The NSL Complex Regulates Housekeeping Genes in Drosophila

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.

Dosage Compensation inDrosophila

“…MOF recruitment is particularly important as MOF also participates in the nonspecific lethal (NSL) or MBD-R2 complex in both sexes (Raja et al 2010;Feller et al 2012;Lam et al 2012). The NSL complex is found at 5 ′ ends of most active genes, coincident with MSL complex-independent H4K16 acetylation, and is essential for viability in both sexes.…”

Evidence of a MOF histone acetyltransferase-containing NSL complex inC. elegans

“…ChIP-seq analysis revealed that it binds preferentially to promoters of housekeeping genes and that the NSL complex is required for efficient recruitment of RNA polymerase II to these promoters. 2 The NSL complex has similarly been found to regulate housekeeping genes in mouse embryonic stem cells (mESCs) 3,4 and to also be required for the expression of key pluripotency factors in these cells. 4 Affinity purification and mass spectrometry analyses have revealed that the Drosophila and human NSL complexes are composed of 9 subunits: MOF/ hMOF, dHCF/HCFC1, OGT/OGT1, WDS/WDR5, MCRS2/MCRS1, MBD-R2/PHF20, NSL1/KANSL1, NSL2/ KANSL2 and NSL3/KANSL3 (Fig.…”

Structural analysis of the KANSL1/WDR5/KANSL2 complex reveals that WDR5 is required for efficient assembly and chromatin targeting of the NSL complex

“…In Drosophila, the complex associates with promoters of >4000 genes, and loss of the NSL complex binding severely affects their expression levels (Raja et al 2010). The majority of the NSL complex-bound targets were shown to belong to housekeeping genes, and the NSL complex was shown to be required for efficient recruitment of RNA polymerase II at their target promoters (Feller et al 2012;Lam et al 2012).…”

“…qPCR was performed using primers corresponding to the promoter (P) and end (E) regions of genes. The list of target and nontarget genes was chosen based on the genome-wide data (Raja et al 2010;Lam et al 2012). ChIP recovery was calculated over the input DNA (shown as percentage [%]).…”