β-actin dependent chromatin remodeling mediates compartment level changes in 3D genome architecture

beta-actin is a crucial component of several chromatin remodeling complexes that 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 (PRCs). While previous work has shown that beta-actin loss can lead to extensive changes in gene expression and heterochromatin organization, it is not known if changes in beta-actin levels can directly influence chromatin remodeling activities of BAF and polycomb proteins. Here we conduct a comprehensive genomic analysis of beta-actin knockout mouse embryonic fibroblasts (MEFs) using ATAC-Seq, HiC-seq, RNA-Seq and ChIP-Seq of various epigenetic marks. We demonstrate that beta-actin levels can induce changes in chromatin structure by affecting the complex interplay between chromatin remodelers such as BAF/BRG1 and EZH2. Our results show that changes in beta-actin levels and associated chromatin remodeling activities can not only impact local chromatin accessibility but also induce reversible changes in 3D genome architecture. Our findings reveal that beta-actin-dependent chromatin remodeling plays a role in shaping the chromatin landscape and influences the regulation of genes involved in development and differentiation. beta-actin loss can affect gene expression and heterochromatin organization. Here the authors conduct a comprehensive genomic analysis of beta-actin knockout mouse embryonic fibroblasts (MEFs) to investigate the impact of changes in beta-actin levels on 3d genome architecture and chromatin remodeling activities of BAF and polycomb proteins.

Automated summary

The study demonstrates that changes in beta-actin levels can influence chromatin structure and 3D genome architecture, as well as the chromatin remodeling activities of BAF and polycomb proteins in mouse embryonic fibroblasts.