Specific Sequence Determinants of miR-15/107 MicroRNA Gene Group Targets

Authors

Peter T. Nelson, University of KentuckyFollow
Wang-Xia Wang, University of KentuckyFollow
Guogen Mao, University of KentuckyFollow
Bernard R. Wilfred, University of KentuckyFollow
Kevin Xie, University of Kentucky
Mary H. Jennings, University of KentuckyFollow
Zhen Gao, Washington University in St. Louis
Xiaowei Wang, Washington University in St. Louis

Abstract

MicroRNAs (miRNAs) target mRNAs in human cells via complex mechanisms that are still incompletely understood. Using anti-Argonaute (anti-AGO) antibody co-immunoprecipitation, followed by microarray analyses and downstream bioinformatics, 'RIP-Chip' experiments enable direct analyses of miRNA targets. RIP-Chip studies (and parallel assessments of total input mRNA) were performed in cultured H4 cells after transfection with miRNAs corresponding to the miR-15/107 gene group (miR-103, miR-107, miR-16 and miR-195), and five control miRNAs. Three biological replicates were run for each condition with a total of 54 separate human Affymetrix Human Gene 1.0 ST array replicates. Computational analyses queried for determinants of miRNA:mRNA binding. The analyses support four major findings: (i) RIP-Chip studies correlated with total input mRNA profiling provides more comprehensive information than using either RIP-Chip or total mRNA profiling alone after miRNA transfections; (ii) new data confirm that miR-107 paralogs target coding sequence (CDS) of mRNA; (iii) biochemical and computational studies indicate that the 3' portion of miRNAs plays a role in guiding miR-103/7 to the CDS of targets; and (iv) there are major sequence-specific targeting differences between miRNAs in terms of CDS versus 3'-untranslated region targeting, and stable AGO association versus mRNA knockdown. Future studies should take this important miRNA-to-miRNA variability into account.

Document Type

Article

Publication Date

10-2011

Notes/Citation Information

Published in Nucleic Acids Research, v. 39, no. 18, p. 8163-8172.

© The Author(s) 2011. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Digital Object Identifier (DOI)

https://doi.org/10.1093/nar/gkr532

Funding Information

National Institutes of Health, Bethesda, MD (grants R01 NS061933, R01 GM089784 and K08 NS050110); Alzheimer Association (NIRG-89917). Funding for open access charge: National Institutes of Health (grants R21AG036875, R01NS061933).

Repository Citation

Nelson, Peter T.; Wang, Wang-Xia; Mao, Guogen; Wilfred, Bernard R.; Xie, Kevin; Jennings, Mary H.; Gao, Zhen; and Wang, Xiaowei, "Specific Sequence Determinants of miR-15/107 MicroRNA Gene Group Targets" (2011). Pathology and Laboratory Medicine Faculty Publications. 8.
https://uknowledge.uky.edu/pathology_facpub/8