|
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) |
|
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) |
GSM4518939 |
β-actin knockout Mouse Embryonic Fibroblast rep2 (ChIP-seq) |
GSM4518940 |
β-actin heterozygous Mouse Embryonic Fibroblast rep1 (ChIP-seq) |
GSM4518941 |
β-actin heterozygous Mouse Embryonic Fibroblast rep2 (ChIP-seq) |
GSM4518942 |
Wild Type Mouse Embryonic Fibroblast (ChIP-seq) |
GSM4518943 |
β-actin knockout Mouse Embryonic Fibroblast (ChIP-seq) |
GSM4518944 |
β-actin heterozygous Mouse Embryonic Fibroblast (ChIP-seq) |
|
This SubSeries is part of SuperSeries: |
GSE149987 |
Role of beta-actin in mouse embryonic fibroblasts (MEFs) |
|
Relations |
BioProject |
PRJNA630705 |
SRA |
SRP260264 |