A unique histone 3 lysine 14 chromatin signature underlies tissue-specific gene regulation

Organismal development and cell differentiation critically depend on chromatin state transitions. The in vivo functions of individual histone modifications, however, remain incompletely understood. Whereas acetylation of histone 3 lysines 9 and 27 (H3K9ac and H3K27ac) and methylation of H3K4 are common in transcriptionally active genes, certain developmentally regulated genes lack these modifications. Here, we show that a key set of genes lacking canonical histone marks are decorated with H3K14ac in Drosophila melanogaster. We created flies with a mutant histone H3 containing a lysine 14-to-arginine substitution, and demonstrate that H3K14 is essential for the expression of genes devoid of canonical histone modifications in the embryonic gut and in the larval wing imaginal disc. As a result, H3K14R mutant animals die as second instar larvae, and mutant mitotic clones cause defects in the wing margin of adult flies. We find that the bromodomain in Brahma (Brm), the catalytic subunit of the Drosophila SWI/SNF complex BAP, recognizes H3K14ac and that brm acts in the same genetic pathway as H3K14R. Our results show that acetylation of a single lysine is essential at genes devoid of canonical histone marks and uncover an important requirement for H3K14 in tissue-specific gene regulation. Overall design: Analysis of gene expression from 3 different samples by RNA-seq (H3K14R mutant and controls), genomic distribution of H3K14ac in embryo and wing disc by ChIP-seq, chromatin accessibility in embryos (H3K14R mutant and controls) by ATAC-seq and RNA Polymerase II occupancy in wild-type and H3K14R embryos by CUT and TAG .