DNA binding drives the association of BRG1/hBRM bromodomains with nucleosomes

Abstract

BRG1 and BRM, central components of the BAF (mSWI/SNF) chromatin remodelling complex, are critical in chromatin structure regulation. Here, we show that the human BRM (hBRM) bromodomain (BRD) has moderate specificity for H3K14ac. Surprisingly, we also find that both BRG1 and hBRM BRDs have DNA-binding activity. We demonstrate that the BRDs associate with DNA through a surface basic patch and that the BRD and an adjacent AT-hook make multivalent contacts with DNA, leading to robust affinity and moderate specificity for AT-rich elements. Although we show that the BRDs can bind to both DNA and H3K14ac simultaneously, the histone-binding activity does not contribute substantially to nucleosome targeting in vitro. In addition, we find that neither BRD histone nor DNA binding contribute to the global chromatin affinity of BRG1 in mouse embryonic stem cells. Together, our results suggest that association of the BRG1/hBRM BRD with nucleosomes plays a regulatory rather than targeting role in BAF activity.

Temporal regulation of chromatin during myoblast differentiation

“…The presence of bromodomains, which promote binding to acetylated chromatin (101, 102) in at least three subunits of SWI/SNF complexes, including the Brm and Brg1 ATPase subunits, suggests a mechanism that enables association of the SWI/SNF enzymes with chromatin. While likely not essential for every SWI/SNF-mediated cellular function (103-106), a bromodomain inhibitor specific for the three SWI/SNF bromodomain proteins nevertheless negatively impacts myoblast differentiation (107), suggesting a contributing role for bromodomain-mediated chromatin interactions. Similarly, knockdown of either the Prmt5 or Carm1 methyltransferases precludes SWI/SNF enzyme binding and function (78, 79), indicating that dimethylation of histone arginines or other PRMT substrates and/or the interaction of a reader of dimethylated histone arginines is a necessary prerequisite for ATP-dependent remodeling of differentiation-specific loci.…”

A role for histone acetylation in regulating transcription elongation

“…Interestingly, the tandem bromodomains within the RSC4 subunit have been biochemically shown to preferentially bind H4K14ac [31]. Furthermore, the central ATPase of the human Swi-Snf (BAF) chromatin remodelling complex contains a bromodomain that also shows specificity for H3K14ac, highlighting the potential importance of this mark upon ATP-dependent chromatin remodelling complex recruitment [32]. …”

The Molecular Basis of Specific DNA Binding by the BRG1 AT-hook and Bromodomain

“…Nucleic acid binding activity has only been demonstrated for a few BDs [15,16]. However, we have predicted that ~30% of known BDs will bind to nucleic acids [15], highlighting the importance of better understanding this function. Previous studies indicate that the BRG1 BD is not essential for global chromatin association of the BAF complex.…”

“…Both bromodomains (BDs) have previously been characterized to bind acetylated-lysine on histone tails, with a moderate preference for histone H3 acetylated at lysine 14 (H3K14ac) [12][13][14]. In addition to its histone binding activity, we have recently discovered that both BDs can associate with DNA [15]. Nucleic acid binding activity has only been demonstrated for a few BDs [15,16].…”

“…In addition to its histone binding activity, we have recently discovered that both BDs can associate with DNA [15]. Nucleic acid binding activity has only been demonstrated for a few BDs [15,16]. However, we have predicted that ~30% of known BDs will bind to nucleic acids [15], highlighting the importance of better understanding this function.…”