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Human Molecular Genetics Advance Access published online on October 20, 2005
Human Molecular Genetics, doi:10.1093/hmg/ddi397
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© The Author 2005. Published by Oxford University Press. All rights reserved
Received August 30, 2005
Revised October 13, 2005
Accepted October 13, 2005

Article

Physiological identification of human transcripts translationally regulated by a specific microRNA

Mika Nakamoto 1, Peng Jin 1, William T. O'Donnell 1, and Stephen T. Warren 2*

1 Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
2 Department of Human Genetics, 615 Michael Street, Suite 301 Whitehead, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA

* To whom correspondence should be addressed.
Stephen T. Warren, E-mail: swarren{at}emory.edu


  Abstract

One mechanism by which endogenous microRNAs (miRNAs) function is to suppress translation of target mRNAs. Computational identification of target mRNAs is hampered by the partial complementarity between miRNAs and their targets and the lack of in vivo approaches to identify targets. Here we identify mRNAs that are regulated by specific endogenous miRNA by detecting shifts in individual mRNA abundance in polyribosome profiles following miRNA knockdown via siRNA. We have identified human genes whose mRNAs were found at significantly increased levels in the heavy polyribosome fractions following miRNA miR-30a-3p knockdown. Where antibody was available, targets showed an increase in protein levels following the miRNA knockdown and a decrease following miRNA overexpression. Although all identified transcripts have sequences that partially complement miR-30a-3p, none were identified by commonly used computational means. These data suggest that the functional interaction between miRNAs and mRNA targets is more complex than previously realized and describe an approach to refine predictive algorithms.


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