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Individual transcription factors modulate both the micromovement of chromatin and its long-range structure [Hi-C]

ABSTRACT: Individual transcription factors modulate both the micromovement of chromatin and its long-range structure [Hi-C]

PROVIDER: PRJNA1092630 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28477144_1.fastq.gz	Fastqsanger.gz
	SRR28477144_2.fastq.gz	Fastqsanger.gz
	SRR28477145_1.fastq.gz	Fastqsanger.gz
	SRR28477145_2.fastq.gz	Fastqsanger.gz
	SRR28477146_1.fastq.gz	Fastqsanger.gz

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Individual transcription factors modulate both the micromovement of chromatin and its long-range structure [Hi-C]

Project description:The control of eukaryotic gene expression is intimately connected to highly dynamic chromatin structures. Gene regulation relies on activator and repressor transcription factors (TFs) that induce local chromatin opening and closing. However, it is unclear how nucleus-wide chromatin organization responds dynamically to the activity of specific TFs. Here we examined how two TFs with opposite effects on local chromatin accessibility modulate chromatin dynamics nucleus-wide. We combine High-resolution Diffusion mapping (Hi-D) and Dense Flow reConstruction and Correlation (DFCC) in living cells to obtain an imaging-based, nanometer-scale analysis of local diffusion processes and long-range coordinated movements of both chromatin and TFs. We show that the expression of either an individual transcriptional activator (CDX2) or repressor (SIX6) with large numbers of binding sites increases chromatin mobility nucleus-wide, yet they induce opposite coherent chromatin motions at the micron scale. Hi-C analysis of higher-order chromatin structures shows that induction of the pioneer factor CDX2 leads both to changes in local chromatin interactions and the distribution of A and B compartments, thus relating the micromovement of chromatin with changes in compartmental structures. Given that inhibition of transcription initiation and elongation by RNA Pol II has a partial impact on the global chromatin dynamics induced by CDX2, we suggest that CDX2 overexpression alters chromatin structure dynamics both dependently and independently of transcription. Our biophysical analysis shows that sequence-specific TFs can influence chromatin structure on multiple architectural levels, arguing that local chromatin changes brought by TFs alter long-range chromatin mobility and its organization.

2024-04-01 | GSE262602 | GEO

Individual transcription factors modulate both the micromovement of chromatin and its long-range structure

Project description:Individual transcription factors modulate both the micromovement of chromatin and its long-range structure

| PRJNA1092625 | ENA

Individual transcription factors modulate both the micromovement of chromatin and its long-range structure [RNA-Seq]

2024-04-01 | GSE262603 | GEO

Individual transcription factors modulate both the micromovement of chromatin and its long-range structure [ChIP-Seq]

2024-04-01 | GSE262601 | GEO

Individual transcription factors modulate both the micromovement of chromatin and its long-range structure [ChIP-Seq]

Project description:Individual transcription factors modulate both the micromovement of chromatin and its long-range structure [ChIP-Seq]

| PRJNA1092628 | ENA

Individual transcription factors modulate both the micromovement of chromatin and its long-range structure [RNA-Seq]

Project description:Individual transcription factors modulate both the micromovement of chromatin and its long-range structure [RNA-Seq]

| PRJNA1092629 | ENA

Individual transcription factors modulate both the micromovement of chromatin and its long-range structure

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

2024-04-01 | GSE262605 | GEO

Comparison of Hi-C results using in-solution versus in-nucleus ligation

Project description:Chromosome conformation capture (3C) and derivative (4C, 5C and Hi-C) methods employ ligation of diluted cross-linked chromatin complexes, intended to favor proximity-dependent, intra-complex ligation. We previously described an alternative Hi-C protocol with ligation in preserved nuclei rather than in solution. Here we directly compare Hi-C methods employing "in-nucleus ligation" and the standard "in-solution ligation". The results show that in-nucleus ligation captures chromatin interactions more consistently over a wider range of distances, and significantly reduces both experimental noise and bias. Thus in-nucleus ligation not only simplifies the experimental procedures, but also produces higher quality data with benefits for the entire range of 3C applications. We created Hi-C libraries by two different methods, in-solution ligation and in-nucleus ligation, from two biological replicates each of mouse foetal liver cells (mouse-1 and mouse-2) and human ES cells (human-1 and human-2) or the mixture of these two species. We also sequenced a random ligation library prepared by reversal of the cross-links and purification of the DNA prior to ligation.

2015-08-12 | E-GEOD-70181 | biostudies-arrayexpress

Hi-C and Haplotagging datasets for Zemin et al long-range read paper

Project description:Hi-C and Haplotagging datasets for Zemin et al long-range read paper

| PRJEB58366 | ENA

Comparison of Hi-C results using in-solution versus in-nucleus ligation

2015-08-12 | GSE70181 | GEO