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Enhancer RNAs make multivalent interactions with NELF to stimulate Pol II pause release [Exo-seq]

ABSTRACT: Enhancer RNAs make multivalent interactions with NELF to stimulate Pol II pause release [Exo-seq]

PROVIDER: PRJNA684922 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13248081.fastq.gz	Fastqsanger.gz
	SRR13248082.fastq.gz	Fastqsanger.gz
	SRR13248083.fastq.gz	Fastqsanger.gz

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Enhancer RNAs make multivalent interactions with NELF to stimulate Pol II pause release

Project description:Enhancer RNAs make multivalent interactions with NELF to stimulate Pol II pause release

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Enhancer RNAs make multivalent interactions with NELF to stimulate Pol II pause release [SHAPE]

Project description:Enhancer RNAs make multivalent interactions with NELF to stimulate Pol II pause release [SHAPE]

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Enhancer RNAs make multivalent interactions with NELF to stimulate Pol II pause release [Exo-seq]

Project description:5’ ExoSeq of total RNA (rRNA & signal recognition particle RNA depleted) from mouse cortical neurons before and after membrane depolarization by potassium chloride (KCl).

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Enhancer RNAs stimulate Pol II pause release by harnessing multivalent interactions to NELF

Project description:UV-light-induced protein-RNA cross-linking followed by MS analysis was used to identify RNA-binding regions of enhancer RNAs (eRNAs) to the negative elongation factor (NELF) complex, and NELF as part of the paused elongation complex (PEC) of human RNA polymerase II.

2022-03-08 | PXD030569 | Pride

Enhancer RNAs make multivalent interactions with NELF to stimulate Pol II pause release

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

2022-03-08 | GSE163113 | GEO

Enhancer RNAs make multivalent interactions with NELF to stimulate Pol II pause release [SHAPE]

Project description:A SHAPE-MaP structure probing experiment was performed on 40 eRNAs. The eRNA transcription start sites (TSSs) were identified by 5'-ExoSeq. The 5' end fragment (1-200 nucleotides) of each eRNA was cloned from mouse cortical neurons and the eRNAs were produced by in vitro transcription. Each eRNA was treated in one sample with DMSO (control) and in a second sample with the SHAPE reagent 1-Methyl-7-nitroisatoic anhydride (1M7). The 1M7 chemical will react preferentially with the ribose 2'OH of the flexible nucleotides in single stranded regions and the produced adduct will lead to mutations during reverse transcription.

2022-03-08 | GSE163112 | GEO

Enhancer RNAs harness multivalent interactions to detach NELF from paused Pol II [GROSEQ, eCLIPSEQ, CHIPSEQ]

Project description:Enhancer RNAs (eRNAs) are a class of non-coding RNAs that originate from enhancers. Although eRNA transcription is a canonical feature of functionally activated enhancers in various organisms and cell types, its functionality in gene regulation has not been firmly established. This is in part due to a lack of knowledge regarding the molecular features required for eRNA function. Using the eRNA-dependent regulation of RNA polymerase II (Pol II) pause release as a model, we examined the requirement of sequence, structure and length for the ability of eRNAs to detach NELF from paused Pol II. We found no common structural or sequence motif that dictates eRNA function. Instead, efficient NELF release requires a single eRNA molecule to make multiple contacts with several NELF subunits as well as the presence of unpaired guanosine nucleosides. By revealing the molecular determinants for eRNA function, our study mechanistically links eRNAs to Pol II pause release and provides new insight into the regulation of metazoan transcription.

2022-03-08 | GSE164556 | GEO

Enhancer RNAs stimulate Pol II pause release by harnessing multivalent interactions to NELF.

Project description:Enhancer RNAs (eRNAs) are long non-coding RNAs that originate from enhancers. Although eRNA transcription is a canonical feature of activated enhancers, the molecular features required for eRNA function and the mechanism of how eRNAs impinge on target gene transcription have not been established. Thus, using eRNA-dependent RNA polymerase II (Pol II) pause release as a model, we here investigate the requirement of sequence, structure and length of eRNAs for their ability to stimulate Pol II pause release by detaching NELF from paused Pol II. We find eRNAs not to exert their function through common structural or sequence motifs. Instead, eRNAs that exhibit a length >200 nucleotides and that contain unpaired guanosines make multiple, allosteric contacts with NELF subunits -A and -E to trigger efficient NELF release. By revealing the molecular determinants of eRNA function, our study establishes eRNAs as an important player in Pol II pause release, and it provides new insight into the regulation of metazoan transcription.

| S-EPMC9068813 | biostudies-literature

Enhancer RNAs harness multivalent interactions to detach NELF from paused Pol II [GROSEQ, eCLIPSEQ, CHIPSEQ]

Project description:Enhancer RNAs harness multivalent interactions to detach NELF from paused Pol II [GROSEQ, eCLIPSEQ, CHIPSEQ]

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NELF-A phosphorylation site identification

Project description:NELF-A phosphorylation by P-TEFb is a key event in the pausing release. We conduct IMAC-LC-MS-MS to identified NELF-A phosphorylation site by activation P-TEFb kinase.

2016-03-23 | PXD003433 | Pride

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