Most mammalian mRNAs are conserved targets of microRNAs

TLDR

MicroRNAs are small RNAs that bind to mRNA sites, especially seed matches in 3′UTRs, which are preferentially conserved. The study overhauled a motif‑conservation tool and applied it to human 3′UTRs, nearly tripling the number of identified conserved miRNA target sites. The updated tool incorporates additional genomes, models mutational biases, dinucleotide and UTR conservation, and uses an improved background model that detects new site types such as offset 6mers and yields statistically powerful predictions of individual miRNA target sites. The analysis identified over 45,000 conserved miRNA target sites in human 3′UTRs, with more than 60 % of protein‑coding genes under selective pressure to maintain miRNA pairing; broadly conserved miRNAs have many more conserved targets than mammalian‑specific ones, and the tool’s probability of preferential conservation correlates with.

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 3′ untranslated regions (3′UTRs), are preferentially conserved. Here, we overhauled our tool for finding preferential conservation of sequence motifs and applied it to the analysis of human 3′UTRs, 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 3′UTRs 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 3′ 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 3′-compensatory sites), are available at the TargetScan website, which displays the P CT for each site and each predicted target.