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

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus

PROVIDER: GSE262605 | GEO | 2024/04/01

REPOSITORIES: GEO

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

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 | GSE262603 | GEO

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

2024-04-01 | GSE262602 | 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

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 [Hi-C]

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

| PRJNA1092630 | ENA

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

Transcription factors mediate long-range enhancer-promoter interactions.

Project description:We examined how remote enhancers establish physical communication with target promoters to activate gene transcription in response to environmental signals. Although the natural IFN-beta enhancer is located immediately upstream of the core promoter, it also can function as a classical enhancer element conferring virus infection-dependent activation of heterologous promoters, even when it is placed several kilobases away from these promoters. We demonstrated that the remote IFN-beta enhancer "loops out" the intervening DNA to reach the target promoter. These chromatin loops depend on sequence-specific transcription factors bound to the enhancer and the promoter and thus can explain the specificity observed in enhancer-promoter interactions, especially in complex genetic loci. Transcription factor binding sites scattered between an enhancer and a promoter can work as decoys trapping the enhancer in nonproductive loops, thus resembling insulator elements. Finally, replacement of the transcription factor binding sites involved in DNA looping with those of a heterologous prokaryotic protein, the lambda repressor, which is capable of loop formation, rescues enhancer function from a distance by re-establishing enhancer-promoter loop formation.

| S-EPMC2779200 | biostudies-literature

Forkhead transcription factors establish origin timing and long-range clustering in S. cerevisiae

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

2012-01-20 | GSE33704 | GEO

Dynamic long-range chromatin interactions control Myb proto-oncogene transcription during erythroid development.

Project description:The key haematopoietic regulator Myb is essential for coordinating proliferation and differentiation. ChIP-Sequencing and Chromosome Conformation Capture (3C)-Sequencing were used to characterize the structural and protein-binding dynamics of the Myb locus during erythroid differentiation. In proliferating cells expressing Myb, enhancers within the Myb-Hbs1l intergenic region were shown to form an active chromatin hub (ACH) containing the Myb promoter and first intron. This first intron was found to harbour the transition site from transcription initiation to elongation, which takes place around a conserved CTCF site. Upon erythroid differentiation, Myb expression is downregulated and the ACH destabilized. We propose a model for Myb activation by distal enhancers dynamically bound by KLF1 and the GATA1/TAL1/LDB1 complex, which primarily function as a transcription elongation element through chromatin looping.

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