A population-based statistical approach identifies parameters characteristic of human microRNA-mRNA interactions

Abstract

Background: MicroRNAs are approximately 17-24 nt. noncoding RNAs found in all eukaryotes that degrade messenger RNAs via RNA interference (if they bind in a perfect or near-perfect complementarity to the target mRNA), or arrest translation (if the binding is imperfect). Several microRNA targets have been identified in lower organisms, but only one mammalian microRNA target has yet been validated experimentally.

Results: We carried out a population-wide statistical analysis of how human microRNAs interact complementarily with human mRNAs, looking for characteristics that differ significantly as compared with scrambled control sequences. These characteristics were used to identify a set of 71 outlier mRNAs unlikely to have been hit by chance. Unlike the case in C. elegans and Drosophila, many human microRNAs exhibited long exact matches (10 or more bases in a row), up to and including perfect target complementarity. Human microRNAs hit outlier mRNAs within the protein coding region about 2/3 of the time. And, the stretches of perfect complementarity within microRNA hits onto outlier mRNAs were not biased near the 5'-end of the microRNA. In several cases, an individual microRNA hit multiple mRNAs that belonged to the same functional class.

Conclusions: The analysis supports the notion that sequence complementarity is the basis by which microRNAs recognize their biological targets, but raises the possibility that human microRNA-mRNA target interactions follow different rules than have been previously characterized in Drosophila and C. elegans.

Figure 1

microRNAs and their scrambled counterparts interact differently with the population of human mRNAs. Shown are all exact hits ≥ 10 bases long (not counting G:U matches) produced on human RefSeq mRNAs by the set of nonredundant microRNAs, vs. the average of 10 replications of scrambled control sequences. Shown is the number of hits as a function of exact hit length. Only the longest hit was counted: e.g., for a hit of length 18, the two subsets of length 17 in the same hit position were not counted.

Figure 2

Distribution of gapped-BLAST scores in hits made by microRNAs and scrambled counterparts. Without permitting G:U matches in the extension phase, the microRNAs had better average gapped-BLAST scores than scrambled counterparts across all mRNAs in the "10+ set" (153.00 ± 0.03 vs. 150.98 ± 0.01, mean ± s.e.m., p < 0.0001). With permitting G:U matches in the extension phase, the microRNA set showed significantly fewer G:U matches overall relative to scrambled counterparts, even when holding constant the length of the exact hit (2.891 ± 0.004 vs. 2.939 ± 0.001, p < 0.0001).

Figure 3

Number of distinct mRNA sequences which received hits from two or more distinct microRNAs, as a function of the minimum distance between hits. Distance of 0 or 1 was excluded because this might be produced by partial overlap of microRNA sequences.

Figure 4

Individual microRNAs hit multiple targets on the candidate list, more often than expected by chance.