title: miRepress: modelling gene expression regulation by microRNA with non-conventional binding sites.
abstract: Some earlier studies have reported an alternative mode of microRNA-target interaction. We detected target regions within mRNA transcripts from AGO PAR-CLIP that did not contain any conventional microRNA seed pairing but only had non-conventional binding sites with microRNA 3' end. Our study from 7 set of data that measured global protein fold change after microRNA transfection pointed towards the association of target protein fold change with 6-mer and 7-mer target sites involving microRNA 3' end. We developed a model to predict the degree of microRNA target regulation in terms of protein fold changes from the number of different conventional and non-conventional target sites present in the target, and found significant correlation of its output with protein expression changes. We validated the effect of non-conventional interactions with target by modulating the abundance of microRNA in a human breast cancer cell line MCF-7. The validation was done using luciferase assay and immunoblot analysis for our predicted non-conventional microRNA-target pair WNT1 (3' UTR) and miR-367-5p and immunoblot analysis for another predicted non-conventional microRNA-target pair MYH10 (coding region) and miR-181a-5p. Both experiments showed inhibition of targets by transfection of microRNA mimics that were predicted to have only non-conventional sites.
authors.forename: Suman
authors.initials: S
authors.lastname: Ghosal
authors.affiliation: Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, West Bengal, 700032, India.
authors.forename: Shekhar
authors.initials: S
authors.lastname: Saha
authors.forename: Shaoli
authors.initials: S
authors.lastname: Das
authors.affiliation: Gyanxet, BF 286 Salt Lake, Kolkata, West Bengal, 700064, India.
authors.forename: Rituparno
authors.initials: R
authors.lastname: Sen
authors.affiliation: Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, West Bengal, 700032, India.
authors.forename: Swagata
authors.initials: S
authors.lastname: Goswami
authors.affiliation: Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, West Bengal, 700032, India.
authors.forename: Siddhartha S
authors.initials: SS
authors.lastname: Jana
authors.affiliation: Gyanxet, BF 286 Salt Lake, Kolkata, West Bengal, 700064, India.
authors.forename: Jayprokas
authors.initials: J
authors.lastname: Chakrabarti
mesh_terms: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D001665:Binding Sites / Q000235:genetics; D002460:Cell Line; D019295:Computational Biology / Q000379:methods*; D015870:Gene Expression; D005786:Gene Expression Regulation; D017930:Genes, Reporter; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D008954:Models, Biological; D018995:Myosin Heavy Chains / Q000737:chemistry / Q000235:genetics; D024501:Nonmuscle Myosin Type IIB / Q000737:chemistry / Q000235:genetics; D059372:Nucleotide Motifs; D016366:Open Reading Frames; D011485:Protein Binding; D017510:Protein Folding; D034622:RNA Interference; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics; D015203:Reproducibility of Results
chemical_list: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D035683:MicroRNAs; D012333:RNA, Messenger; D024501:Nonmuscle Myosin Type IIB; C103815:nonmuscle myosin type IIB heavy chain; D018995:Myosin Heavy Chains