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CTCF tunes gene expression in a loop-dependent and -independent manner [Hi-C]

ABSTRACT: BL-Hi-C was performed in CTCF AID cells with or without overexpression of wild-type or Y226A/F228A double mutant CTCF to verify that mutant CTCF cannot mediate significant chromatin loops.

ORGANISM(S): Mus musculus

PROVIDER: GSE274884 | GEO | 2026/05/06

REPOSITORIES: GEO

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CTCF tunes gene expression in a loop-dependent and -independent manner [ChIP-Seq]

Project description:ChIP experiments were performed to investigate the changes of CTCF and several chromatin remodeling subunits following CTCF degradation in mouse embryonic stem cells and found that acute CTCF degradation reduced the binding of CHD4 and CHD8.

2026-05-06 | GSE274792 | GEO

CTCF tunes gene expression in a loop-dependent and -independent manner [ATAC-Seq]

Project description:This study was aimed to investigate the influence of CTCF degradation on chromatin accessibility, and discovered that CTCF loss reduced chromatin accessbility

2026-05-06 | GSE274789 | GEO

CTCF tunes gene expression in a loop-dependent and -independent manner [MNase HiChIP]

Project description:CTCF, RAD21 and H3K27ac MNase HiChIP experiments were performed to capture their mediated chromatin interactions. Our data showed that the change in H3K27ac mediated chromatin interactions was minimal upon acute CTCF loss.

2026-05-06 | GSE274794 | GEO

CTCF tunes gene expression in a loop-dependent and -independent manner [RNA-seq]

Project description:In this study, we aimed to investigate changes in gene expression following CTCF degradation, and found that CTCF primarily regulated gene expression in a loop-independent manner when it bound at gene promoters.

2026-05-06 | GSE274773 | GEO

CTCF tunes gene expression in a loop-dependent and -independent manner [TT-seq]

Project description:By using TT-seq, we investigated whether CTCF regulated gene expression by repressing antisense transcription. Our results showed that only few genes were regulated in this way, and CTCF might exert its loop-independent regulatory role through other mechanisms.

2026-05-06 | GSE274797 | GEO

CTCF tunes gene expression in a loop-dependent and -independent manner [MNase-based 4C-seq]

Project description:By designing specific primers targeting different genomic loci, M4C was used to capture chromatin interactions mediated by these loci and to reveal the changes in chromatin interactions upon acute CTCF loss.

2026-05-06 | GSE274799 | GEO

Dissecting developmental disorders caused by CTCF mutation at R567 [Hi-C]

Project description:In this study, we performed BL-Hi-C experiments to investigate the influence of CTCF mutation on higher-order chromatin structures.

2024-05-06 | GSE214687 | GEO

CTCF tunes gene expression in a loop-dependent and -independent manner

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

2026-05-06 | GSE275003 | GEO

CTCF N-terminal Domain Regulates Clustered Protocadherin Gene Expression by Enhancing Cohesin Processivity [ChIP-seq]

Project description:CTCF structures 3D genome folding by anchoring or forestalling cohesin loop extrusion, but the exact mechanism remains obscure. Here, using clustered protocadherins (cPcdh) as model genes, we report that CTCF stabilizes or facilitates cohesin loop extrusion by enhancing its processivity. Specifically, we show that, compared with the Pcdh alpha and gamma clusters, the Pcdh beta cluster is greatly affected upon CTCFY226A/F228A mutation in the N-terminal domain. Given the long-range distance of the Pcdh beta cluster from the distal enhancer, this finding has interesting implications in CTCF regulation of cohesin processivity along the linear chromatin during DNA loop extrusion. In particular, the effect on cohesin processivity upon CTCFY226A/F228A mutation is conspicuously similar to that of WAPL overexpression, demonstrating that, contrary to the general view of blocking or forestalling cohesin, CTCF actually enhances or facilitates cohesin loop extrusion.

2025-02-15 | GSE285578 | GEO

CTCF couples long-range loop extrusion and diffusion to mediate a diverse Igk repertoire

Project description:Dynamic genome folding is important for V(D)J recombination at the immunoglobulin kappa (Igk) locus, which recombines Jk and Vk gene segments across a 3.2 Mb region in both deletional and inversional orientations. Chromatin loop extrusion and diffusion are considered two key mechanisms underlying Igk folding, but how they coordinate remains unclear. Here we show that CTCF is a key regulator coupling loop extrusion and diffusion during Igk V-J rearrangement, promoting recombination in both orientations across long genomic distances. Mechanistically, the CTCF N-terminus promotes long-range loop extrusion that facilitates distal Vk usage by stabilizing cohesin against WAPL release, and also forms loop barriers enabling chromatin diffusion for inversional Vk joining. In CTCF N-terminal-deficient B cells, defects in inversional Vk joining are not restored by WAPL depletion but are instead largely rescued by a dCas9-blockade targeted to the Vk-Jk intergenic region, mimicking the CTCF barrier. Our findings thus highlight how CTCF coordinates distinct genome-folding mechanisms through its dual roles in cohesin stabilization and extrusion barrier formation to ensure the generation of a diverse Igk repertoire.

2025-11-18 | PXD070894 | Pride

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