Research article

The relationship between the evolution of microRNA targets and the length of their UTRs

Chao Cheng¹ , Nitin Bhardwaj¹ and Mark Gerstein^1,2,3

¹  Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA

²  Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA

³  Department of Computer Science, Yale University, New Haven, CT 06520, USA

author email corresponding author email

BMC Genomics 2009, 10:431doi:10.1186/1471-2164-10-431

Published:	14 September 2009

Abstract

Background

MicroRNAs (miRNAs) are endogenous small RNA molecules that modulate the gene expression at the post-transcription levels in many eukaryotic cells. Their widespread and important role in animals is gauged by estimates that ~25% of all genes are miRNA targets.

Results

We perform a systematic investigation of the relationship between miRNA regulation and their targets' evolution in two mammals: human and mouse. We find genes with longer 3' UTRs are regulated by more distinct types of miRNAs. These genes correspondingly tend to have slower evolutionary rates at the protein level. Housekeeping genes are another class of genes that evolve slowly. However, they have a distinctly different type of regulation, with shorter 3'UTRs to avoid miRNA targeting.

Conclusion

Our analysis suggests a two-way evolutionary mechanism for miRNA targets on the basis of their cellular roles and the length of their 3' UTRs. Functionally critical genes that are spatially or temporally expressed are stringently regulated by miRNAs. While housekeeping genes, however conserved, are selected to have shorter 3'UTRs to avoid miRNA regulation.