H4K16 acetylation marks active genes and enhancers of embryonic stem cells, but does not alter chromatin compaction

Abstract

Compared with histone H3, acetylation of H4 tails has not been well studied, especially in mammalian cells. Yet, H4K16 acetylation is of particular interest because of its ability to decompact nucleosomes in vitro and its involvement in dosage compensation in flies. Here we show that, surprisingly, loss of H4K16 acetylation does not alter higher-order chromatin compaction in vivo in mouse embryonic stem cells (ESCs). As well as peaks of acetylated H4K16 and KAT8 histone acetyltransferase at the transcription start sites of expressed genes, we report that acetylation of H4K16 is a new marker of active enhancers in ESCs and that some enhancers are marked by H3K4me1, KAT8, and H4K16ac, but not by acetylated H3K27 or EP300, suggesting that they are novel EP300 independent regulatory elements. Our data suggest a broad role for different histone acetylation marks and for different histone acetyltransferases in long-range gene regulation.

Selective Recognition of H3.1K36 Dimethylation/H4K16 Acetylation Facilitates the Regulation of All-trans-retinoic Acid (ATRA)-responsive Genes by Putative Chromatin Reader ZMYND8

“…3B). Genome-wide distribution of H3K36Me2 and H4K16Ac epigenetic marks has been previously reported (27)(28)(29). The NSD2 (Nuclear receptor SET Domain-containing family of histone lysine methyltransferase) target genes, for example TGFA, MET, and RRAS2, were found to have high H3K36Me2 occupancy (Fig.…”

“…We at first investigated the cause of selective enrichment of ZMYND8 at the gene body. H3K36Me2 and H4K16Ac have been shown to be significantly enriched at the gene body by ChIP-Seq studies in different cell lines (27)(28)(29). To understand whether the preferential recruitment of ZMYND8 to the gene body of the ATRA-inducible genes in SH-SY5Y cells is through its modified histone-binding ability, we analyzed the histone PTM on these genes (Fig.…”

High-resolution mapping of H4K16 and H3K23 acetylation reveals conserved and unique distribution patterns inArabidopsisand rice

“…65 The mechanism regarding the differential expression pattern of H4K16ac-enriched genes in pollen is unclear. It is possible that, like in human HEK293 cells, 37 H4K16ac has distinct effects on transcription in pollen. In the future, it will be important to directly examine the roles of H4K16ac in regulating transcriptional activity in the different stages of the development.…”

“…1B), but is enriched at promoters and transcribed regions of active genes in human. 37,38,40 To explore the conservation of H4K16ac and H3K23ac distribution patterns in plants, we determined their genome-wide occupancy in rice by using ChIP-seq.…”

“…In mouse embryonic stem cells, H4K16ac is critical in releasing compacted chromatin for transcriptional activation. 37 However, H4K16ac has little impact on transcription in the differentiated HEK293 cells. 38 Compared to the large amount of studies on H4K16ac in fungi and animals, its biological function in plants is completely unknown.…”