Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors [ChIRP-seq]

ABSTRACT: Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors [ChIRP-seq]

PROVIDER: PRJNA728712 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors [ChIRP-seq]

Project description:Many lncRNAs have been discovered using transcriptomic data, however, it is unclear what fraction of lncRNAs is functional and what structural properties affect their phenotype. MUNC lncRNA (also known as DRReRNA) acts as an enhancer RNA for the Myod1 gene in cis and stimulates the expression of other promyogenic genes in trans by recruiting the cohesin complex. Here, experimental probing of the RNA structure revealed that MUNC contains multiple structural domains not detected by prediction algorithms in the absence of experimental information. We show that these specific and structurally distinct domains are required for induction of promyogenic genes, for binding genomic sites and gene expression regulation, and for binding the cohesin complex. Myod1 induction and cohesin interaction comprise only a subset of MUNC phenotype. Our study reveals unexpectedly complex, structure-driven functions for the MUNC lncRNA and emphasizes the importance of experimentally determined structures for understanding structure-function relationships in lncRNAs.

2022-01-21 | GSE174195 | GEO

Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors [SHAPE-MaP]

2022-01-21 | GSE174217 | GEO

Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors [RNA-seq]

2022-01-21 | GSE174203 | GEO

Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors

Project description:Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors

| PRJNA728862 | ENA

Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors [RNA-seq]

Project description:Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors [RNA-seq]

| PRJNA728732 | ENA

Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors [SHAPE-MaP]

Project description:Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors [SHAPE-MaP]

| PRJNA728866 | ENA

Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors

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

2022-01-21 | GSE174218 | GEO

Dissecting the functions of mycobacteria RbpA structural domains

Project description:Dissecting the functions of mycobacteria RbpA structural domains

| PRJNA419075 | ENA

Dissecting the functions of mycobacteria RbpA structural domains

Project description:RNA polymerase (RNAP) binding protein RbpA contributes to the formation of stable RNAP-promoter open complexes (RPo) and is essential for viability in mycobacteria. Based on structural and biochemical data, four domains have been identified in the RbpA protein: a N-terminal tail (NTT) domain of unknown function, a core domain (CD) that contacts the RNAP β’ subunit in a recently solved crystal structure, a basic linker (BL) that binds DNA, and a s-interaction domain (SID) that binds group I and group II s-factors. However, limited in vivo studies have been performed in mycobacteria and how the individual structural domains of RbpA contribute to RbpA function and mycobacterial gene expression remains mostly unknown. We dissected the roles of the RbpA structural domains in mycobacteria using a panel of rbpA mutants that target individual RbpA domains. The function of each RbpA domain was required for Mycobacterium tuberculosis viability and optimal growth in Mycobacterium smegmatis. We determined that the RbpA SID is both necessary and sufficient for RbpA interaction with the RNAP holoenzyme, indicating that the primary function of the CD is not solely association with the RNAP. We show that RbpA BL and SID are required for stabilization of RPo complexes at the ribosomal RNA rrnAP3 promoter in vitro, while the NTT and CD are dispensable. Finally, we determine that the NTT and CD impact gene expression of a distinct set of genes from that affected by the BL and SID activities. Our findings highlight specific outcomes for the activities of the individual functional domains in RbpA.

2018-05-03 | GSE107123 | GEO

Long Non-Coding RNA LEENE Promotes Angiogenesis and Ischemic Recovery (ChIRP-Seq)

Project description:Chromatin-associated long non-coding RNAs (ca-lncRNAs) play important roles in transcriptional regulation. To comprehensively investigate the chromatin interactome of an enhancer-derived ca-lncRNA, LEENE, we performed the Chromatin isolation by RNA purification (ChIRP) to pull down LEENE-associated DNAs, which were subjected to DNA-seq. Specifically, we used 10 previously validated tiling nucleotides targeting different domains based on the predicted secondary structure. LEENE was overexpressed by adenovirus to enhance the ChIRP-seq signals.

2023-02-08 | GSE205278 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data