SWI/SNF regulates half of its targets without the need of ATP-driven nucleosome remodeling by Brahma

BMC Genomics
Antonio Jordán-PlaNeus Visa

Abstract

Brahma (BRM) is the only catalytic subunit of the SWI/SNF chromatin-remodeling complex of Drosophila melanogaster. The function of SWI/SNF in transcription has long been attributed to its ability to remodel nucleosomes, which requires the ATPase activity of BRM. However, recent studies have provided evidence for a non-catalytic function of BRM in the transcriptional regulation of a few specific genes. Here we have used RNA-seq and ChIP-seq to identify the BRM target genes in S2 cells, and we have used a catalytically inactive BRM mutant (K804R) that is unable to hydrolyze ATP to investigate the magnitude of the non-catalytic function of BRM in transcription regulation. We show that 49% of the BRM target genes in S2 cells are regulated through mechanisms that do not require BRM to have an ATPase activity. We also show that the catalytic and non-catalytic mechanisms of SWI/SNF regulation operate on two subsets of genes that differ in promoter architecture and are linked to different biological processes. This study shows that the non-catalytic role of SWI/SNF in transcription regulation is far more prevalent than previously anticipated and that the genes that are regulated by SWI/SNF through ATPase-dependent and ATPase-independen...Continue Reading

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Citations

Jan 26, 2020·International Journal of Molecular Sciences·Dominika M Gratkowska-ZmudaTomasz J Sarnowski
Mar 7, 2020·Signal Transduction and Targeted Therapy·Lisha DuQing Yang
Apr 17, 2020·Signal Transduction and Targeted Therapy·Lisha DuQing Yang
Apr 4, 2021·International Journal of Molecular Sciences·Yulii V ShidlovskiiEnnio Giordano

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Datasets Mentioned

BETA
GSE95236

Methods Mentioned

BETA
ChIP-seq
RNA-seq
in
PCR
immunoprecipitation
MNase-seq
ChIP

Software Mentioned

Limma
Biostrings Stringr
REVIGO
Preseq
HTSeq
IGV genome browser
GraphPad
ngs
Metagene
R

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