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Expression data from Rad21 knock-down in ES cells

ABSTRACT: The Cohesin complex has recently been described to regulate gene expression. We wanted to determine the gene expression profile specific in mouse ES cells after depletion of the Cohesin subunit Rad21. We used microarrays to detail the global programme of gene expression underlying depletion of Rad21 and identified distinct early development related genes up-regulated and many pluripotency related genes downregulated. Rad21 was depleted in R1/E ES cells for 48h using esiRNAs against Rad21. An esiRNA against non-targeting Luciferase was used as a negative control

ORGANISM(S): Mus musculus

SUBMITTER: Maciej Paszkowski-Rogacz

PROVIDER: E-GEOD-23923 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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RAD21 cooperates with pluripotency transcription factors in the maintenance of embryonic stem cell identity.

Nitzsche Anja A Paszkowski-Rogacz Maciej M Matarese Filomena F Janssen-Megens Eva M EM Hubner Nina C NC Schulz Herbert H de Vries Ingrid I Ding Li L Huebner Norbert N Mann Matthias M Stunnenberg Hendrik G HG Buchholz Frank F

PloS one 20110512 5

For self-renewal, embryonic stem cells (ESCs) require the expression of specific transcription factors accompanied by a particular chromosome organization to maintain a balance between pluripotency and the capacity for rapid differentiation. However, how transcriptional regulation is linked to chromosome organization in ESCs is not well understood. Here we show that the cohesin component RAD21 exhibits a functional role in maintaining ESC identity through association with the pluripotency transc ...[more]

PMID: 21589869

Similar Datasets

The Cohesin Complex Cooperates with Pluripotency Transcription Factors in the Maintenance of Embryonic Stem Cell Identity

Project description:Embryonic stem cells (ESCs) cells run a self-renewal gene expression program, requiring the expression of certain transcription factors accompanied by a particular chromosome organization to maintain a balance between pluripotency and the capacity for rapid differentiation. However, how transcriptional regulation is linked to chromosome organization in ESCs remains enigmatic. Here we show that Cohesin exhibits a functional role in maintaining ESC identity through association with the pluripotency transcriptional network. ChIP-seq analyses of the cohesin subunit Rad21 reveal an ESC specific cohesin binding pattern that is characterized by a CTCF independent colocalization of cohesin with pluripotency related transcription factors. Upon ESC differentiation, these binding sites disappear and instead new CTCF independent Rad21 binding sites emerge, which are enriched for binding sites of transcription factors implicated in early differentiation. Furthermore, knock-down of cohesin subunits causes expression changes that are reminiscent of the depletion of key pluripotency transcription factors, demonstrating the functional relevance of the cohesin - pluripotency transcriptional network association. Finally, we show that Nanog physically interacts with the cohesin interacting proteins Stag1 and Wapl, further substantiating this association. Based on these findings we propose that a dynamic placement of cohesin by pluripotency transcription factors contributes to a chromosome organization supporting the ESC expression program. This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2011-05-19 | E-GEOD-24030 | biostudies-arrayexpress

Expression data from Rad21 knock-down in ES cells

Project description:The Cohesin complex has recently been described to regulate gene expression. We wanted to determine the gene expression profile specific in mouse ES cells after depletion of the Cohesin subunit Rad21. We used microarrays to detail the global programme of gene expression underlying depletion of Rad21 and identified distinct early development related genes up-regulated and many pluripotency related genes downregulated.

2011-05-19 | GSE23923 | GEO

Rad21-mediated NF-κB signaling limits hematopoietic stem cell self-renewal in aging and inflammation

Project description:MTD project_description Inflammation and decreased stem cell function characterize organism aging, yet the relationship between these factors remains incompletely understood. This study shows that aged hematopoietic stem and progenitor cells exhibit increased ground-stage NF-κB activity, which enhances their responsiveness to undergo differentiation and loss of self-renewal in response to inflammation. The study identifies Rad21/cohesin as a critical mediator of NF-κB signals, by increasing chromatin accessibility of inter-/intra-genic and enhancer regions. Rad21/NF-κB are required for normal differentiation, but limit self-renewal of hematopoietic stem cells (HSCs) during aging and inflammation in an NF-κB dependent manner. HSCs from aged mice fail to downregulate Rad21/cohesin and inflammation/differentiation inducing signals in the resolution phase after acute inflammation. and The inhibition of cohesin/NF-κB is sufficient to revert the hypersensitivity of aged HSPCs to inflammation-induced differentiation. During aging, myeloid-biased HSCs with disrupted and naturally occurring reduced expression of Rad21/cohesin are increasingly selected over lymphoid-biased HSCs. Together, Rad21/cohesin mediated NF-κB signaling limits HSPC function during aging and selects for cohesin deficient HSCs with myeloid skewed differentiation.

2018-11-28 | PXD011537 | Pride

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

A combined RNAi and localization approach for dissecting long noncoding RNAs reveals a function of Panct1 in ES cells

Project description:Long non-coding RNAs (lncRNAs) regulate diverse biological pathways. Unlike protein coding genes, where methods to comprehensibly study their functional roles in cellular systems are available, techniques to systematically investigate lncRNAs have largely remained unexplored. Here, we report a technology for combined Knockdown and Localization Analysis of Non-coding RNAs (c-KLAN) that merges phenotypic characterization and localization approaches to study lncRNAs. Using a library of endoribonuclease prepared short interfering RNAs (esiRNAs) coupled with a pipeline for synthesizing labeled riboprobes for RNA fluorescence in situ hybridization (FISH), we demonstrate the utility of c-KLAN by identifying a novel transcript Panct1 (Pluripotency associated non-coding transcript 1) that regulates embryonic stem cell identity. We postulate that c-KLAN should be generally useful in the discovery of lncRNAs implicated in various biological processes. In this experiment, the levels of Panct1(AK156552) have been depleted by RNAi and the expression levels of all genes have been monitored 72 hours post transfection with esiRNAs against Panct1. An esiRNA against non-targeting Luciferase was used as a negative control.

2012-02-15 | E-GEOD-29798 | biostudies-arrayexpress

RAD21-TEV NLS-TEV RNAseq - extended cohesin depletion

Project description:RAD21-TEV NLS-TEV RNAseq - extended cohesin depletion

| PRJNA679484 | ENA

Cohesin maintains replication timing to suppress DNA damage on cancer genes [PEM-seq: RAD21-shRNA]

Project description:Cohesin loss-of-function mutations are frequently observed in tumors, but the mechanism is unclear. Here, we found that depletion of RAD21, a core subunit of cohesin, leads to massive genome-wide DNA breaks, up to five-fold, and 147 translocation hotspot genes that are co-mutated with cohesin in multiple cancers. Increased DNA damages are independent of RAD21-loss-induced transcription alteration and loop anchor elimination. However, damage-induced chromosomal translocations coincide with the asymmetrically distributed Okazaki fragments of DNA replication, suggesting that RAD21 depletion causes replication stresses evidenced by the slower replication speed and increased stalled forks. Mechanistically, approximately 30% of the human genome exhibits an earlier replication timing after RAD21 depletion, caused by the early initiation of >900 extra dormant origins. Correspondingly, most translocation hotspot genes lie in timing-altered regions. Therefore, we conclude that cohesin dysfunction causes replication stresses induced by excessive DNA replication initiation, resulting in gross DNA damages that may promote tumorigenesis.

2023-05-18 | GSE230504 | GEO

Expression analysis of mock- or RAD21-transduced Kasumi1 cells

Project description:We recently identified recurrent mutations of cohesin complex in myeloid neoplasms through whole-exome sequencing analysis. RAD21 is one of the main components of the cohesin complex. In this study, to investigate the biological impact of wild-type RAD21 on Kasumi1 cells harboring RAD21 mutation, Kasumi1 cells were retrovirally transduced with either mock or wild-type RAD21, and expression array was performed. Expression analysis was performed for mock- or wild-type RAD21-transduced Kasumi-1 cells in triplicate. The experiment was performed twice independently.

2013-07-16 | E-GEOD-47641 | biostudies-arrayexpress

Drosophila retrotransposon and inverted repeat-derived endogenous siRNAs are differentially processed in distinct cellular locations

Project description:Endogenous small interfering (esi)RNAs repress mRNA levels and retrotransposon (retroTn) mobility in Drosophila somatic cells. EsiRNAs are primarily generated from transposon and inverted repeat (hairpin) loci in Drosophila culture cells. After discovering a nucleus specific physical interaction between the essential esiRNA cleavage enzyme Dcr2 and Symplekin, a component of the core cleavage complex (CCC) required for 3’ end processing of mRNAs, we investigated cellular localization of esiRNA biogenesis and overlap between these pathways. We found that knockdown of CCC components perturbs esiRNA levels and that retroTn precursor transcripts are highly enriched in the nucleus while hairpin RNAs are predominantly cytoplasmic. Additionally, retroTn and hairpin-derived esiRNAs have distinct physical characteristics. Combined, these observations support a novel mechanism in which differences in localization of esiRNA precursors impacts esiRNA biogenesis; hairpin-derived esiRNAs are generated in the cytoplasm independent of Dcr2-Symplekin interactions, while retroTns are processed in the nucleus.

2017-06-01 | GSE82128 | GEO

Expression analysis of mock- or RAD21-transduced Kasumi1 cells

2013-07-16 | GSE47641 | GEO