ICRs) (Quenneville et al 2011). To test this hypothesis, we capitalized on our previous demonstration that tethering to Escherichia coli Tet operator-derived TetO motifs of a fusion protein in which KRAB is linked to the DNA-binding domain of the Tet repressor (tTR-KRAB) results in the progressive DNA methylation of adjacent sequences in ES cells (Quenneville et al 2012). We thus engineered a new set of lentivectors containing an array of TetO sites upstream or not of various SVA inserts placed antisense, 59 of the PRKG1-GFP cassette (Fig.…”

“…In murine ES cells, TRIM28-induced repression leads to DNA methylation, which is thought to result in permanent silencing of EREs (Quenneville et al 2012;Rowe et al 2013a). We thus examined the methylation status of EREs in human ES cells by correlating publicly available ENCODE (Encyclopedia of DNA Elements) Project DNA methylation data with our TRIM28 ChIP-seq results.…”

“…In murine embryonic stem cells, this protein is important for self-renewal (Hu et al 2009;Seki et al 2010). 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).…”