title: The effect of central loops in miRNA:MRE duplexes on the efficiency of miRNA-mediated gene regulation.
abstract: MicroRNAs (miRNAs) guide posttranscriptional repression of mRNAs. Hundreds of miRNAs have been identified but the target identification of mammalian mRNAs is still a difficult task due to a poor understanding of the interaction between miRNAs and the miRNA recognizing element (MRE). In recent research, the importance of the 5' end of the miRNA:MRE duplex has been emphasized and the effect of the tail region addressed, but the role of the central loop has largely remained unexplored. Here we examined the effect of the loop region in miRNA:MRE duplexes and found that the location of the central loop is one of the important factors affecting the efficiency of gene regulation mediated by miRNAs. It was further determined that the addition of a loop score combining both location and size as a new criterion for predicting MREs and their cognate miRNAs significantly decreased the false positive rates and increased the specificity of MRE prediction.
authors.affiliation: Department of Biological Science and Biotechnology, Tsinghua University, Beijing, People's Republic of China.
authors.forename: Wenbin
authors.initials: W
authors.lastname: Ye
authors.forename: Qing
authors.initials: Q
authors.lastname: Lv
authors.forename: Chung-Kwun Amy
authors.initials: CK
authors.lastname: Wong
authors.forename: Sean
authors.initials: S
authors.lastname: Hu
authors.forename: Chao
authors.initials: C
authors.lastname: Fu
authors.forename: Zhong
authors.initials: Z
authors.lastname: Hua
authors.forename: Guoping
authors.initials: G
authors.lastname: Cai
authors.forename: Guoxi
authors.initials: G
authors.lastname: Li
authors.forename: Burton B
authors.initials: BB
authors.lastname: Yang
authors.forename: Yaou
authors.initials: Y
authors.lastname: Zhang
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics*; D000465:Algorithms; D000818:Animals; D019556:COS Cells; D002417:Cattle; D015687:Cell Hypoxia; D002522:Chlorocebus aethiops; D017931:DNA Primers; D004797:Enzyme-Linked Immunosorbent Assay; D005786:Gene Expression Regulation; D006801:Humans; D008156:Luciferases / Q000378:metabolism; D051379:Mice; D035683:MicroRNAs / Q000502:physiology*; D009154:Mutation; D002679:Pan troglodytes; D051381:Rats; D014162:Transfection; D042461:Vascular Endothelial Growth Factor A / Q000235:genetics*
chemical_list: D020413:3' Untranslated Regions; D017931:DNA Primers; D035683:MicroRNAs; D042461:Vascular Endothelial Growth Factor A; D008156:Luciferases