|
| 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 |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Jun 24, 2019 |
| Last update date |
May 13, 2020 |
| 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) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
|
| Samples (6)
|
|
| Relations |
| BioProject |
PRJNA550354 |
| SRA |
SRP211805 |
Less...
More...