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SAFB associates with nascent RNAs and can promote gene expression in mouse embryonic stem cells [RIP-seq]

ABSTRACT: SAFB associates with nascent RNAs and can promote gene expression in mouse embryonic stem cells [RIP-seq]

PROVIDER: PRJNA872559 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21177827.fastq.gz	Fastqsanger.gz
	SRR21177828.fastq.gz	Fastqsanger.gz
	SRR21177829.fastq.gz	Fastqsanger.gz
	SRR21177830.fastq.gz	Fastqsanger.gz
	SRR21177831.fastq.gz	Fastqsanger.gz

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SAFB associates with nascent RNAs and can promote gene expression in mouse embryonic stem cells

Project description:SAFB associates with nascent RNAs and can promote gene expression in mouse embryonic stem cells

| PRJNA872560 | ENA

SAFB associates with nascent RNAs and can promote gene expression in mouse embryonic stem cells [ChIP-seq]

Project description:SAFB has roles in gene repression, and we asked whether PRC2 was involved in this process

2023-08-31 | GSE211905 | GEO

SAFB associates with nascent RNAs and can promote gene expression in mouse embryonic stem cells [RNA-seq]

Project description:SAFB associates with nascent RNAs and can promote gene expression in mouse embryonic stem cells [RNA-seq]

| PRJNA872552 | ENA

SAFB associates with nascent RNAs and can promote gene expression in mouse embryonic stem cells [ChIP-seq]

Project description:SAFB associates with nascent RNAs and can promote gene expression in mouse embryonic stem cells [ChIP-seq]

| PRJNA872547 | ENA

Identification of SAFB and HnrnpU interactors

Project description:Scaffold Attachment Factor B (SAFB) is a conserved RNA Binding Protein (RBP) that is essential for early mammalian development. However, the RNAs that associate with SAFB in mouse embryonic stem cells have not been characterized. Here, we addressed this unknown using RNA-seq and SAFB RNA immunoprecipitation followed by RNA-seq (RIP-seq) in wild-type mouse embryonic stem cells (ESCs) and in ESCs in which SAFB and SAFB2 were knocked out. The transcript most enriched in SAFB association was the lncRNA Malat1, which contains a series of purine-rich motifs in its 5 end. Beyond Malat1, SAFB predominantly associated with introns of protein-coding genes also through purine-rich motifs. Knockout of SAFB/2 led to down- and upregulation of genes in multiple biological pathways. The nascent transcripts of many downregulated genes associated with high levels of SAFB in wild-type cells, implying that SAFB binding promotes the expression of these genes. Reintroduction of SAFB into double-knockout cells restored gene expression towards wild-type levels, an effect that was again observable at the level of nascent transcripts. Proteomic analyses indicate an enrichment of nuclear speckle-associated, SR proteins in FLAG-tagged SAFB immunoprecipitated samples. Comparison to immunoprecipitates made from FLAG-tagging of another nuclear-enriched RNA-binding protein called HNRNPU (also known as SAF-A) identified both similarities and differences. Perhaps most notably, we observed a stronger enrichment for speckle-associated proteins in SAFB immunoprecipitations and a strong enrichment for paraspeckle-associated proteins in HNRNPU immunoprecipitations. Our findings suggest that among other potential functions in mouse embryonic stem cells, SAFB directly promotes the expression of a subset of genes through its ability to bind purine regions in nascent RNA.

2023-07-20 | PXD038103 | Pride

SAFB associates with nascent RNAs and can promote gene expression in mouse embryonic stem cells [RNA-seq]

Project description:We performed gene expression profiling analysis using data obtained from RIP-seq inputs of 7 different cell lines.

2023-08-31 | GSE211915 | GEO

SAFB associates with nascent RNAs and can promote gene expression in mouse embryonic stem cells [RIP-seq]

Project description:RNA-IPs in WT and SAFB1/2 DKO mESCs.

2023-08-31 | GSE211917 | GEO

SAFB associates with nascent RNAs and can promote gene expression in mouse embryonic stem cells

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

2023-08-31 | GSE211920 | GEO

The nuclear matrix protein SAFB maintains heterochromatin architecture through RNA-dependent phase separation [RIP-seq]

Project description:Eukaryotic chromosomes fold into topologically associating domains (TADs), which further gather in active (A) or inactive (B) genomic compartments. Here we show that Scaffold Attachment Factor B (SAFB), a nuclear matrix-associated protein with RNA binding functions, modulates global chromatin condensation in a dosage-dependent manner. Upon the depletion of SAFB, the genome coverage of Lamina-associated-domains (LADs) decreases from 53.33% to 45.93%, and both inter- and intra-TAD chromatin-chromatin interactions in compartment B decrease significantly. In the nucleus, SAFB favorably co-localizes with H3K9me3, a marker of heterochromatin, and the disruption of SAFB leads to a collapse of H3K9me3 foci. Furthermore, we show that SAFB proteins can form liquid-liquid phase separation in the cell and in vitro. Intriguingly, SAFB interacts with RNAs from repetitive elements enriched in heterochromatin (e.g., Major Satellites and LINE1), which can promote SAFB-mediated phase separation, depending on the density of SAFB recognizing motifs in the RNAs.

2019-12-01 | GSE141084 | GEO

HOXA9 forms a repressive complex with nuclear matrix-associated protein SAFB to maintain acute myeloid leukemia [RNA-seq]

Project description:This study identifies HOXA9 protein interactome in acute myeloid leukemia cells. Integrated genomic, transcriptomic and proteomic analyses further demonstrated that the HOXA9-SAFB-chromatin complex associates with NuRD and HP1γ to repress the expression of factors associated with differentiation and apoptosis in leukemia maintenance.

2022-12-27 | GSE221700 | GEO

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