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CTCF and Cohesin (Rad21) ChIP-seq in female mouse liver

ABSTRACT: CTCF and Cohesin (Rad21) ChIP-seq in female mouse liver

PROVIDER: PRJNA542215 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9030030.fastq.gz	Fastqsanger.gz
	SRR9030031.fastq.gz	Fastqsanger.gz
	SRR9030032.fastq.gz	Fastqsanger.gz
	SRR9030026.fastq.gz	Fastqsanger.gz
	SRR9030027.fastq.gz	Fastqsanger.gz

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CTCF and Cohesin (Rad21) ChIP-seq in female mouse liver

Project description:Sequencing files provided here include mouse liver ChIP-seq for CTCF and the cohesin subunit Rad21. These files are part of a larger study ("CTCF and Cohesin link sex-biased distal regulatory elements to sex-biased gene expression in mouse liver") where we compare CTCF and cohesin binding in male and female mouse liver as well as differences in chromatin conformation (DNA looping).

2020-07-07 | GSE130908 | GEO

ChIP-seq analyses of CTCF binding in liver samples from CAST/EiJ and SPRET/EiJ (Mus spretus) mice, and of the cohesin subunit RAD21 in C57BL/6J mouse liver

Project description:We explored the relationship between the evolutionary dynamics of CTCF binding and the functional stability of higher order genome structures, by performing ChIP-seq experiments in closely related Mus species or strains and intersecting with Hi-C-derived topologically associating domains (TADs) and expression data. All experiments were performed in adult male liver samples in 3 biological replicates and with an input control set. We also generated RAD21 (cohesin subunit) ChIP-seq from a replicate of adult male mouse (C57BL/6J) liver to determine localization of cohesin with respect to CTCF.

2019-11-20 | E-MTAB-8014 | biostudies-arrayexpress

CTCF and Cohesin (Rad21) ChIP-seq in male mouse liver

Project description:Sequencing files provided here include mouse liver ChIP-seq for CTCF and the cohesin subunit Rad21. These files are part of a larger study where we describe features of Topologically Associating Domains (TADs) and their impact on liver gene expression, then use these features to computationally predict subTAD structures not otherwise readily identifiable due to the low resolution of Hi-C. Our findings reveal that CTCF-based subTAD loops maintain key insulating properties of TADs, and support the proposal that subTADs are formed by the same loop extrusion mechanism and contribute to nuclear architecture as intra-TAD scaffolds that further constrain enhancer-promoter interactions. This allows high expression of super enhancer target genes and individual genes within inactive TADs, and may be a broadly conserved mechanism of genomic regulation.

2018-05-11 | GSE102997 | GEO

Mapping of cohesin, CTCF and a collection of tissue-specific and ubiquitous transcriptional regulators using ChIP-seq in primary wild type and Rad21-cohesin haploinsufficient mouse liver

Project description:Mapping of cohesin, CTCF and a collection of tissue-specific and ubiquitous transcriptional regulators using ChIP-seq in primary mouse liver. The following antibodies were used: CTCF (upstate, 07729), STAG1 (abcam, ab4457), STAG2 (abcam, 4464), RAD21 (abcam, ab992), CEBPA (santa cruz, sc9314), HNF4A (aviva systems biology, ARP31946), FOXA1 (abcam, ab5089), FOXA2 (santa cruz, sc6554), HNF6 (santa cruz, sc13050), HNF1A (santa cruz, sc6547), PREP1 (santa cruz, sc6245), NRSF/REST (santa cruz, sc25398), GABPA (santa cruz, sc22810), E2F4 (santa cruz, sc1082), p300 (santa cruz, sc585), CBP (santa cruz, sc369), RNAP2 (abcam, ab5408), H3K4me1 (abcam, ab8895), H3K4me3 (abcam, ab8580), H3K36me3 (abcam, ab9050), H3K79me2 (abcam, ab3594), H2AK5ac (abcam, 1764)

2012-06-22 | E-MTAB-941 | biostudies-arrayexpress

Chromatin immunoprecipitation of mouse B3 pre-B cells and VL3 thymocytes to identify cohesin and CTCF binding sites

Project description:Identification of cohesin (Rad21) and CTCF binding sites in ~2% of the mouse genome in B3 pre-B cells stably expressing FLAG-tagged Rad21 using anti-FLAG (Sigma F3165) and anti-CTCF (Upstate 07729) antibodies

2008-01-31 | E-TABM-401 | biostudies-arrayexpress

Genome-wide identification of CTCF and Cohesin binding sites in neonatal mouse brain

Project description:ChIP-seq for CTCF and Rad21 in 3 week old mouse brain from reciprocal BxC and CxB crosses. One biological replicate of each. Examination of CTCF and Cohesin binding sites in neonetal mouse brain

2013-06-20 | E-GEOD-35140 | biostudies-arrayexpress

CTCF/cohesin organize the ground state of chromatin-nuclear speckle association [hela rad21-aid RNA-seq]

Project description:The interchromatin space in the cell nucleus contains various membrane-less nuclear bodies. Recent findings indicate that nuclear speckles, comprising a distinct nuclear body, exhibit interactions with certain chromatin regions in a ground state. Key questions are how this ground state of chromatin-nuclear speckle association is established and what are the gene regulatory roles of this layer of nuclear organization. We report here that chromatin structural factors CTCF and cohesin are required for full ground state association between DNA and nuclear speckles. Disruption of ground state DNA-speckle contacts via either CTCF depletion or cohesin depletion had minor effects on basal level expression of speckle-associated genes, however we show strong negative effects on stimulus-dependent induction of speckle-associated genes. We identified a putative speckle targeting motif (STM) within cohesin subunit RAD21 and demonstrated that the STM is required for chromatin-nuclear speckle association. In contrast to reduction of CTCF or RAD21, depletion of the cohesin releasing factor WAPL stabilized cohesin on chromatin and DNA-speckle contacts, resulting in enhanced inducibility of speckle-associated genes. In addition, we observed disruption of chromatin-nuclear speckle association in patient derived cells with Cornelia de Lange syndrome (CdLS), a congenital neurodevelopmental diagnosis involving defective cohesin pathways, thus revealing nuclear speckles as an avenue for therapeutic inquiry. In summary, our findings reveal a mechanism to establish the ground organizational state of chromatin-speckle association, to promote gene inducibility, and with relevance to human disease.

2024-11-08 | GSE273618 | GEO

ChIP-seq data in mESCs show ZFP661 suppresses cohesin binding at CTCF barriers

Project description:In this assay, we aimed to investigate the occupancy of ZFP661 in the mouse genome and its possible role in regulating the occupancies of CTCF and cohesin, which are two key factors in establishing 3D chromatin structures. To achieve this, we performed ChIP-seq in ZFP661-3HA endogenously tagged mESCs (for ZFP661), Zfp661 knockout (KO) mESCs (for CTCF and RAD21), and ZFP661-3HA overexpressing (OE) mESCs (for ZFP661, CTCF, RAD21, KAP1, and H3K9me3). Our results reveal that 1) ZFP661 binding peaks were co-occupied with those of CTCF; 2) ZFP661 binds exclusively inside the CTCF loop anchors; and 3) ZFP661 can suppress cohesin binding at CTCF barriers without altering CTCF binding.

2023-05-09 | GSE231866 | GEO

Transcription profiling of zebrafish embryos homozygous mutant for the cohesin subunit Rad21

Project description:Rad21 is a subunit of cohesin. The main function of cohesin is to hold replicated chromosomes together until cells divide, but it also plays a role in gene expression. To find out which genes might be regulated by cohesin, a study was conducted to look for global changes in gene expression in zebrafish embryos lacking cohesin component Rad21. The zebrafish Rad21 mutant used for expression analysis was rad21nz171, an allele isolated in a forward genetic screen for regulators of runx1. Experiment Overall Design: RNA from rad21nz171 mutant and wild type zebrafish embryos collected at 24 hours post-fertilization (h.p.f.) and 48 h.p.f. was hybridized to Affymetrix microarrays (Gene Chip zebrafish genome arrays cat. no. 900488). Four pools of 50 embryos for each genotype and time point were used as the RNA source, and RNA from each pool was hybridized independently such that the experiment had four biological replicates.

2009-11-10 | E-GEOD-18795 | biostudies-arrayexpress

CTCF and cohesin regulate chromatin loop stability with distinct dynamics

Project description:The study investigates the nuclear organization and the binding dynamics of CTCF and cohesin by super-resolution microscopy and ChIP-seq. We determined the genome-wide binding profile of CTCF and Rad21 cohesin subunit in wild type mouse ES cells and compared them to a double FLAG-Halo-mCTCF/mRad21-SNAPf-V5 knock-in mES line, generated by CRISPR/Cas9-mediated genome editing to perform imaging experiments.

2017-05-03 | GSE90994 | GEO

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