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ATAC-Seq analysis of beta actin knockout mouse embryonic fibroblasts expressing NLS-tagged beta-actin

ABSTRACT: ATAC-Seq analysis of beta actin knockout mouse embryonic fibroblasts expressing NLS-tagged beta-actin

PROVIDER: PRJNA880776 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21591080_1.fastq.gz	Fastqsanger.gz
	SRR21591080_2.fastq.gz	Fastqsanger.gz
	SRR21591081_1.fastq.gz	Fastqsanger.gz
	SRR21591081_2.fastq.gz	Fastqsanger.gz

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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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ATAC-Seq analysis of beta actin knockout mouse embryonic fibroblasts expressing NLS-tagged beta-actin

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

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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

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

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Sequencing analysis of beta-actin KO MEFs expressing NLS-beta-actin

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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

Sequencing analysis of beta-actin KO MEFs expressing NLS-beta-actin

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-09-19 | GSE213434 | GEO

Transcription profiling by array of human MCF-7 cells with ER-beta tagged with TAP-tag at the C-term or N-term or expressing ER-alpha tagged

Project description:MCF-7 TET Off cells (MCF-7 wt) were used to produce stable clones expressing ER-beta tagged with TAP-tag respectively at the C-term and at the N-term (C-TAP-ER-beta and N-TAP-ER-beta) or expressing ER-alpha tagged (C-TAP-ER-alpha). All were grown in Dulbecco's modified Eagle's medium (DMEM). Then cells were lysed and RNA extracted were pooled. For mRNA expression profiling, 500 ng total RNA were reverse transcribed and used for synthesis of cDNA and biotinylated cRNA. Finally cRNA were hybridized for 18 hours on Illumina HumanHT-12 v3.0 BeadChips and after scanning, data analysis was performed.

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Hi-C sequencing analysis of wild-type, β-actin knockout and β-actin hetereozygous mouse embryonic fibroblasts

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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