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

ABSTRACT: 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.

ORGANISM(S): Mus musculus

PROVIDER: GSE274799 | GEO | 2026/05/06

REPOSITORIES: GEO

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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

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

2026-05-06 | GSE275003 | GEO

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

Project description: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.

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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 [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

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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

Robust 4C-seq data analysis to screen for regulatory DNA interactions

Project description:Regulatory DNA elements can control expression of distant genes via physical interactions. Here, we present a cost-effective methodology and computational analysis pipeline for robust characterization of the physical organization around selected promoters and other functional elements using Chromosome Conformation Capture combined with high-throughput sequencing (4C-seq) data. Our approach can be multiplexed and routinely integrated with other functional genomics assays to facilitate physical characterization of gene regulation. A high resolution 4C-seq protocol involving two restriction digests and a revised analysis pipeline was applied to several viewpoints in four genomic loci (the well-characterized alpha-globin and beta-globin loci, and the novel Oct4 and Satb1 loci), allowing robust detection of physical interactions between regulatory DNA elements.

2012-09-04 | E-GEOD-40420 | biostudies-arrayexpress

4C-seq experiment on mouse skeletal muscle and DP thymocytes

Project description:Purpose: The aim of this study is to investigate enhancer promoter interactions in skeletal muscle Methods: 50 ng of purified DNA were used as a template for PCR with bait-specific primers (Table S5) containing Illumina adapter termini. PCR reactions were pooled and, after primer removal with 1.8x AMPure XP beads, DNA was sequenced with the HiSeq 4000 (Illumina), as single-end 50 bp reads. Sequences were trimmed to remove primer and bait fragment sequence with the sabre tool (https://github.com/najoshi/sabre), mapped to the genome with Bowtie and converted to restriction fragment space as in van de Werken et al., 2012 (van de Werken et al., 2012). Interactions were called on single 4C experiments with peakC (Geeven et al., 2018), using a sliding window of 21 fragments.

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UMI-4C for quantitative and targeted chromosomal contact profiling

Project description:We developed a targeted chromosome conformation capture (4C) approach that uses unique molecular identifiers (UMI) to derive high complexity quantitative chromosome contact profiles with controlled signal to noise ratios. We demonstrate that the method improves the sensitivity and specificity for detection of long-range chromosomal interactions, and that it allows the design of interaction screens with predictable statistical power. UMI-4C robustly quantifies contact intensity changes between cell types and conditions, opening the way toward incorporation of long-range interactions in quantitative models of gene regulation. We constructed UMI-4C profiles of 13 different genomic loci (viewpoints) in five different cell lines, in order to study the 3D chromatin contact maps of these selected loci. The coordinates for these viewpoints are: G1p1 chrX:48646542; baitG1_3_5kb chrX:48641393; bait_50kb chrX:48595987; bait_165kb chrX:48476525; ANK1 chr8:41654693; hbb_3HS chr11:5221346; hbb_HBB chr11:5248714; hbb_HBBP1_G1 chr11:5266532; HBB_HBE chr11:5292159; HBB_HS2 chr11:5301345; HBB_HS3 chr11:5306690; HBB_HS5 chr11:5313539; HBB_HBD chr11:5256597

2016-06-15 | E-GEOD-76763 | biostudies-arrayexpress

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