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

TLDR

H4K16 acetylation, though understudied in mammals, is known to loosen nucleosomes in vitro and contribute to dosage compensation in flies. In mouse embryonic stem cells, H4K16 acetylation marks active genes and enhancers yet its loss does not alter chromatin compaction, underscoring a broad role for acetylation marks in long‑range gene regulation.

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.