BRD9 KO RNA seq (primary cells)-Highly discriminative globin gene activation by the non-canonical BAF chromatin remodeling complex

The regulation of the switch from fetal (HBG) to adult (HBB and HBD) beta-globin gene expression has served as a paradigm for clinically relevant developmental transcriptional control. Mechanistic studies of this switch have focused overwhelmingly on HBG repressors with comparatively little attention paid to potential HBG activators. We found that in adult type HUDEP2 erythroid cells, the ATP-dependent chromatin remodeler BRG1 preferentially activates the HBG genes as well as the minor adult HBD gene. BRG1 is a core catalytic subunit of three BAF complexes, canonical BAF, polybromo BAF, and non-canonical BAF (ncBAF) that regulate chromatin accessibility in distinct gene- and cell-type contexts. Using comprehensive CRISPR mediated dissection of these complexes in HUDEP2 and primary adult erythroid cells, we pinpointed the HBG and HBD selective activation function of BRG1 to the ncBAF complex. Loss of the ncBAF complex subunits BRD9 and BAF60A preferentially decreased HBG and HBD transcription while accelerating erythroid differentiation and hemoglobinization. Pharmacologic depletion of BRD9 acutely decreased chromatin accessibility at the HBD and HBG promoters and reduced their transcriptional activities. This surprising demonstration of BAF complex selectivity within a multi-gene cluster extends our understanding of BAF complex functions and identifies a potential target for therapeutic manipulation of beta-like globin genes. Overall design: We performed RNA seq analysis in 3 healthy donor erythroid cells derived from CD34+ HSPC after BRD9 knockout. Total RNA was isolated form erythoid cells after 10 days of erythroid differentiation targetted with CRISPR control sgRNA (AAVS1 targetting) or BRD9 targetting. Transcriptome changes were analysed by bulk RNA-seq after ribosomal RNA removal.