Acute depletion of BRG1 reveals its primary function as an activator of transcription

Gang Ren, Wai Lim Ku, Guangzhe Ge, Jackson A. Hoffman, Jee Youn Kang, Qingsong Tang, Kairong Cui, Yong He, Yukun Guan, Bin Gao, Chengyu Liu, Trevor K. Archer and Keji Zhao ()
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Gang Ren: National Heart, Lung, and Blood Institute, NIH
Wai Lim Ku: National Heart, Lung, and Blood Institute, NIH
Guangzhe Ge: National Heart, Lung, and Blood Institute, NIH
Jackson A. Hoffman: Research Triangle Park
Jee Youn Kang: National Heart, Lung, and Blood Institute, NIH
Qingsong Tang: National Heart, Lung, and Blood Institute, NIH
Kairong Cui: National Heart, Lung, and Blood Institute, NIH
Yong He: National Institutes of Health
Yukun Guan: National Institutes of Health
Bin Gao: National Institutes of Health
Chengyu Liu: National Heart, Lung, and Blood Institute, NIH
Trevor K. Archer: Research Triangle Park
Keji Zhao: National Heart, Lung, and Blood Institute, NIH

Nature Communications, 2024, vol. 15, issue 1, 1-16

Abstract: Abstract The mammalian SWI/SNF-like BAF complexes play critical roles during animal development and pathological conditions. Previous gene deletion studies and characterization of human gene mutations implicate that the complexes both repress and activate a large number of genes. However, the direct function of the complexes in cells remains largely unclear due to the relatively long-term nature of gene deletion or natural mutation. Here we generate a mouse line by knocking in the auxin-inducible degron tag (AID) to the Smarca4 gene, which encodes BRG1, the essential ATPase subunit of the BAF complexes. We show that the tagged BRG1 can be efficiently depleted by osTIR1 expression and auxin treatment for 6 to 10 h in CD4 + T cells, hepatocytes, and fibroblasts isolated from the knock-in mice. The acute depletion of BRG1 leads to decreases in nascent RNAs and RNA polymerase II binding at a large number of genes, which are positively correlated with the loss of BRG1. Further, these changes are correlated with diminished accessibility at DNase I Hypersensitive Sites (DHSs) and p300 binding. The acute BRG1 depletion results in three major patterns of nucleosome shifts leading to narrower nucleosome spacing surrounding transcription factor motifs and at enhancers and transcription start sites (TSSs), which are correlated with loss of BRG1, decreased chromatin accessibility and decreased nascent RNAs. Acute depletion of BRG1 severely compromises the Trichostatin A (TSA) -induced histone acetylation, suggesting a substantial interplay between the chromatin remodeling activity of BRG1 and histone acetylation. Our data suggest BRG1 mainly plays a direct positive role in chromatin accessibility, RNAPII binding, and nascent RNA production by regulating nucleosome positioning and facilitating transcription factor binding to their target sites.

Date: 2024
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DOI: 10.1038/s41467-024-48911-z

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