The sufficient minimal set of miRNA seed types

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 interact...

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Published in	Bioinformatics (Oxford, England) Vol. 27; no. 10; pp. 1346 - 1350
Main Authors	Ellwanger, Daniel C., Büttner, Florian A., Mewes, Hans-Werner, Stümpflen, Volker
Format	Journal Article
Language	English
Published	Oxford Oxford University Press 15.05.2011
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 Gene silencing Seeds RNA interference Seed Micro RNA
Online Access	Get full text
ISSN	1367-4803 1367-4811 1367-4811
DOI	10.1093/bioinformatics/btr149

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Abstract	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. Contact: florian.buettner@helmholtz-muenchen.de v.stuempflen@helmholtz-muenchen.de Supplementary Information: Supplementary data are available at Bioinformatics online.
AbstractList	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. Contact: florian.buettner@helmholtz-muenchen.de v.stuempflen@helmholtz-muenchen.de Supplementary Information: Supplementary data are available at Bioinformatics online. 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. Contact: florian.buettner@helmholtz-muenchen.de v.stuempflen@helmholtz-muenchen.de Supplementary Information: Supplementary data are available at Bioinformatics online. 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.MOTIVATIONPairing 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.RESULTSWe 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. 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.
Author	Mewes, Hans-Werner Ellwanger, Daniel C. Büttner, Florian A. Stümpflen, Volker
AuthorAffiliation	1 Institute of Bioinformatics and Systems Biology (MIPS), Helmholtz Zentrum München - German Research Center for Environmental Health, D-85764 Neuherberg and 2 Chair of Genome-oriented Bioinformatics, Technische Universität München, Center of Life and Food Science, D-85350 Freising-Weihenstephan, Germany
AuthorAffiliation_xml	– name: 1 Institute of Bioinformatics and Systems Biology (MIPS), Helmholtz Zentrum München - German Research Center for Environmental Health, D-85764 Neuherberg and 2 Chair of Genome-oriented Bioinformatics, Technische Universität München, Center of Life and Food Science, D-85350 Freising-Weihenstephan, Germany
Author_xml	– sequence: 1 givenname: Daniel C. surname: Ellwanger fullname: Ellwanger, Daniel C. – sequence: 2 givenname: Florian A. surname: Büttner fullname: Büttner, Florian A. – sequence: 3 givenname: Hans-Werner surname: Mewes fullname: Mewes, Hans-Werner – sequence: 4 givenname: Volker surname: Stümpflen fullname: Stümpflen, Volker
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Snippet	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... 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...
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SubjectTerms	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
Title	The sufficient minimal set of miRNA seed types
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