10.6084/M9.FIGSHARE.C.4105967.V1
Jordán-Pla, Antonio
Antonio
Jordán-Pla
Simei Yu
Waldholm, Johan
Johan
Waldholm
Källman, Thomas
Thomas
Källman
Ann-Kristin Östlund Farrants
Visa, Neus
Neus
Visa
SWI/SNF regulates half of its targets without the need of ATP-driven nucleosome remodeling by Brahma
Figshare
2018
Collection
Biophysics
Biochemistry
29999 Physical Sciences not elsewhere classified
FOS: Physical sciences
Genetics
FOS: Biological sciences
Molecular Biology
Immunology
FOS: Clinical medicine
69999 Biological Sciences not elsewhere classified
80699 Information Systems not elsewhere classified
FOS: Computer and information sciences
Developmental Biology
Cancer
Computational Biology
2018-05-19
2018-05-19
2018
10.1186/s12864-018-4746-2
10.6084/m9.figshare.c.4105967
CC BY 4.0
Abstract Background 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. Results 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. Conclusions 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-independent mechanisms have specialized roles in different cellular and developmental processes.