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Mesoscale chromatin confinement facilitates target search of pioneer transcription factors in live cells [ChIP-seq]

ABSTRACT: Mesoscale chromatin confinement facilitates target search of pioneer transcription factors in live cells [ChIP-seq]

PROVIDER: PRJNA841668 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27376335_1.fastq.gz	Fastqsanger.gz
	SRR27376335_2.fastq.gz	Fastqsanger.gz
	SRR27376336_1.fastq.gz	Fastqsanger.gz
	SRR27376336_2.fastq.gz	Fastqsanger.gz
	SRR27376337_1.fastq.gz	Fastqsanger.gz

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Mesoscale chromatin confinement facilitates target search of pioneer transcription factors in live cells

Project description:Mesoscale chromatin confinement facilitates target search of pioneer transcription factors in live cells

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Mesoscale chromatin confinement facilitates target search of pioneer transcription factors in live cells [RNA-seq]

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Mesoscale chromatin confinement facilitates target search of pioneer transcription factors in live cells [ATAC-seq]

Project description:Mesoscale chromatin confinement facilitates target search of pioneer transcription factors in live cells [ATAC-seq]

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Mesoscale chromatin confinement facilitates target search of pioneer transcription factors in live cells [RNA-seq]

Project description:To dissect the molecular mechanisms of the transcription factor FOXA2 accessing nucleosomal targets and controlling cell fates, we combined live-cell single-molecule imaging, genome editing, chromatin binding, chromatin accessibility, and RNA sequence analysis. Using the hESC differentiation cellular system to anterior primitive streak (APS) and definitive endoderm (DE), we demonstrated by RNA-seq that FOXA2 is a lineage-determining transcription factor for DE formation and that its intrinsically disordered C-terminal domain (CTD) is essential for its normal function. Through ChIP-seq and ATAC-seq at multiple time points of exogenous expression, we also showed that the CTD is required for FOXA2 effectively accessing targets in closed chromatin and altering chromatin accessibility. Together with the single-molecule kinetics captured by fluorescence microscopy, this study uncovers new mechanistic insights on the activity of lineage-determining transcription factors in engaging chromatin and accessing nucleosomal targets.

2024-04-29 | GSE203640 | GEO

Mesoscale chromatin confinement facilitates target search of pioneer transcription factors in live cells [ATAC-seq]

2024-04-29 | GSE203649 | GEO

Mesoscale chromatin confinement facilitates target search of pioneer transcription factors in live cells [ChIP-seq]

2024-04-29 | GSE203644 | GEO

Mesoscale chromatin confinement facilitates target search of pioneer transcription factors in live cells

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

2024-04-28 | GSE203650 | GEO

Confinement stress in HR and LR trout lines

Project description:This SuperSeries is composed of the following subset Series: GSE25440: Individual variation in confinement response at 168h GSE25473: Time course study of confinement stress in HR and LR trout lines Refer to individual Series

2010-11-24 | E-GEOD-25584 | biostudies-arrayexpress

An Intrinsic Disordered Region Mediated Confinement State Contributes to Dynamics and Function of Transcription Factors

Project description:In this study we used single-molecule tracking and machine-learning based classification to directly measure the nuclear mobility of the glucocorticoid receptor (GR) in live cells. We revealed two distinct and dynamic sub-diffusive populations. One accounts for specific binding to chromatin, while the other represents a confinement state that requires an intrinsically disordered region (IDR), consistent with liquid-liquid condensate subdomains. Further analysis showed that the dwell times of both subpopulations follow a power-law distribution, consistent with a broad distribution of affinities on the GR cistrome and interactome. Altogether, our data link IDRs with a confinement state that is functionally distinct from specific chromatin binding and modulates the transcriptional output by increasing the local concentration of TFs at specific sites.

2021-01-14 | GSE154771 | GEO

Eukaryotic cytoplasm is widely structured via mesoscale condensates

Project description:Compartmentalization is an essential feature of eukaryotic life and is achieved both via membrane-bound organelles, such as mitochondria, and membrane-less biomolecular condensates, such as the nucleolus. Known biomolecular condensates typically exhibit liquid-like properties and are visualized by microscopy on the scale of ~1µm. They have been studied mostly by microscopy, examining select individual proteins. So far, several dozen biomolecular condensates are known, serving a multitude of functions, for example, in the regulation of transcription, RNA processing or signalling and their malfunction can cause diseases. However, it remains unclear to what extent biomolecular condensates are utilized in cellular organization and at what length scale they typically form. Here we examine native cytoplasm from Xenopus egg extract on a global scale with quantitative proteomics, filtration, size exclusion and dilution experiments. These assays reveal that at least 18% of the proteome is organized into mesoscale biomolecular condensates at the scale of ~100nm and appear to be stabilized by RNA or gelation. We confirmed mesoscale sizes via imaging below the diffraction limit by investigating protein permeation into porous substrates with defined pore sizes. Our results show that eukaryotic cytoplasm organizes extensively via biomolecular condensates, but at surprisingly short length scales.

2023-11-02 | GSE232651 | GEO

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