How cBAF and PBAF regulate the nucleosomal and subnucleosomal landscape of promoters, enhancers and REST repressor binding sites

Abstract

BAF (SWI/SNF) chromatin remodeling complexes belong to three subfamilies, cBAF, PBAF, and ncBAF, that regulate the nucleosomal organization and accessibility of transcription factors (TFs) DNA binding sites at cis-regulatory elements (CREs). However, the functional specificities of these complexes at promoters, enhancers, and other categories of CREs are poorly understood. Here, we examined how the BAF complexes regulate the nucleosomal and subnucleosomal landscape in which transcription initiation occurs in vivo. We first described how these complexes regulate the earliest step of transcription preinitiation complex (PIC) assembly, which is defined by the binding of the general transcription factors TBP and TFIIA. We show that in the presence of a TATA box, PIC formation occurs onto a core promoter or enhancer region still wrapped into a fragile nucleosome or a subnucleosomal particle. Conversely, without a TATA box, PIC assembles onto genomic templates mostly stripped of histones. We establish that cBAF, but not PBAF or ncBAF, regulates this chromatin organization and the first step of PIC formation at promoters and enhancers. We observed that individual subunits of cBAF have specific functions at promoters: the BRG1 ATPase and SMARCB1 regulate the production of fragile nucleosomes and subnucleosomal particles, while ARID1A stimulates the binding of TBP/TFIIA independently of the ATPase subunit. In contrast, all three subunits are systematically required for both chromatin organization and TBP/TFIIA binding at enhancers. Finally, we revealed that a subset of PBAF subunits controls the nucleosomal and subnucleosomal landscape at REST repressor binding sites. Our integrative study identified specific functions of cBAF and PBAF subunits in controlling the binding of TFs and the nucleosomal and subnucleosomal organization of CREs.