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ChIP-Seq of H3K27ac in Actb-/- MEFs expressing NLS-tagged beta-actin

ABSTRACT: Genome-wide ChIP-Seq of H3K27ac in β-actin KO MEFs expressing NLS-tagged beta-actin to assess the role of nulcear actin in regulating histone acetylation

ORGANISM(S): Mus musculus

PROVIDER: GSE213432 | GEO | 2022/09/19

REPOSITORIES: GEO

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RNA-Seq analysis of beta-actin knockout MEFs expressing NLS-tagged beta-actin

Project description:RNA-Seq analysis of beta-actin knockout MEFs expressing NLS-tagged beta-actin to study role of actin in transcription

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Project description: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.

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β-actin RNA-BioID

Project description:Function and fate of mRNAs is controlled by RNA binding proteins (RBPs) but determining the proteome of a specific mRNA in vivo is still challenging. RNA proximity biotinylation on the transported β-actin mRNA tagged with MS2 aptamers (RNA-BioID) is used to characterize the dynamic proteome of the β-actin mRNP in mouse embryonic fibroblasts (MEFs). We have identified > 60 β-actin associated RBPs including all six previously known as well as novel interactors. By investigating the dynamics of the β-actin mRNP in MEFs, we expand the set of β-actin mRNA associated RBPs and characterize the changes of the interacting proteome upon serum-induced mRNA localization. We report that the KH-domain containing protein FUBP3 represents a new β-actin associated RBP that binds to its 3’-untranslated region outside the known RNA localization element but is required for β-actin RNA localization. RNA-BioID will allow to obtain a dynamic view on the composition of endogenous mRNPs.

2020-03-12 | PXD010694 | Pride

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