Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chip-on-ChEPseq analysis of RAD21 cohesin subunit cleaved by separase in a human cancer cell line

ABSTRACT: The goal of the study was to map the epigenomic positions of proteolyzed RAD21 human protein in mitotic DLD-1 cells with proprietary antibodies against the neo-epitope (RAD21*) generated by cleavage with separase. The study involved chromatin IP analyzed by high-throughput sequencing analysis using immortalized human cancer cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE216058 | GEO | 2022/11/07

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Chip-on-ChEPseq analysis of RAD21 cohesin subunit cleaved by separase in a human cancer cell line

Project description:Chip-on-ChEPseq analysis of RAD21 cohesin subunit cleaved by separase in a human cancer cell line

| PRJNA891852 | ENA

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

Rad21 is the core subunit of cohesin complex in directing genome organization

Project description:In eukaryotes, the nuclear chromatin in the interphase is a hierarchical organization. Previous studies have suggested that cohesin-DNA interactions play important architectural functions for chromatin structure in the interphase. In this study, we applied super-resolution imaging, single-molecule imaging to measure the distribution of cohesin subunits. Hi-C and RNA-seq were used to reveal the 3D genome structures alterations and the relationship with breast cancer upon Rad21 up-regulation. Hi-C experiment showed that the contact frequency of short distance was increased while that of long distance was decreased in the absence of Rad21 up-regulation. Chromatin interactions between A and B compartments increased and compartmentalization strength was reduced significantly upon Rad21 up-regulation. Correspondingly, accumulated contacts were shown at TAD corners and inter-TAD interactions increased. These observations support cohesin loop extrusion model and lead us to propose the unique role of Rad21-loader interaction in cohesin loading and further cohesin extrusion. Moreover, we combined transcriptome changes and chromatin structure alterations upon Rad21 up-regulation and revealed the correlation between Rad21 and breast cancer by affecting chromatin architecture.

2022-05-01 | GSE183186 | GEO

Expression data from zebrafish embryos homozygous mutant for the cohesin subunit Rad21

2009-10-30 | GSE18795 | GEO

Cohesin subunit RAD21: From biology to disease.

Project description:RAD21 (also known as KIAA0078, NXP1, HR21, Mcd1, Scc1, and hereafter called RAD21), an essential gene, encodes a DNA double-strand break (DSB) repair protein that is evolutionarily conserved in all eukaryotes from budding yeast to humans. RAD21 protein is a structural component of the highly conserved cohesin complex consisting of RAD21, SMC1a, SMC3, and SCC3 [STAG1 (SA1) and STAG2 (SA2) in metazoans] proteins, involved in sister chromatid cohesion. This function is essential for proper chromosome segregation, post-replicative DNA repair, and prevention of inappropriate recombination between repetitive regions. In interphase, cohesin also functions in the control of gene expression by binding to numerous sites within the genome. In addition to playing roles in the normal cell cycle and DNA DSB repair, RAD21 is also linked to the apoptotic pathways. Germline heterozygous or homozygous missense mutations in RAD21 have been associated with human genetic disorders, including developmental diseases such as Cornelia de Lange syndrome (CdLS) and chronic intestinal pseudo-obstruction (CIPO) called Mungan syndrome, respectively, and collectively termed as cohesinopathies. Somatic mutations and amplification of the RAD21 have also been widely reported in both human solid and hematopoietic tumors. Considering the role of RAD21 in a broad range of cellular processes that are hot spots in neoplasm, it is not surprising that the deregulation of RAD21 has been increasingly evident in human cancers. Herein, we review the biology of RAD21 and the cellular processes that this important protein regulates and discuss the significance of RAD21 deregulation in cancer and cohesinopathies.

| S-EPMC7949736 | biostudies-literature

Chip-seq analysis of meiotic Cohesin (mei-Cohesins) subunit REC8 cleaved by separase (REC8*), and SMC3 in Macaca fascicularis testis

Project description:The study aimed to map epigenomic locations of separase-cleaved REC8 using chromatin IP analyzed by high-throughput sequencing on purified germ cells from M. fascicularis testis

2022-11-07 | GSE201989 | GEO

Effect daunorubicin on the binding of the cohesin subunit Rad21 in HCT116 cells [ChIP-seq]

Project description:We used ChIP-seq to measure the binding of the cohesin subunit Rad21 in response to daunorubicin treatment in HCT116 cells

2016-09-30 | GSE86191 | GEO

Expression data from MCF7 cells depleted of the cohesin subunit RAD21 and treated with estrogen or vehicle

Project description:RAD21 is a subunit of cohesin. Cohesin is maninly known for its role in holding sister chromatids together during cell-division but it also plays a role in gene regulation. Genome wide study in MCF7 cells have shown that cohesin co-binds with estrogen receptor alpha at numerous sites. To identify estrogen sensitive genes that are influenced by cohesin, a microarray expression analysis was conducted in MCF7 cells lacking the cohesin subunit RAD21. Global changes in gene expression were identified in cells treated with Control/RAD21 siRNA and stimulated with estrogen/vehicle thereafter.

2016-01-30 | GSE59908 | GEO

The Drosophila cohesin subunit Rad21 is a trithorax group (trxG) protein.

Project description:The cohesin complex is a key player in regulating cell division. Cohesin proteins SMC1, SMC3, Rad21, and stromalin (SA), along with associated proteins Nipped-B, Pds5, and EcoI, maintain sister chromatid cohesion before segregation to daughter cells during anaphase. Recent chromatin immunoprecipitation (ChIP) data reveal extensive overlap of Nipped-B and cohesin components with RNA polymerase II binding at active genes in Drosophila. These and other data strongly suggest a role for cohesion in transcription; however, there is no clear evidence for any specific mechanisms by which cohesin and associated proteins regulate transcription. We report here a link between cohesin components and trithorax group (trxG) function, thus implicating these proteins in transcription activation and/or elongation. We show that the Drosophila Rad21 protein is encoded by verthandi (vtd), a member of the trxG gene family that is also involved in regulating the hedgehog (hh) gene. In addition, mutations in the associated protein Nipped-B show similar trxG activity i.e., like vtd, they act as dominant suppressors of Pc and hh(Mrt) without impairing cell division. Our results provide a framework to further investigate how cohesin and associated components might regulate transcription.

| S-EPMC2527924 | biostudies-literature

RAD21-TEV NLS-TEV RNAseq - extended cohesin depletion

Project description:RNA-seq of vehicle and doxycycline treated Rad21-TEV primary neuron transduced with NLS-TEV, inducing extended cohesin depletion

2021-02-28 | GSE161797 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data