Imperfect centered miRNA binding sites are common and can mediate functional repression of target mRNAs
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE55059 | GEO | 2014/02/14
SECONDARY ACCESSION(S): PRJNA238342
REPOSITORIES: GEO
Similar Datasets
Project description:BackgroundMicroRNAs (miRNAs) bind to mRNAs and target them for translational inhibition or transcriptional degradation. It is thought that most miRNA-mRNA interactions involve the seed region at the 5' end of the miRNA. The importance of seed sites is supported by experimental evidence, although there is growing interest in interactions mediated by the central region of the miRNA, termed centered sites. To investigate the prevalence of these interactions, we apply a biotin pull-down method to determine the direct targets of ten human miRNAs, including four isomiRs that share centered sites, but not seeds, with their canonical partner miRNAs.ResultsWe confirm that miRNAs and their isomiRs can interact with hundreds of mRNAs, and that imperfect centered sites are common mediators of miRNA-mRNA interactions. We experimentally demonstrate that these sites can repress mRNA activity, typically through translational repression, and are enriched in regions of the transcriptome bound by AGO. Finally, we show that the identification of imperfect centered sites is unlikely to be an artifact of our protocol caused by the biotinylation of the miRNA. However, the fact that there was a slight bias against seed sites in our protocol may have inflated the apparent prevalence of centered site-mediated interactions.ConclusionsOur results suggest that centered site-mediated interactions are much more frequent than previously thought. This may explain the evolutionary conservation of the central region of miRNAs, and has significant implications for decoding miRNA-regulated genetic networks, and for predicting the functional effect of variants that do not alter protein sequence.
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Project description:Whole transcriptome Identification of direct targets identify a new class of miRNA::mRNA interactions. HEK293T cells were transfected with biotinylated miRNAs. The miRNAs and target mRNA were pulled down with streptavidin and compared to a mock transfected control.
2013-12-01 | E-GEOD-40408 | biostudies-arrayexpress
Project description:Whole transcriptome identification of direct targets identify a new class of miRNA::mRNA interactions. This is a qualitative experiment to check transcript structure of mRNAs that bind to miR-17-5p. HEK293T cells were transfected with biotinylated miRNAs. The miRNAs and target mRNA were pulled down with streptavidin and profiled using stranded RNA-seq.
2014-02-14 | E-GEOD-55058 | biostudies-arrayexpress
Project description:Whole transcriptome Identification of direct targets identify a new class of miRNA::mRNA interactions.
2013-12-01 | GSE40408 | GEO
Project description:Whole transcriptome identification of direct targets identify a new class of miRNA::mRNA interactions.
2014-02-14 | GSE55058 | GEO
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