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Nuclear receptor activation leads to functional changes in CTCF-defined chromatin structure [HiChIP]

ABSTRACT: Nuclear receptor activation leads to functional changes in CTCF-defined chromatin structure [HiChIP]

PROVIDER: PRJNA778665 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16849263_1.fastq.gz	Fastqsanger.gz
	SRR16849263_2.fastq.gz	Fastqsanger.gz
	SRR16849264_1.fastq.gz	Fastqsanger.gz
	SRR16849264_2.fastq.gz	Fastqsanger.gz
	SRR16849265_1.fastq.gz	Fastqsanger.gz

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Nuclear receptor activation leads to functional changes in CTCF-defined chromatin structure [HiChIP]

Project description:The aim of the project was to investigate the effect of nuclear receptor activation, particularly of the vitamin D receptor, on CTCF-defined 3D chromatin structure, and associated functional changes in the transcriptional response of THP-1 cells.

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Nuclear receptor activation leads to functional changes in CTCF-defined chromatin structure

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Project description:Nuclear receptor activation leads to functional changes in CTCF-defined chromatin structure [Hi-C]

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CTCF HiChIP data in A673 Ewing sarcoma cell lines (siCT & siSA2)

Project description:STAG2, a member of cohesin, is one of the most recurrently mutated genes in human cancer. Here, we investigated STAG2 function in the context of Ewing sarcoma, an aggressive bone tumor driven by EWS-FLI1 oncogene chimeric transcription factor. A673 Ewing sarcoma cell line was trasfected with siCT or 2 different siRNA targetting STAG2 during 72h and CTCF HiChIP experiments were preformed for each conditions. Analyses of HiChIP data show that STAG2 knowck-down alters CTCF-anchored loop extrusion.

2021-04-29 | GSE156650 | GEO

CTCF HiChIP experiments in cells treatd with control shRNA or BHLHE40 shRNA

Project description:In this study, we investigated CTCF mediated chromatin interactions by HiChIP experiment in control shRNA and BHLHE40-depleted HeLa-S3 cells.

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DNA methylation insulates exons from CTCF loops with nuclear speckles (HiChIP)

Project description:DNA methylation insulates exons from CTCF loops with nuclear speckles (HiChIP)

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Nuclear receptor activation leads to functional changes in CTCF-defined chromatin structure

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

2022-04-27 | GSE190464 | GEO

Nuclear receptor activation leads to functional changes in CTCF-defined chromatin structure [Hi-C]

Project description:The aim of the project was to investigate the effect of nuclear receptor activation, particularly of the vitamin D receptor, on chromatin structure, and associated functional changes in the transcriptional response of THP-1 cells.

2022-04-27 | GSE190463 | GEO

DNA methylation insulates exons from CTCF loops with nuclear speckles (HiChIP)

Project description:CTCF is necessary for the formation and maintenance of many DNA loops and Topologically Associating Domains, but the genomic features that influence CTCF looping are incompletely understood. We characterized the downstream effects of treating cells with a DNMT1 inhibitor and acute depletion of nuclear speckles to study the factors that influence CTCF looping.

2024-11-11 | GSE217754 | GEO

High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion [HiChIP]

Project description:Cohesin-mediated DNA loop extrusion enables gene regulation by distal enhancers through the establishment of chromosome structure and long-range enhancer-promoter interactions. The best characterized cohesin-related structures, such as topologically associating domains (TADs) anchored at convergent CTCF binding sites, represent static conformations. Consequently, loop extrusion dynamics remain poorly understood. To better characterize static and dynamically extruding chromatin loop structures, we use MNase-based 3D genome assays to simultaneously determine CTCF and cohesin localization as well as the 3D contacts they mediate. Here we present CTCF Analyzer (with) Multinomial Estimation (CAMEL), a tool that identifies CTCF footprints at near base-pair resolution in CTCF MNase HiChiP. We also use Region Capture Micro-C to identify a CTCF-adjacent footprint that is attributed to cohesin occupancy. We leverage this substantial advance in resolution to determine that the fully extruded (CTCF-CTCF loop) state is rare genome-wide with locus-specific variation from ~1-10%. We further investigate the impact of chromatin state on loop extrusion dynamics and find that active regulatory elements impede cohesin extrusion. These findings support a model of topological regulation whereby the transient, partially extruded state facilitates enhancer-promoter contacts that can regulate transcription.

2025-01-14 | GSE285007 | GEO

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