Abstract
MOF is the major histone H4 lysine 16-specific (H4K16) acetyltransferase in mammals and Drosophila. In flies, it is involved in the regulation of X-chromosomal and autosomal genes as part of the MSL and the NSL complexes, respectively. While the function of the MSL complex as a dosage compensation regulator is fairly well understood, the role of the NSL complex in gene regulation is still poorly characterized. Here we report a comprehensive ChIP–seq analysis of four NSL complex members (NSL1, NSL3, MBD-R2, and MCRS2) throughout the Drosophila melanogaster genome. Strikingly, the majority (85.5%) of NSL-bound genes are constitutively expressed across different cell types. We find that an increased abundance of the histone modifications H4K16ac, H3K4me2, H3K4me3, and H3K9ac in gene promoter regions is characteristic of NSL-targeted genes. Furthermore, we show that these genes have a well-defined nucleosome free region and broad transcription initiation patterns. Finally, by performing ChIP–seq analyses of RNA polymerase II (Pol II) in NSL1- and NSL3-depleted cells, we demonstrate that both NSL proteins are required for efficient recruitment of Pol II to NSL target gene promoters. The observed Pol II reduction coincides with compromised binding of TBP and TFIIB to target promoters, indicating that the NSL complex is required for optimal recruitment of the pre-initiation complex on target genes. Moreover, genes that undergo the most dramatic loss of Pol II upon NSL knockdowns tend to be enriched in DNA Replication–related Element (DRE). Taken together, our findings show that the MOF-containing NSL complex acts as a major regulator of housekeeping genes in flies by modulating initiation of Pol II transcription.
Highlights
In the past decade, our understanding of eukaryotic transcriptional regulation has changed from the notion of a ‘‘generic entity that functions by a single universal mechanism’’ [1] to the acknowledgement of diversity in promoter types and functions
Using genome-wide chromatin binding profiles, we find that the NonSpecific Lethal (NSL) complex, a histone acetyltransferase-containing complex, is bound to the majority of constitutively active gene promoters
We show that NSLbound genes display specific sets of DNA motifs, welldefined nucleosome free regions, and broad transcription initiation patterns
Summary
Our understanding of eukaryotic transcriptional regulation has changed from the notion of a ‘‘generic entity that functions by a single universal mechanism’’ [1] to the acknowledgement of diversity in promoter types and functions. Acetylation itself may disrupt interactions between nucleosomes and cause chromatin decompaction [6,7] Both mechanisms can contribute to reduced nucleosome occupancies at transcriptional start sites (TSSs), thereby providing an open chromatin environment for GTF binding [8]. HATs can be classified into two predominant families: the GCN5-related N-acetyltransferase (GNAT) family (e.g. Gcn and p300) [9] and the Moz-Ybf2/Sas3-Sas2-Tip (MYST) family (e.g. Tip and MOF) [10]. These enzymes often function as part of multi-protein complexes, presumably to increase substratespecificity and to impose tight regulation of their enzymatic activity. In Drosophila, the MSL complex is targeted to the transcribed regions of X-chromosomal
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