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: Suman Ghosal, Shekhar Saha, Shaoli Das, Rituparno Sen, Swagata Goswami, Siddhartha S Jana, Jayprokas Chakrabarti
• Journal: Scientific reports (Sci Rep) Vol. 6 Pg. 22334 (Feb 29 2016) ISSN: 2045-2322 [Electronic] England
• PMID: 26923536 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)

Chemical References

• 3' Untranslated Regions
• 5' Untranslated Regions
• MicroRNAs
• RNA, Messenger
• Nonmuscle Myosin Type IIB
• nonmuscle myosin type IIB heavy chain
• Myosin Heavy Chains

Topics

• 3' Untranslated Regions
• 5' Untranslated Regions
• Binding Sites (genetics)
• Cell Line
• Computational Biology (methods)
• Gene Expression
• Gene Expression Regulation
• Genes, Reporter
• Humans
• MicroRNAs (genetics)
• Models, Biological
• Myosin Heavy Chains (chemistry, genetics)
• Nonmuscle Myosin Type IIB (chemistry, genetics)
• Nucleotide Motifs
• Open Reading Frames
• Protein Binding
• Protein Folding
• RNA Interference
• RNA, Messenger (chemistry, genetics)
• Reproducibility of Results