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https://doi.org/10.1371/journal.pcbi.0030238
Title: | Intragenomic matching reveals a huge potential for miRNA-mediated regulation in plants | Authors: | Lindow M. Jacobsen A. Nygaard S. Mang Y. Krogh A. |
Keywords: | microRNA microRNA vegetable protein Arabidopsis article base pairing gene control gene interaction gene targeting genetic analysis genome nonhuman plant plant genetics populus trichocarpa prediction rice chromosome map gene expression regulation genetics methodology phenotype plant plant genome sequence analysis sequence homology species difference Arabidopsis thaliana Oryza sativa Populus trichocarpa Chromosome Mapping Gene Expression Regulation, Plant Genome, Plant MicroRNAs Phenotype Plant Proteins Plants Sequence Analysis, RNA Sequence Homology, Nucleic Acid Species Specificity |
Issue Date: | 2007 | Publisher: | Public Library of Science | Citation: | Lindow M., Jacobsen A., Nygaard S., Mang Y., Krogh A. (2007). Intragenomic matching reveals a huge potential for miRNA-mediated regulation in plants. PLoS Computational Biology 3 (11) : 2379-2390. ScholarBank@NUS Repository. https://doi.org/10.1371/journal.pcbi.0030238 | Abstract: | 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 ?1,200, ?2,500, and ?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. © 2007 Lindow et al. | Source Title: | PLoS Computational Biology | URI: | https://scholarbank.nus.edu.sg/handle/10635/165613 | ISSN: | 1553734X | DOI: | 10.1371/journal.pcbi.0030238 |
Appears in Collections: | Elements Staff Publications |
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