NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE149961 Query DataSets for GSE149961
Status Public on May 01, 2021
Title Genome-wide ChIP-Seq maps of EZH2 distribution between Wild Type (WT), Actb+/- (HET), and Actb-/- (KO) Mouse Embryonic Fibroblast
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary β-actin is a crucial component of several chromatin remodeling complexes which control chromatin structure and accessibility. The mammalian Brahma-associated factor (BAF) is one such complex that plays essential roles in development and differentiation by regulating the chromatin state of critical genes and opposing the repressive activity of polycomb repressive complexes. While previous work has shown that β-actin loss can lead to extensive changes in gene expression and heterochromatin organization, it is not known if changes in β-actin levels can directly influence chromatin remodeling activities of BAF and polycomb proteins. Here we conduct a comprehensive genomic analysis of β-actin knockout mouse embryonic fibroblasts (MEFs) using ATAC-Seq, HiC-seq, RNA-Seq and ChIP-Seq of various epigenetic marks. We demonstrate that β-actin levels can affect the complex interplay between chromatin remodelers such as BAF/BRG1 and EZH2 in a dosage-dependent manner. Our results show that changes in β-actin levels and associated chromatin remodeling activities can not only impact local chromatin accessibility but also induce reversable changes in 3D genome architecture. Our findings support a novel role for β-actin levels in shaping the chromatin landscape during development and differentiation.
 
Overall design ChIP-Seq was performed for 6 samples (3 different genotypes with two biological replicates each)
 
Contributor(s) Mahmood SR, Xie X, ElSaid NH, Gunsalus KC, Percipalle P
Citation(s) 34475390
Submission date May 06, 2020
Last update date Sep 29, 2021
Contact name Piergiorgio Percipalle
E-mail(s) pp69@nyu.edu
Organization name New York University Abu Dhabi
Department Biology Department, Science Division
Street address Saadiyat Campus, Abu Dhabi
City Abu Dhabi
State/province Abu Dhabi
ZIP/Postal code 129188
Country United Arab Emirates
 
Platforms (1)
GPL21626 NextSeq 550 (Mus musculus)
Samples (9)
GSM4518936 Wild Type Mouse Embryonic Fibroblast rep1 (ChIP-seq)
GSM4518937 Wild Type Mouse Embryonic Fibroblast rep2 (ChIP-seq)
GSM4518938 β-actin knockout Mouse Embryonic Fibroblast rep1 (ChIP-seq)
This SubSeries is part of SuperSeries:
GSE149987 Role of beta-actin in mouse embryonic fibroblasts (MEFs)
Relations
BioProject PRJNA630705
SRA SRP260264

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
GSE149961_HET_ezh2_merged_cleaned.bw 289.1 Mb (ftp)(http) BW
GSE149961_KO_ezh2_merged_cleaned.bw 272.5 Mb (ftp)(http) BW
GSE149961_RAW.tar 1.5 Gb (http)(custom) TAR (of BW)
GSE149961_WT_ezh2_merged_cleaned.bw 99.6 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap