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

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus

PROVIDER: GSE163113 | GEO | 2022/03/08

REPOSITORIES: GEO

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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 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).

2022-03-08 | GSE163111 | GEO

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

| PRJNA684920 | ENA

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]

| PRJNA684923 | ENA

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

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

| PRJNA684922 | ENA

NELF Regulates a Promoter-Proximal Step Distinct from RNA Pol II Pause-Release.

Project description: Not available

| S-EPMC7402197 | biostudies-literature

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

NELF regulates a promoter-proximal step distinct from RNA Pol II pause-release

Project description:RNA polymerase II (Pol II) is generally paused at promoter-proximal regions in most metazoans, and based on in vitro studies, this function has been attributed to the negative elongation factor (NELF). Here, we show that upon rapid depletion of NELF, Pol II fails to be released into gene bodies, stopping instead around the +1 nucleosomal dyad-associated region. The transition to the 2nd pause region is independent of positive transcription elongation factor P-TEFb. During the heat shock response, Pol II is rapidly released from pausing at heat shock induced genes, while most genes are paused and transcriptionally downregulated during the heat shock response. We find that both aspects of the heat shock response remain intact upon NELF loss. We find that NELF depletion results in global loss of cap-binding complex from chromatin without global reduction of nascent transcript 5’ cap stability. Thus, our studies implicate NELF functioning in early elongation complexes distinct from Pol II pause-release.

2020-03-09 | GSE144786 | GEO

Enhancer RNA facilitates NELF release from immediate early genes.

Project description: Not available

| S-EPMC4186258 | biostudies-literature