Transcriptomics

Dataset Information

310

Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: miRNA inhibition data


ABSTRACT: To obtain evidence that Argonaute (AGO) crosslink-centered regions (CCRs) indeed contain functional miRNA-binding sites, we blocked 25 of the most abundant miRNAs in HEK 293 cells (Figure 5C of PMID 20371350) by transfection of a cocktail of 2'-O-methyl-modified antisense oligoribonucleotides and monitored the changes in mRNA stability by microarrays (Figure 7A of PMID 20371350). Consistent with previous studies of individual miRNAs (Grimson et al., 2007), the magnitude of the destabilization effects of transcripts containing at least one CCR depended on the length of the seed-complementary region and dropped from 9-mer to 8-mer to 7-mer to 6-mer matches (Figure 7B of PMID 20371350). We did not find evidence for significant destabilization of transcripts that only contained imperfectly paired seed regions. The top 25 expressed miRNAs expressed in HEK 293 cells were inhibited by transfection of a cocktail of 25 antisense 2'-O-Me oligoribonucleotides and the gene expression was compared to mock-transfected cells.

ORGANISM(S): Homo sapiens  

SUBMITTER: Thomas Tuschl   Markus Hafner 

PROVIDER: E-GEOD-21577 | ArrayExpress | 2010-05-27

SECONDARY ACCESSION(S): GSE21577PRJNA129319

REPOSITORIES: GEO, ArrayExpress

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Publications


RNA transcripts are subject to posttranscriptional gene regulation involving hundreds of RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs) expressed in a cell-type dependent fashion. We developed a cell-based crosslinking approach to determine at high resolution and transcriptome-wide the binding sites of cellular RBPs and miRNPs. The crosslinked sites are revealed by thymidine to cytidine transitions in the cDNAs prepared from immunopurified RNPs of 4-thio  ...[more]

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