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MyoD induced enhancer RNA interacts with hnRNPL protein via CAAA motif to activate target gene transcription during myogenic differentiation [RNA-Seq]

ABSTRACT: MyoD induced enhancer RNA interacts with hnRNPL protein via CAAA motif to activate target gene transcription during myogenic differentiation [RNA-Seq]

PROVIDER: PRJNA472071 | ENA |

REPOSITORIES: ENA

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MyoD induced enhancer RNA interacts with hnRNPL protein via CAAA motif to activate target gene transcription during myogenic differentiation

Project description:Evidence of widespread transcription at active enhancers became apparent. However, our understanding about the functions of enhancer RNAs (eRNAs) and their mechanistic roles remains incomplete. Here, we study eRNA regulation and function using skeletal myoblast differentiation as a paradigm. We provide a panoramic view of enhancer transcription and uncover reprogramming in enhancer transcription occurring during myogenic differentiation. We demonstrate the critical role of MyoD in activating eRNAs production. Results from in depth dissection of two eRNAs transcribed from super enhancers (seRNA-1 and -2) suggest that seRNAs can promote myogenic differentiation in vitro and in vivo; the induction of the seRNAs is in coordination with the activation of the neighboring genes and seRNA loss largely impairs their expression. Mechanistically, we elucidate these seRNAs specifically bind to heterogeneous nuclear ribonucleoprotein L (hnRNPL) and modulate hnRNPL binding to the target promoter. A CAAA tract on the seRNA was identified to be essential in mediating the interaction between seRNA-1 and hnRNPL. Disruption of seRNA-hnRNPL interaction attenuates Pol II and H3K36me3 deposition at the target genes, in coincidence with the reduction of their expression. Furthermore, analyses of hnRNPL binding transcriptome-wide reveals its association with eRNAs is a general phenomenon in multiple cells. Collectively, we propose that eRNA-hnRNPL interaction contributes to target mRNA activation.

2019-10-03 | GSE114659 | GEO

MyoD induced enhancer RNA interacts with hnRNPL protein via CAAA motif to activate target gene transcription during myogenic differentiation [RNA-Seq]

2019-10-03 | GSE114658 | GEO

MyoD induced enhancer RNA interacts with hnRNPL protein via CAAA motif to activate target gene transcription during myogenic differentiation [GRO-Seq]

2019-10-03 | GSE114657 | GEO

MyoD induced enhancer RNA interacts with hnRNPL protein via CAAA motif to activate target gene transcription during myogenic differentiation [CLIP-Seq]

2019-10-03 | GSE114656 | GEO

MyoD induced enhancer RNA interacts with hnRNPL protein via CAAA motif to activate target gene transcription during myogenic differentiation

Project description:MyoD induced enhancer RNA interacts with hnRNPL protein via CAAA motif to activate target gene transcription during myogenic differentiation

| PRJNA472068 | ENA

MyoD induced enhancer RNA interacts with hnRNPL protein via CAAA motif to activate target gene transcription during myogenic differentiation [CLIP-Seq]

Project description:MyoD induced enhancer RNA interacts with hnRNPL protein via CAAA motif to activate target gene transcription during myogenic differentiation [CLIP-Seq]

| PRJNA472070 | ENA

MyoD induced enhancer RNA interacts with hnRNPL protein via CAAA motif to activate target gene transcription during myogenic differentiation [GRO-Seq]

Project description:MyoD induced enhancer RNA interacts with hnRNPL protein via CAAA motif to activate target gene transcription during myogenic differentiation [GRO-Seq]

| PRJNA472072 | ENA

MyoD induced enhancer RNA interacts with hnRNPL to activate target gene transcription during myogenic differentiation.

Project description: Not available

| S-EPMC6923398 | biostudies-literature

NTRAS hnRNPL RNA sequencing in HUVECs

Project description:In the current project with aim to unequivocally characterize a novel splicing-regulatory network that proves to be a central mediator of endothelial barrier function and vascular integrity. At the core of this network is the endothelial enriched lncRNA NTRAS (annotated as RP11-354k1.1) is shown to control alternative splicing decisions in HUVECs through interplaying with splicing factor hnRNPL. Specifically, in the project we show that NTRAS sequesters the splicing factor hnRNPL through a CA dinucleotide motif, to enhance TJP1 exon 20 usage, thereby TJP1α+ isoform. In turn disrupting TJP1α+ isoform expression impaired endothelial barrier function. Collectively, this splicing-regulatory network might prove fundamental in unlocking new interventions strategic to prevent or reverse vascular leakage.

2022-01-10 | E-MTAB-11311 | biostudies-arrayexpress

Motif Variation Regulates the Affinity Landscape and Epigenetic State of the MyoD Cistrome

Project description:The cis-regulatory code is the cellular lexicon by which the transcriptional machinery converts sequence information within cis-regulatory modules (CRMs) into gene expression output. Tissue-specific transcription factors such as MyoD orchestrate gene expression programs by binding to short DNA motifs called E-boxes within their target CRMs to modulate chromatin state and to fine-tune gene expression output. Despite extensive research, how the relatively short and ubiquitously distributed E-box motifs contribute to binding specificity, assembly and the functional output of the transcriptional machinery remains poorly understood. Here, we have carried out an integrative analysis of the relationship between MyoD occupancy, nucleosome positioning, CRMs-associated histone marks and motif sequences within the myogenic CRMs in differentiating muscle cells. Our data suggests that variant sequences within MyoD-binding motifs and their multiplicity within the CRMs, as well as the spatial arrangement of the motifs, in combination confer binding affinity of MyoD, nucleosome occupancy and the epigenetic state of the myogenic CRMs. Our comparative genomic analysis of single nucleotide polymorphism (SNPs) across publically available data from 17 strains of laboratory mice suggests that variant sequences within MyoD-bound motifs, but not their genome-wide counterparts, are under selection. Taken together, our data suggests that variant sequences within MyoD-binding motifs are retained and have functional role to confer a dynamic range of affinities, enabling MyoD to establish a broad spectrum of activity across myogenic CRMs.

2018-01-02 | GSE80588 | GEO

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