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Abstract
We predict regulatory targets of vertebrate microRNAs (miRNAs) by identifying mRNAs
with conserved complementarity to the seed (nucleotides 2-7) of the miRNA. An overrepresentation
of conserved adenosines flanking the seed complementary sites in mRNAs indicates that
primary sequence determinants can supplement base pairing to specify miRNA target
recognition. In a four-genome analysis of 3' UTRs, approximately 13,000 regulatory
relationships were detected above the estimate of false-positive predictions, thereby
implicating as miRNA targets more than 5300 human genes, which represented 30% of
our gene set. Targeting was also detected in open reading frames. In sum, well over
one third of human genes appear to be conserved miRNA targets.