The NSL complex–mediated nucleosome landscape is required to maintain transcription fidelity and suppression of transcription noise

We report that the Drosophila Non-Specific Lethal (NSL) complex is necessary to maintain this stereotypical nucleosomal organization at promoters. Upon NSL1 depletion, nucleosomes invade the NDRs at TSSs of NSL-bound genes. NSL complex member NSL3 binds to TATA-less promoters in a sequence-dependent manner. We showed that the NSL complex is necessary and sufficient to recruit NURF chromatin remodeling complex to target promoters. The NSL complex is not only essential for transcription but is required for accurate TSS selection for genes with multiple TSSs. Further, loss of NSL complex leads to an increase in transcriptional noise. Thus, the NSL complex establishes a canonical nucleosomal organization that enables transcription and determines TSS fidelity. We performed (in 2-3 replicates) Mnase-seq (GST control, NSL1, INO80, NURF-301), ChIP-seq (NSL1, NURF-301 with Input control), MAPCap (upon knockdown of NSL1, with GST control), RNA-seq (upon knockdown of NSL1, with GST control), gDIP (genomic-DNA immunopurification, with GFP control, Input control, GST control, MCRS2, NSL1 and NSL3) and scRNAseq (upon knockdown of NSL1, with GST control) to systematically analyze how the NSL complex regulates transcription.