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The sufficient minimal set of miRNA seed types.
Bioinformatics 27, 1346-1350 (2011)
Publ. Version/Full Text Volltext
DOI
PMC
MOTIVATION: Pairing between the target sequence and the 6-8 nt long seed sequence of the miRNA presents the most important feature for miRNA target site prediction. Novel high-throughput technologies such as Argonaute HITS-CLIP afford meanwhile a detailed study of miRNA:mRNA duplices. These interaction maps enable a first discrimination between functional and non-functional target sites in a bulky fashion. Prediction algorithms apply different seed paradigms to identify miRNA target sites. Therefore, a quantitative assessment of miRNA target site prediction is of major interest. RESULTS: We identified a set of canonical seed types based on a transcriptome wide analysis of experimentally verified functional target sites. We confirmed the specificity of long seeds but we found that the majority of functional target sites are formed by less specific seeds of only 6 nt indicating a crucial role of this type. A substantial fraction of genuine target sites arenon-conserved. Moreover, the majority of functional sites remain uncovered by common prediction methods.
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Publication type
Article: Journal article
Document type
Scientific Article
Keywords
mammalian micrornas; site accessibility; target recognition; messenger-rnas; prediction; protein; impact; identification; determinants; expression
ISSN (print) / ISBN
1367-4803
e-ISSN
1367-4811
Journal
Bioinformatics
Quellenangaben
Volume: 27,
Issue: 10,
Pages: 1346-1350
Publisher
Oxford University Press
Publishing Place
Oxford
Non-patent literature
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Reviewing status
Peer reviewed