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Identification of proteins and miRNAs that specifically bind an mRNA in vivo

ABSTRACT: Identification of proteins and miRNAs that specifically bind an mRNA in vivo

PROVIDER: PRJNA541231 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9016770.fastq.gz	Fastqsanger.gz
	SRR9016780.fastq.gz	Fastqsanger.gz
	SRR9016790.fastq.gz	Fastqsanger.gz
	SRR9016771.fastq.gz	Fastqsanger.gz
	SRR9016781.fastq.gz	Fastqsanger.gz

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Identification of proteins and miRNAs that specifically bind an mRNA in vivo [small RNA]

Project description:Identification of proteins and miRNAs that specifically bind an mRNA in vivo [small RNA]

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Identification of proteins and miRNAs that specifically bind an mRNA in vivo [total RNA]

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Identification of proteins and miRNAs that specifically bind an mRNA in vivo [small RNA]

Project description:Understanding regulation of an mRNA requires knowledge of its regulators. However, methods for reliable de-novo identification of proteins binding to a particular RNA are scarce and were so far only successfully applied to abundant noncoding RNAs in cell culture. Here, we present vIPR, an RNA-protein crosslink, RNA pulldown, and shotgun proteomics approach to identify proteins bound to a selected mRNA in C. elegans. Applying vIPR to the germline-specific transcript gld-1 led to enrichment of known and novel interactors. By comparing enrichment upon gld-1 and lin-41 pulldown, we demonstrate that vIPR recovers both common and specific RNA-binding proteins, and we validate DAZ-1 as a novel and specific gld-1 regulator. Finally, combining vIPR with small RNA sequencing, we recover known and biologically important transcript-specific miRNA interactions, and we identify miR-84 as a specific interactor of the gld-1 transcript. We envision that vIPR provides a platform for investigating RNA in vivo regulation in diverse biological systems.

2019-08-08 | GSE130732 | GEO

Identification of proteins and miRNAs that specifically bind an mRNA in vivo [total RNA]

2019-08-08 | GSE130730 | GEO

Identification of proteins and miRNAs that specifically bind an mRNA in vivo.

Project description:Understanding regulation of an mRNA requires knowledge of its regulators. However, methods for reliable de-novo identification of proteins binding to a particular RNA are scarce and were thus far only successfully applied to abundant noncoding RNAs in cell culture. Here, we present vIPR, an RNA-protein crosslink, RNA pulldown, and shotgun proteomics approach to identify proteins bound to selected mRNAs in C. elegans. Applying vIPR to the germline-specific transcript gld-1 led to enrichment of known and novel interactors. By comparing enrichment upon gld-1 and lin-41 pulldown, we demonstrate that vIPR recovers both common and specific RNA-binding proteins, and we validate DAZ-1 as a specific gld-1 regulator. Finally, combining vIPR with small RNA sequencing, we recover known and biologically important transcript-specific miRNA interactions, and we identify miR-84 as a specific interactor of the gld-1 transcript. We envision that vIPR will provide a platform for investigating RNA in vivo regulation in diverse biological systems.

| S-EPMC6746756 | biostudies-literature

Identification of proteins and miRNAs that specifically bind an mRNA in vivo

2019-08-12 | PXD013720 | Pride

Identification of proteins and miRNAs that specifically bind an mRNA in vivo

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

2019-08-08 | GSE130733 | GEO

miRNAs specifically bound by PrPc during C2C12 cell differentiation

Project description:miRNAs specifically bound by PrPc during C2C12 cell differentiation

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identify the possible proteins that specifically bind to the 59-bp nucleotide sequence containing rs2280381

Project description:we performed DNA-affinity precipitation assay (DAPA) followed by mass spectrometry to identify the possible proteins that specifically bind to the 59-bp nucleotide sequence containing rs2280381 using U-937 cell nuclear extracts.

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Denaturing purifications demonstrate that PRC2 and other widely-reported chromatin proteins do not appear to bind directly to RNA in vivo [ChIP-seq]

Project description:The Polycomb Repressive Complex 2 (PRC2) has been reported to bind to many RNAs and has become a central player in reports describing the mechanisms of how long non-coding RNAs (lncRNAs) regulate gene expression. Based largely on these observations of PRC2, many additional chromatin proteins have similarly been reported to bind RNA to enact their functions. Yet, there is a growing discrepancy between the biochemical evidence supporting specific lncRNA-PRC2 interactions and functional evidence demonstrating that PRC2 is often dispensable for lncRNA function. Here we revisit the evidence supporting broad RNA binding by PRC2 and other chromatin proteins and show that many previously reported RNA-protein interactions do not represent in vivo interactions. We find that denaturing purification of in vivo crosslinked RNA-protein complexes leads to loss of detectable PRC2-RNA interactions. Similarly, we fail to detect in vivo RNA binding of other chromatin-associated proteins previously reported to bind RNA (CTCF, YY1, WDR5, and others), despite accurately mapping bona fide RNA-protein binding sites across a range of proteins including several specific chromatin-associated proteins (SPEN, CHTOP, TET2, and others). Taken together, these results argue for a critical re-evaluation of the broad role of RNA binding to orchestrate various chromatin regulatory mechanisms.

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