Genome-Wide Analysis of KAP1 Binding Suggests Autoregulation of KRAB-ZNFs

Abstract

We performed a genome-scale chromatin immunoprecipitation (ChIP)-chip comparison of two modifications (trimethylation of lysine 9 [H3me3K9] and trimethylation of lysine 27 [H3me3K27]) of histone H3 in Ntera2 testicular carcinoma cells and in three different anatomical sources of primary human fibroblasts. We found that in each of the cell types the two modifications were differentially enriched at the promoters of the two largest classes of transcription factors. Specifically, zinc finger (ZNF) genes were bound by H3me3K9 and homeobox genes were bound by H3me3K27. We have previously shown that the Polycomb repressive complex 2 is responsible for mediating trimethylation of lysine 27 of histone H3 in human cancer cells. In contrast, there is little overlap between H3me3K9 targets and components of the Polycomb repressive complex 2, suggesting that a different histone methyltransferase is responsible for the H3me3K9 modification. Previous studies have shown that SETDB1 can trimethylate H3 on lysine 9, using in vitro or artificial tethering assays. SETDB1 is thought to be recruited to chromatin by complexes containing the KAP1 corepressor. To determine if a KAP1-containing complex mediates trimethylation of the identified H3me3K9 targets, we performed ChIP-chip assays and identified KAP1 target genes using human 5-kb promoter arrays. We found that a large number of genes of ZNF transcription factors were bound by both KAP1 and H3me3K9 in normal and cancer cells. To expand our studies of KAP1, we next performed a complete genomic analysis of KAP1 binding using a 38-array tiling set, identifying ;7,000 KAP1 binding sites. The identified KAP1 targets were highly enriched for C 2 H 2 ZNFs, especially those containing Krü ppel-associated box (KRAB) domains. Interestingly, although most KAP1 binding sites were within core promoter regions, the binding sites near ZNF genes were greatly enriched within transcribed regions of the target genes. Because KAP1 is recruited to the DNA via interaction with KRAB-ZNF proteins, we suggest that expression of KRAB-ZNF genes may be controlled via an auto-regulatory mechanism involving KAP1.

Silencing of proviruses in embryonic cells: efficiency, stability and chromatin modifications

“…It is not clear whether both marks are present on all silenced proviruses or whether individual proviruses are marked only by one or the other modification. Recent findings in human [23] and mouse ES cells [24] indicate that although rare, the mutual occupancy of these marks is possible. The data indicate that at least two distinct histone methyltransferases are simultaneously active in marking the viral chromatin of the newly incoming MLVs, and the two marks are consistent with the existence of redundant pathways mediating the virus silencing.…”

Roles of Kruppel-associated Box (KRAB)-associated Co-repressor KAP1 Ser-473 Phosphorylation in DNA Damage Response

“…Genomic analysis of KAP1 binding has identified about 7000 KAP1 binding sites throughout the human genome (54). Interestingly, the identified KAP1 targets are highly enriched for C2H2 ZNFs, particularly those containing KRAB domains, suggesting that KAP1 may also be involved in mediating transcription of numerous KRAB-ZFPs (42,54).…”

Heterochromatin protein 1α: a hallmark of cell proliferation relevant to clinical oncology

“…Indeed, in Drosophila , HP1 is involved in the regulation of cell cycle genes (De Lucia et al, 2005) and could even actively promote gene expression by stimulating H3K36 demethylation (Lin et al, 2008). Human HP1 plays a role in silencing Cyclin E by the tumour suppressor Rb (Nielsen et al, 2001b), and interacts with the co‐repressor protein KAP1, the genomic targets of which include genes involved in crucial cellular pathways (O'Geen et al, 2007). However, there is currently no evidence in mammalian cells that regulation of gene expression would be a unique property of HP1α, not shared by HP1β and γ.…”