title: 3'LIFE: a functional assay to detect miRNA targets in high-throughput.
abstract: MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene output at the post-transcriptional level by targeting degenerate elements primarily in 3'untranslated regions (3'UTRs) of mRNAs. Individual miRNAs can regulate networks of hundreds of genes, yet for the majority of miRNAs few, if any, targets are known. Misexpression of miRNAs is also a major contributor to cancer progression, thus there is a critical need to validate miRNA targets in high-throughput to understand miRNAs' contribution to tumorigenesis. Here we introduce a novel high-throughput assay to detect miRNA targets in 3'UTRs, called Luminescent Identification of Functional Elements in 3'UTRs (3'LIFE). We demonstrate the feasibility of 3'LIFE using a data set of 275 human 3'UTRs and two cancer-relevant miRNAs, let-7c and miR-10b, and compare our results to alternative methods to detect miRNA targets throughout the genome. We identify a large number of novel gene targets for these miRNAs, with only 32% of hits being bioinformatically predicted and 27% directed by non-canonical interactions. Functional analysis of target genes reveals consistent roles for each miRNA as either a tumor suppressor (let-7c) or oncogenic miRNA (miR-10b), and preferentially target multiple genes within regulatory networks, suggesting 3'LIFE is a rapid and sensitive method to detect miRNA targets in high-throughput.
authors: School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ 85287, USA Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, 1001 S. McAllister Dr., Tempe, AZ 85287, USA.
authors: Justin M
authors: JM
authors: Wolter
authors: School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ 85287, USA Barrett, The Honors College, Arizona State University, 751 E Lemon Mall, Tempe, AZ 85287, USA.
authors: Kasuen
authors: K
authors: Kotagama
authors: Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, 1001 S. McAllister Dr., Tempe, AZ 85287, USA.
authors: Alexandra C
authors: AC
authors: Pierre-Bez
authors: School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ 85287, USA.
authors: Mari
authors: M
authors: Firago
authors: School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ 85287, USA Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, 1001 S. McAllister Dr., Tempe, AZ 85287, USA Barrett, The Honors College, Arizona State University, 751 E Lemon Mall, Tempe, AZ 85287, USA mangone@asu.edu.
authors: Marco
authors: M
authors: Mangone
mesh_terms: D020413:3' Untranslated Regions; D001483:Base Sequence; D017124:Conserved Sequence; D057809:HEK293 Cells; D006801:Humans; D008163:Luminescent Measurements / Q000379:methods*; D035683:MicroRNAs / Q000378:metabolism*; D009369:Neoplasms / Q000235:genetics; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism
chemical_list: D020413:3' Untranslated Regions; D035683:MicroRNAs; D012333:RNA, Messenger