Intragenomic matching reveals a huge potential for miRNA-mediated regulation in plants.

microRNAs (miRNAs) are important post-transcriptional regulators, but the extent of this regulation is uncertain, both with regard to the number of miRNA genes and their targets. Using an algorithm based on intragenomic matching of potential miRNAs and their targets coupled with support vector machi...

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Autores principales:	Morten Lindow, Anders Jacobsen, Sanne Nygaard, Yuan Mang, Anders Krogh
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2007
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/b974e44039b84d73b66eeef242b63fd4
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spelling	oai:doaj.org-article:b974e44039b84d73b66eeef242b63fd42021-11-25T05:41:30ZIntragenomic matching reveals a huge potential for miRNA-mediated regulation in plants.1553-734X1553-735810.1371/journal.pcbi.0030238https://doaj.org/article/b974e44039b84d73b66eeef242b63fd42007-11-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.0030238https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358microRNAs (miRNAs) are important post-transcriptional regulators, but the extent of this regulation is uncertain, both with regard to the number of miRNA genes and their targets. Using an algorithm based on intragenomic matching of potential miRNAs and their targets coupled with support vector machine classification of miRNA precursors, we explore the potential for regulation by miRNAs in three plant genomes: Arabidopsis thaliana, Populus trichocarpa, and Oryza sativa. We find that the intragenomic matching in conjunction with a supervised learning approach contains enough information to allow reliable computational prediction of miRNA candidates without requiring conservation across species. Using this method, we identify approximately 1,200, approximately 2,500, and approximately 2,100 miRNA candidate genes capable of extensive base-pairing to potential target mRNAs in A. thaliana, P. trichocarpa, and O. sativa, respectively. This is more than five times the number of currently annotated miRNAs in the plants. Many of these candidates are derived from repeat regions, yet they seem to contain the features necessary for correct processing by the miRNA machinery. Conservation analysis indicates that only a few of the candidates are conserved between the species. We conclude that there is a large potential for miRNA-mediated regulatory interactions encoded in the genomes of the investigated plants. We hypothesize that some of these interactions may be realized under special environmental conditions, while others can readily be recruited when organisms diverge and adapt to new niches.Morten LindowAnders JacobsenSanne NygaardYuan MangAnders KroghPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 3, Iss 11, p e238 (2007)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Morten Lindow Anders Jacobsen Sanne Nygaard Yuan Mang Anders Krogh Intragenomic matching reveals a huge potential for miRNA-mediated regulation in plants.
description	microRNAs (miRNAs) are important post-transcriptional regulators, but the extent of this regulation is uncertain, both with regard to the number of miRNA genes and their targets. Using an algorithm based on intragenomic matching of potential miRNAs and their targets coupled with support vector machine classification of miRNA precursors, we explore the potential for regulation by miRNAs in three plant genomes: Arabidopsis thaliana, Populus trichocarpa, and Oryza sativa. We find that the intragenomic matching in conjunction with a supervised learning approach contains enough information to allow reliable computational prediction of miRNA candidates without requiring conservation across species. Using this method, we identify approximately 1,200, approximately 2,500, and approximately 2,100 miRNA candidate genes capable of extensive base-pairing to potential target mRNAs in A. thaliana, P. trichocarpa, and O. sativa, respectively. This is more than five times the number of currently annotated miRNAs in the plants. Many of these candidates are derived from repeat regions, yet they seem to contain the features necessary for correct processing by the miRNA machinery. Conservation analysis indicates that only a few of the candidates are conserved between the species. We conclude that there is a large potential for miRNA-mediated regulatory interactions encoded in the genomes of the investigated plants. We hypothesize that some of these interactions may be realized under special environmental conditions, while others can readily be recruited when organisms diverge and adapt to new niches.
format	article
author	Morten Lindow Anders Jacobsen Sanne Nygaard Yuan Mang Anders Krogh
author_facet	Morten Lindow Anders Jacobsen Sanne Nygaard Yuan Mang Anders Krogh
author_sort	Morten Lindow
title	Intragenomic matching reveals a huge potential for miRNA-mediated regulation in plants.
title_short	Intragenomic matching reveals a huge potential for miRNA-mediated regulation in plants.
title_full	Intragenomic matching reveals a huge potential for miRNA-mediated regulation in plants.
title_fullStr	Intragenomic matching reveals a huge potential for miRNA-mediated regulation in plants.
title_full_unstemmed	Intragenomic matching reveals a huge potential for miRNA-mediated regulation in plants.
title_sort	intragenomic matching reveals a huge potential for mirna-mediated regulation in plants.
publisher	Public Library of Science (PLoS)
publishDate	2007
url	https://doaj.org/article/b974e44039b84d73b66eeef242b63fd4
work_keys_str_mv	AT mortenlindow intragenomicmatchingrevealsahugepotentialformirnamediatedregulationinplants AT andersjacobsen intragenomicmatchingrevealsahugepotentialformirnamediatedregulationinplants AT sannenygaard intragenomicmatchingrevealsahugepotentialformirnamediatedregulationinplants AT yuanmang intragenomicmatchingrevealsahugepotentialformirnamediatedregulationinplants AT anderskrogh intragenomicmatchingrevealsahugepotentialformirnamediatedregulationinplants
_version_	1718414539891933184

Intragenomic matching reveals a huge potential for miRNA-mediated regulation in plants.

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