PBRM1 bromodomains associate with RNA to facilitate chromatin association

Abstract

PBRM1 is a subunit of the PBAF chromatin remodeling complex, which is mutated in 40–50% of clear cell renal cell carcinoma patients. It is thought to largely function as a chromatin binding subunit of the PBAF complex, but the molecular mechanism underlying this activity is not fully known. PBRM1 contains six tandem bromodomains which are known to cooperate in binding of nucleosomes acetylated at histone H3 lysine 14 (H3K14ac). Here, we demonstrate that the second and fourth bromodomains from PBRM1 also bind nucleic acids, selectively associating with double stranded RNA elements. Disruption of the RNA binding pocket is found to compromise PBRM1 chromatin binding and inhibit PBRM1-mediated cellular growth effects.

Cancer-associated polybromo-1 bromodomain 4 missense variants variably impact bromodomain ligand binding and cell growth suppression

“…We also performed EMSA analyses to determine PBRM1-BD4 missense variant DNA binding. Notably, we find that although the PBRM1-BD4 E583K substitution lies within the putative PBRM1-BD4 nucleic acid binding pocket ( 60 ), it maintains nucleic acid binding relative to WT ( Figs. 3 D and S4 ).…”

“…We and others recently showed that PBRM1 bromodomains bind nucleic acids at a site overlapping the canonical Kac binding site ( 60 ). Several residues defining the putative PBRM1-BD4 nucleic acid binding pocket ( 60 ) are near ( e.g.…”

“…We and others recently showed that PBRM1 bromodomains bind nucleic acids at a site overlapping the canonical Kac binding site ( 60 ). Several residues defining the putative PBRM1-BD4 nucleic acid binding pocket ( 60 ) are near ( e.g. , R522, Y555, H599) or include (E583) the residues we consider in the cancer-associated PBRM1-BD4 missense variants analyzed in this study ( i.e.…”

Rational design and development of selective BRD7 bromodomain inhibitors and their activity in prostate cancer

“…We found previously that a single BD mutation in (or even full deletion of) the polybromo-1 (PBRM1) PBAF subunit can slightly reduce but not abrogate PBAF global chromatin association. 17,46,47 In contrast, a single BD mutation or inhibition of the BRD9 subunit completely dissociates GBAF from chromatin. 17,48 To determine whether our BRD7 inhibitors can displace BRD9 from chromatin at cellularly active concentrations, we performed a cell fractionation assay.…”

Rational Design and Development of Selective BRD7 Bromodomain Inhibitors and Their Activity in Prostate Cancer

“…PBAF contains a total of eight BDs across three separate subunits. We found previously that a single BD mutation in (or even full deletion of) the polybromo-1 (PBRM1) PBAF subunit can slightly reduce but not abrogate PBAF global chromatin association. ,, In contrast, a single BD mutation or inhibition of the BRD9 subunit completely dissociates GBAF from chromatin. , To determine whether our BRD7 inhibitors can displace BRD9 from chromatin at cellularly active concentrations, we performed a cell fractionation assay. We treated HEK293T cells with 10 μM of the compounds or DMSO and collected nuclear-soluble and chromatin-insoluble fractions.…”