Most mammalian mRNAs are conserved targets of microRNAs

Abstract

MicroRNAs (miRNAs) are small endogenous RNAs that pair to sites in mRNAs to direct post-transcriptional repression. Many sites that match the miRNA seed (nucleotides 2-7), particularly those in 3Ј untranslated regions (3ЈUTRs), are preferentially conserved. Here, we overhauled our tool for finding preferential conservation of sequence motifs and applied it to the analysis of human 3ЈUTRs, increasing by nearly threefold the detected number of preferentially conserved miRNA target sites. The new tool more efficiently incorporates new genomes and more completely controls for background conservation by accounting for mutational biases, dinucleotide conservation rates, and the conservation rates of individual UTRs. The improved background model enabled preferential conservation of a new site type, the "offset 6mer," to be detected. In total, >45,000 miRNA target sites within human 3ЈUTRs are conserved above background levels, and >60% of human protein-coding genes have been under selective pressure to maintain pairing to miRNAs. Mammalian-specific miRNAs have far fewer conserved targets than do the more broadly conserved miRNAs, even when considering only more recently emerged targets. Although pairing to the 3Ј end of miRNAs can compensate for seed mismatches, this class of sites constitutes less than 2% of all preferentially conserved sites detected. The new tool enables statistically powerful analysis of individual miRNA target sites, with the probability of preferentially conserved targeting (P CT ) correlating with experimental measurements of repression. Our expanded set of target predictions (including conserved 3Ј-compensatory sites), are available at the TargetScan website, which displays the P CT for each site and each predicted target.[Supplemental material is available online at www.genome.org.]MicroRNAs are ∼22-nucleotide (nt) endogenous RNAs that derive from distinctive hairpin precursors in plants and animals (Bartel 2004). After incorporation into a silencing complex, which contains at its core an Argonaute protein, an miRNA can pair to an mRNA and thereby specify the post-transcriptional repression of that protein-coding message, either by transcript destabilization, translational repression, or both. MicroRNAs constitute one of the more abundant classes of gene-regulatory molecules in animals, with hundreds of distinct miRNAs confidently identified in both human and mouse (Landgraf et al. 2007). A central goal for understanding the functions of all these small regulatory RNAs has been to determine which messages are targeted for repression.The search for biological targets of metazoan miRNAs has benefited greatly from the comparative analysis of orthologous mRNAs. Targets of miRNAs can be predicted above the background of false-positive predictions by requiring conserved Watson-Crick pairing to the 5Ј region of the miRNA, known as the miRNA seed (Lewis et al. 2003). Because so many messages have preferentially preserved their pairing to miRNA seeds, targets can be predicted simply by searching for c...

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