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

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

PROVIDER: PRJNA841678 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19367900.fastq.gz	Fastqsanger.gz
	SRR19367883.fastq.gz	Fastqsanger.gz
	SRR19367884.fastq.gz	Fastqsanger.gz
	SRR19367885.fastq.gz	Fastqsanger.gz
	SRR19367886.fastq.gz	Fastqsanger.gz

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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.

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

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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.

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