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Series GSE198517 Query DataSets for GSE198517
Status Public on Nov 02, 2023
Title Inhibition of SWI/SNF broadly disrupts enhancers and reveals remodeler redundancy at promoters
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Appropriate gene expression requires the establishment of accessible chromatin at promoters and enhancers. These patterns are maintained thorugh the action of, such as the SWI/SNF family. Despite this critical role, previous studies have remained inconclusive regarding the direct role of SWI/SNF. Herein, we employ BRM014, a fast-acting small-molecule inhibitor of the SWI/SNF ATPase subunit, to probe the direct response of mouse embryonic stem cells to disruption of appropriate SWI/SNF chromatin remodeling activity. We demonstrate that the immediate role of SWI/SNF inhibition is a broad loss of chromatin accessibility at both promoter and enhancer loci, and this is reflected in an associated reduction in nascent transcription. We determine that this initial perturbation can be compensated for at a majority of gene promoters, such that these elements regain accessibilty and gene expression under prolonged treatment. However, a subset of gene promoters, as well as most enhancers, fail to recover under these conditions. Finally, we identify EP400 as a putative factor driving compensation ability, as the loss of this factor impedes promoter recovery.
Overall design ATAC-seq, PRO-seq, ChIP-seq, RNA-seq. For all experiments, at least two replicates were generated for each condition.

Comparative gene expression profiling analysis of RNA-seq data for A548 and H1299 cells following 12 h treatment with 5 uM BRM014 or DMSO control.
Contributor(s) Ablondi EF, Martin BE, Adelman K
Citation(s) 37922899
Submission date Mar 12, 2022
Last update date Feb 01, 2024
Contact name Karen Adelman
Organization name Harvard Medical School
Department Biological Chemistry and Molecular Pharmacology
Street address 45 Shattuck St. LHRRB-201a
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
Platforms (4)
GPL21626 NextSeq 550 (Mus musculus)
GPL21697 NextSeq 550 (Homo sapiens)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (107)
GSM5949801 mESC_WT_ATAC-seq_rep1
GSM5949802 mESC_WT_ATAC-seq_rep2
GSM5949803 mESC_WT_ATAC-seq_rep3
BioProject PRJNA815672

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE198517_A549_RNAseq_raw_gene_counts.tsv.gz 299.8 Kb (ftp)(http) TSV 102.2 Mb (ftp)(http) BW 58.2 Mb (ftp)(http) BW 39.5 Mb (ftp)(http) BW 106.0 Mb (ftp)(http) BW 101.4 Mb (ftp)(http) BW 59.8 Mb (ftp)(http) BW 96.1 Mb (ftp)(http) BW 60.9 Mb (ftp)(http) BW 197.0 Mb (ftp)(http) BW 244.2 Mb (ftp)(http) BW 239.7 Mb (ftp)(http) BW 227.3 Mb (ftp)(http) BW 223.4 Mb (ftp)(http) BW 120.7 Mb (ftp)(http) BW 122.7 Mb (ftp)(http) BW 140.0 Mb (ftp)(http) BW 140.7 Mb (ftp)(http) BW
GSE198517_H1299_RNAseq_raw_gene_counts.tsv.gz 293.1 Kb (ftp)(http) TSV 49.0 Mb (ftp)(http) BW 50.0 Mb (ftp)(http) BW 45.2 Mb (ftp)(http) BW 52.8 Mb (ftp)(http) BW 52.7 Mb (ftp)(http) BW 48.7 Mb (ftp)(http) BW 45.9 Mb (ftp)(http) BW 45.0 Mb (ftp)(http) BW 42.7 Mb (ftp)(http) BW 50.2 Mb (ftp)(http) BW 34.7 Mb (ftp)(http) BW 48.3 Mb (ftp)(http) BW
GSE198517_MV411_ATACseq_seq_template.xlsx 139.1 Kb (ftp)(http) XLSX 78.0 Mb (ftp)(http) BW 88.2 Mb (ftp)(http) BW 118.4 Mb (ftp)(http) BW 131.4 Mb (ftp)(http) BW 117.2 Mb (ftp)(http) BW 129.7 Mb (ftp)(http) BW 116.4 Mb (ftp)(http) BW 128.7 Mb (ftp)(http) BW 101.1 Mb (ftp)(http) BW 112.4 Mb (ftp)(http) BW
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