ArticleRNA (New York, N.Y.)2012
Analysis of the accessibility of CLIP bound sites reveals that nucleation of the miRNA:mRNA pairing occurs preferentially at the 3'-end of the seed match.
Article in RNA (New York, N.Y.), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
11 citing papers in PubMed, 18 citations in OpenAlex.
- Viral non-coding RNAs: Stealth strategies in the tug-of-war between humans and herpesviruses.Seminars in cell & developmental biology · 2021Review
- RPmirDIP: Reciprocal Perspective improves miRNA targeting prediction.Scientific reports · 2020Article
- microCLIP super learning framework uncovers functional transcriptome-wide miRNA interactions.Nature communications · 2018Article
- mirDIP 4.1-integrative database of human microRNA target predictions.Nucleic acids research · 2018Article
- microRNA-122 target sites in the hepatitis C virus RNA NS5B coding region and 3' untranslated region: function in replication and influence of RNA secondary structure.Cellular and molecular life sciences : CMLS · 2017Article
- PACCMIT/PACCMIT-CDS: identifying microRNA targets in 3' UTRs and coding sequences.Nucleic acids research · 2015Article
- Computational prediction of disease microRNAs in domestic animals.BMC research notes · 2014Article
- Analysis options for high-throughput sequencing in miRNA expression profiling.BMC research notes · 2014Article
- Article
- CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data.Genome biology · 2014Article
- mirMark: a site-level and UTR-level classifier for miRNA target prediction.Genome biology · 2014Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To find out whether the AGO-miRNA complex is more sensitive to the accessibility of a particular region inside the seed match, we analyze in detail the accessibility of a wide set of miRNA binding sites validated by PAR-CLIP and HITS-CLIP experiments. Our analysis reveals that nucleotides at the 3'-end of bound seed matches are significantly more accessible than nucleotides at the 5'-end as well as nucleotides at any positions in the unbound seed matches. We show that the accessibility of a single nucleotide at the 3'-end is more effective than the accessibility of several nucleotides at the 5'-end in discriminating between functional and nonfunctional binding sites. Analysis of mRNA and protein fold changes induced by miRNA overexpression demonstrates that genes with accessible nucleation regions at the 3'-end are down-regulated more strongly than genes whose accessible nucleation regions are located elsewhere within the seed match. We also observed an increase in the precision of the miRNA target prediction algorithm PACMIT when accessibility toward the 3'-end of the seed match was required. The pronounced sensitivity of the AGO-miRNA complex to the accessibility of the 3'-end of the seed match suggests that, in most cases, nucleation occurs in this region. We show that this conclusion is consistent with previous experimental studies.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.