title: Functional conservation of both CDS- and 3'-UTR-located microRNA binding sites between species.
abstract: MicroRNAs (miRNAs) mediate gene regulation posttranscriptionally through pairing of their seed (2-7 nt) to 3'-untranslated regions (3'-UTRs) or coding regions (coding sequences [CDSs]) of their target genes. CDS target sites generally show weaker repression effects than 3'-UTR sites. However, little is known about the conservation of the function, that is, repression effect, for these two groups of target sites. In addition, no systematic analysis of the evolutionary constraint on CDS sites exists to date. To address these questions, we performed RNA-sequencing to quantify the regulatory effect of miR-15a/miR-16 and miR-92a on their CDS and 3'-UTR targets in human and macaque cells. These miRs were knocked down transiently so the repression effect could be tracked immediately. Although on average CDS targets are less derepressed than 3'-UTR targets in both species, both the 3'-UTR targets and the CDS targets are functionally conserved. The evolutionary analysis of miRNA target sites shows that CDS sites are more conserved than nontarget control, albeit to a lesser extent than 3'-UTR sites. In conclusion, CDS target sites are functional, even though they are subject to less functional constraint than 3'-UTR target sites.
authors.affiliation: Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing, China.
authors.forename: Guojing
authors.initials: G
authors.lastname: Liu
authors.affiliation: Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Rui
authors.initials: R
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing, China.
authors.forename: Jin
authors.initials: J
authors.lastname: Xu
authors.affiliation: Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China Department of Ecology and Evolution, University of Chicago luxm@big.ac.cn cw16@uchicago.edu.
authors.forename: Chung-I
authors.initials: CI
authors.lastname: Wu
authors.affiliation: Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing, China luxm@big.ac.cn cw16@uchicago.edu.
authors.forename: Xuemei
authors.initials: X
authors.lastname: Lu
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics*; D000818:Animals; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics*; D002460:Cell Line; D017124:Conserved Sequence; D057809:HEK293 Cells; D006801:Humans; D008253:Macaca mulatta; D035683:MicroRNAs / Q000737:chemistry* / Q000235:genetics*; D016366:Open Reading Frames / Q000235:genetics*
chemical_list: D020413:3' Untranslated Regions; D035683:MicroRNAs
keywords: 3′-UTR targets; CDS targets; conservation; microRNA