title: Genome-scale identification of miRNA-mRNA and miRNA-lncRNA interactions in domestic animals.
abstract: Domestic animals show considerable genetic diversity. Previous studies suggested that animal phenotypes were affected by miRNA-mRNA interplay, but these studies focused mainly on the analysis of one or several miRNA-mRNA interactions. However, in this study, we investigated miRNA-mRNA and miRNA-lncRNA interactions on a genomic scale using miranda and targetscan algorithms. There has been strong directional artificial selection practiced during the domestication of animals. Thus, we investigated SNPs that were located in miRNAs and miRNA binding sites and found that several SNPs located in 3'-UTRs of mRNAs had the potential to affect miRNA-mRNA interactions. In addition, a database, named miRBond, was developed to provide visualization, analysis and downloading of the resulting datasets. Our results open the way to further experimental verification of miRNA-mRNA and miRNA-lncRNA interactions as well as the influence of SNPs upon such interplay.
authors.affiliation: School of Computer Science and Technology, Xidian University, Xi'an, 710071, China.|School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, 710048, China.
authors.forename: A
authors.initials: A
authors.lastname: Li
authors.affiliation: School of Computer Science and Technology, Xidian University, Xi'an, 710071, China.
authors.forename: J
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Department of Molecular and Cell Biology, School of Life Sciences, University of Science and Technology of China, Hefei, 230022, China.|State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
authors.forename: Z
authors.initials: Z
authors.lastname: Zhou
authors.affiliation: School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, 710048, China.
authors.forename: L
authors.initials: L
authors.lastname: Wang
authors.affiliation: School of Computer Science and Technology, Xidian University, Xi'an, 710071, China.
authors.forename: X
authors.initials: X
authors.lastname: Sun
authors.affiliation: Xi'an DongXing Branch, CMST Development Co. Ltd., Xi'an, 710032, China.
authors.forename: Y
authors.initials: Y
authors.lastname: Liu
mesh_terms: D020413:3' Untranslated Regions; D000465:Algorithms; D000818:Animals; D000829:Animals, Domestic / Q000235:genetics*; D001947:Breeding; D002417:Cattle; D002645:Chickens; D035683:MicroRNAs / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D062085:RNA, Long Noncoding / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics*; D013552:Swine
chemical_list: D020413:3' Untranslated Regions; D035683:MicroRNAs; D062085:RNA, Long Noncoding; D012333:RNA, Messenger
keywords: SNP; chicken; cow; miRBond; pig