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Super-enhancer switching in early mammalian development involves eRNA mediated SWI/SNF recruitment [RIP-seq]

ABSTRACT: Super-enhancer switching in early mammalian development involves eRNA mediated SWI/SNF recruitment [RIP-seq]

PROVIDER: PRJNA989588 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25098974.fastq.gz	Fastqsanger.gz
	SRR25098975.fastq.gz	Fastqsanger.gz
	SRR25098976.fastq.gz	Fastqsanger.gz
	SRR25098977.fastq.gz	Fastqsanger.gz
	SRR25098978.fastq.gz	Fastqsanger.gz

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Super-enhancer switching in early mammalian development involves eRNA mediated SWI/SNF recruitment [RIP-seq]

Project description:The RNA transcribed from enhancer regions, referred to as eRNA, has been suggested to directly activate transcription by helping to recruit transcription factors and co-activators. Although there have been specific examples of eRNA functioning in this way, it is not clear how general this may be. We find the AT-hook of SWI/SNF alone binds preferentially RNA and as part of the esBAF complexes likely associates with eRNA that are transcribed from intronic and intergenic regions. SWI/SNF is globally recruited in cis by eRNA to cell-type specific enhancers at two distinct stages in early mammalian development and not at promoters or enhancers that are shared between the two stages. SWI/SNF recruited by eRNA facilitates recruitment and/or activation of MLL3/4, p300/CBP and Mediator co-activators to stage-specific super-enhancers that in the primed embryonic stage activate cell lineage priming related genes. We find a strong connection between ATP-dependent chromatin remodeling and eRNA in cell identity and super-enhancer activation.

2023-07-10 | GSE236261 | GEO

Super-enhancer switching in early mammalian development involves eRNA mediated SWI/SNF recruitment

Project description:Super-enhancer switching in early mammalian development involves eRNA mediated SWI/SNF recruitment

| PRJNA992193 | ENA

Super-enhancer switching in early mammalian development involves eRNA mediated SWI/SNF recruitment [CUT-RUN]

Project description:The RNA transcribed from enhancer regions, referred to as eRNA, has been suggested to directly activate transcription by helping to recruit transcription factors and co-activators. Although there have been specific examples of eRNA functioning in this way, it is not clear how general this may be. We find the AT-hook of SWI/SNF alone binds preferentially RNA and as part of the esBAF complexes associates with eRNA transcribed from intronic and intergenic regions. SWI/SNF is globally recruited in cis by eRNA to cell-type specific enhancers at two distinct stages in early mammalian development and not at promoters or enhancers that are shared between the two stages. SWI/SNF recruited by eRNA facilitates recruitment and/or activation of MLL3/4, p300/CBP and Mediator co-activators to stage-specific super-enhancers that in the primed embryonic stage activate cell lineage priming related genes. We find a strong connection between ATP-dependent chromatin remodeling and eRNA in cell identity and super-enhancer activation.

2023-08-25 | GSE207788 | GEO

Super-enhancer switching in early mammalian development involves eRNA mediated SWI/SNF recruitment [RNAPII_inhibitor CUT&RUN]

2023-07-10 | GSE236752 | GEO

Super-enhancer switching in early mammalian development involves eRNA mediated SWI/SNF recruitment [CUT-RUN]

Project description:Super-enhancer switching in early mammalian development involves eRNA mediated SWI/SNF recruitment [CUT-RUN]

| PRJNA857069 | ENA

Super-enhancer switching in early mammalian development involves eRNA mediated SWI/SNF recruitment [RNAPII_inhibitor CUT&RUN]

Project description:Super-enhancer switching in early mammalian development involves eRNA mediated SWI/SNF recruitment [RNAPII_inhibitor CUT&RUN]

| PRJNA992192 | ENA

Super-enhancer switching in early mammalian development involves eRNA mediated SWI/SNF recruitment

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

2023-07-08 | GSE236753 | GEO

LncRNA adapters determine SWI/SNF complex occupancy at gene regulatory elements [RIP-seq]

Project description:The coordination of chromatin remodeling is essential for DNA accessibility and gene expression control. The highly conserved and ubiquitously expressed SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex plays a key role in regulating gene expression in a context-dependent manner. SWI/SNF actively maintains open chromatin states across the genome and responds dynamically to cellular signals. However, the precise mechanisms determining how SWI/SNF is targeted to specific genomic sites remain elusive. In this study we demonstrate that long non-coding RNAs (lncRNAs) are pivotal in the binding of the SWI/SNF complex to specific genomic targets. The interaction between SWI/SNF and lncRNAs is essential for the recruitment of the complex to gene regulatory elements, where it plays a critical role. We show that trans-acting lncRNAs direct the SWI/SNF complex to cell-specific enhancers, with lncRNA knockdowns leading to a genome-wide redistribution of SWI/SNF away from these enhancers. This redistribution impacts the expression of genes connected to these enhancers, underscoring the critical role of lncRNAs in the specific targeting of SWI/SNF to DNA. This insight into the targeting mechanisms of SWI/SNF by lncRNAs has broad implications, from understanding the processes of gene expression control to identifying therapeutic targets in diseases associated with SWI/SNF dysfunction, such as cancer.

2024-11-27 | GSE262063 | GEO

SWI/SNF remains localized to chromatin in the presence of SCHLAP1 (RIP-seq)

Project description:RNA immunoprecipitation of SWI/SNF in prostate cacner

2018-05-14 | GSE114393 | GEO

A SWI/SNF nucleosome remodeling complex acts in non-coding RNA-mediated transcriptional silencing

Project description:RNA-mediated transcriptional silencing prevents deleterious effects of transposon activity and controls the expression of protein-coding genes. It involves long non-coding RNAs (lncRNAs)1, which in Arabidopsis thaliana are produced by a specialized RNA Polymerase V (Pol V)2. lncRNAs guide Argonaute-siRNA complexes to specific genomic loci and mediate the establishment of DNA methylation3,4. The mechanism by which lncRNAs affect chromatin structure and mRNA production remains mostly unknown. Here we identify the SWI/SNF nucleosome remodeling complex as a component of the RNA-mediated transcriptional silencing pathway. We found that SWI3, an essential subunit of the SWI/SNF complex, physically interacts with a lncRNA-binding IDN2 protein5,6. RNA-mediated DNA methylation and transcriptional silencing was compromised in the swi3 mutant. Moreover, targets of SWI/SNF significantly overlapped with genes controlled by Pol V, which shows that the physical interaction reflects a functional relationship. We further found that non-coding transcription by Pol V affects nucleosome positioning on silenced regions. We propose that lncRNAs mediate transcriptional silencing by guiding the SWI/SNF complex and establishing positioned nucleosomes on specific genomic loci. We further propose that guiding ATP-dependent chromatin remodeling complexes may be a more general function of lncRNAs. RNA-seq of 3 samples (Col-0, nrpe1 [a mutant defective in the largest subunit of Pol V and unable to produce lncRNA], swi3b, idn2) with 3 biological replicates.

2012-12-01 | E-GEOD-38400 | biostudies-arrayexpress

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