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Response of cohesin STAG1 and STAG2 to reduction of NIPBL levels [RNA-Seq]

ABSTRACT: Response of cohesin STAG1 and STAG2 to reduction of NIPBL levels [RNA-Seq]

PROVIDER: PRJNA853746 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19884623.fastq.gz	Fastqsanger.gz
	SRR19884624.fastq.gz	Fastqsanger.gz
	SRR19884625.fastq.gz	Fastqsanger.gz
	SRR19884626.fastq.gz	Fastqsanger.gz
	SRR19884627.fastq.gz	Fastqsanger.gz

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Response of cohesin STAG1 and STAG2 to reduction of NIPBL levels [ChIP-Seq]

Project description:Cohesin mediates sister chromatid cohesion and organizes the genome through the formation of chromatin loops. Two versions of the complex carrying either STAG1 or STAG2 show overlapping and specific functions and both are required to fulfill embryonic development. Cohesin-STAG1 displays longer residence time on chromatin that depends on CTCF and ESCO1 and establishes longer, long-lived chromatin loops together with CTCF. Cohesin-STAG2 shows a preferential interaction with WAPL and mediates shorter loops involved in tissue-specific transcription independently of CTCF. Here we show that the two variants respond in opposite ways to knock down of NIPBL, the putative cohesin loader that is also essential for loop extrusion. Cohesin-STAG1 levels increase on chromatin under this condition and the complex accumulates further at CTCF positions while cohesin-STAG2 is diminished genome-wide. Our data support a model in which NIPBL is not required for association of cohesin with chromatin but it is for loop extrusion, which in turn facilitates stabilization of cohesin-STAG2 at CTCF positions after being loaded elsewhere. In contrast, cohesin-STAG1 is preferentially loaded at CTCF sites independently of NIPBL. Nevertheless, loop formation by these chromatin-bound complexes is impaired and gene expression is severely affected, resembling alterations in Cornelia de Lange patients

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Response of cohesin STAG1 and STAG2 to reduction of NIPBL levels [Hi-C]

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Response of cohesin STAG1 and STAG2 to reduction of NIPBL levels [RNA-Seq]

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Response of cohesin STAG1 and STAG2 to reduction of NIPBL levels

Project description:Response of cohesin STAG1 and STAG2 to reduction of NIPBL levels

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Response of cohesin STAG1 and STAG2 to reduction of NIPBL levels [Hi-C]

Project description:Response of cohesin STAG1 and STAG2 to reduction of NIPBL levels [Hi-C]

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Response of cohesin STAG1 and STAG2 to reduction of NIPBL levels [ChIP-Seq]

Project description:Response of cohesin STAG1 and STAG2 to reduction of NIPBL levels [ChIP-Seq]

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Distinct and overlapping roles of STAG1 and STAG2 in cohesin localization and gene expression in embryonic stem cells [RNA-seq]

Project description:Purpose: Cohesin is a ring-shaped complex that is critical to genome organization and is an important regulator of gene expression. How cohesin accessory proteins contribute to cohesin function remain unclear. The purpose of this study is to assess the roles of cohesin accessory proteins, STAG1 and STAG2, in cohesin localization and gene expression. Method: The role of STAG1 and STAG2 in gene regulation was assessed by performing RNA-seq in wildtype and CRISPR-Cas9 genome edited STAG knockout mouse embryonic stem cells (mESCs). The redundancy of the STAGs was addressed by using siRNA against STAG1 in a STAG2-knockout background.

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Different NIPBL requirements of cohesin-STAG1 and cohesin-STAG2.

Project description:Cohesin organizes the genome through the formation of chromatin loops. NIPBL activates cohesin's ATPase and is essential for loop extrusion, but its requirement for cohesin loading is unclear. Here we have examined the effect of reducing NIPBL levels on the behavior of the two cohesin variants carrying STAG1 or STAG2 by combining a flow cytometry assay to measure chromatin-bound cohesin with analyses of its genome-wide distribution and genome contacts. We show that NIPBL depletion results in increased cohesin-STAG1 on chromatin that further accumulates at CTCF positions while cohesin-STAG2 diminishes genome-wide. Our data are consistent with a model in which NIPBL may not be required for chromatin association of cohesin but it is for loop extrusion, which in turn facilitates stabilization of cohesin-STAG2 at CTCF positions after being loaded elsewhere. In contrast, cohesin-STAG1 binds chromatin and becomes stabilized at CTCF sites even under low NIPBL levels, but genome folding is severely impaired.

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Cohesin Members Stag1 and Stag2 Display Distinct Roles in Chromatin Accessibility and Topological Control of HSC Self-Renewal and Differentiation [RNA_3populations_LSK_GMP_CFUE]

Project description:Transcriptional regulators, including the cohesin complex member STAG2, are recurrently mutated in cancer. The role of STAG2 in gene regulation, hematopoiesis, and tumor suppression remains unresolved. We show that Stag2 deletion in hematopoietic stem and progenitor cells (HSPCs) results in altered hematopoietic function, increased self-renewal, and impaired differentiation. Chromatin immunoprecipitation (ChIP) sequencing revealed that, although Stag2 and Stag1 bind a shared set of genomic loci, a component of Stag2 binding sites is unoccupied by Stag1, even in Stag2-deficient HSPCs. Although concurrent loss of Stag2 and Stag1 abrogated hematopoiesis, Stag2 loss alone decreased chromatin accessibility and transcription of lineage-specification genes, including Ebf1 and Pax5, leading to increased self-renewal and reduced HSPC commitment to the B cell lineage. Our data illustrate a role for Stag2 in transformation and transcriptional dysregulation distinct from its shared role with Stag1 in chromosomal segregation.

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Cohesin Members Stag1 and Stag2 Display Distinct Roles in Chromatin Accessibility and Topological Control of HSC Self-Renewal and Differentiation [ChIP_LinNeg_Stag1Stag2CTCF]

2019-09-26 | GSE138005 | GEO