The sufficient minimal set of miRNA seed types

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 ena...

Full description

Saved in:
Bibliographic Details
Published in:Bioinformatics (Oxford, England) England), 2011-05, Vol.27 (10), p.1346-1350
Main Authors: ELLWANGER, Daniel C, BÜTTNER, Florian A, MEWES, Hans-Werner, STÜMPFLEN, Volker
Format: Article
Language:English
Subjects:
Algorithms
Animals
Base Sequence
Biological and medical sciences
Discovery Note
Eukaryotic Initiation Factors - metabolism
Fundamental and applied biological sciences. Psychology
Gene Expression Profiling
General aspects
Humans
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Mice
MicroRNAs - chemistry
MicroRNAs - genetics
MicroRNAs - metabolism
Oligonucleotide Array Sequence Analysis
Oligonucleotides - genetics
Oligonucleotides - metabolism
RNA, Messenger - genetics
RNA, Messenger - metabolism
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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. 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.
ISSN:1367-4803
1367-4811
DOI:10.1093/bioinformatics/btr149