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Series GSE133196 Query DataSets for GSE133196
Status Public on Jan 01, 2020
Title ATAC-Seq analysis of Mouse Embryonic Fibroblasts (MEFs) to understand the role of β-actin in regulating chromatin states
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 ATAC-Seq analysis was performed for 3 samples using two replicates for each condition. Samples included MEFs wildtype, knockout or heterozygous for β-actin.

Contributor(s) Xie X, Mahmood SR
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Submission date Jun 24, 2019
Last update date May 13, 2020
Contact name Piergiorgio Percipalle
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)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (6)
GSM3901929 β-actin heterozygous MEFs [HET_1]
GSM3901930 β-actin heterozygous MEFs [HET_2]
GSM3901937 β-actin knockout MEFs [KO_1]
BioProject PRJNA550354
SRA SRP211805

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Supplementary file Size Download File type/resource 228.3 Mb (ftp)(http) BW 224.6 Mb (ftp)(http) BW
GSE133196_RAW.tar 720.6 Mb (http)(custom) TAR (of BW) 199.9 Mb (ftp)(http) BW
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Raw data are available in SRA
Processed data provided as supplementary file

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