Mammalian gene regulation through the 3' UTR

Abstract

The untranslated region (UTR) at the 30 end of a mammalian mRNA is typically rich with regulatory motifs that influence the stability, localization, translation and other properties of the message. We explored two classes of motifs, microRNA (miRNA) complementary sites and cleavage and polyadenylation (poly(A)) signals, and provide evidence that specific sequence contextual features are important for their recognition. MiRNAs are 22 nt, non-coding RNAs that function as post-transcriptional gene regulators in animals and plants. They typically interact with target mRNAs through base-pairing predominantly between bases 2-8 (the 'seed' region) at the 50 end of the miRNA and complementary sites in the target 30 UTR ('seed matches'). These interactions result in target mRNA translational repression or deadenylation, or both. Through analysis of mRNA expression data following miRNA or siRNA overexpression or inhibition, we uncovered novel targeting determinants that influence mRNA levels. These include the presence of distinct seed match types and sequence context, in particular that increased AU content and conservation were independently associated with greater target down-regulation. Our results demonstrate that mRNA fold change increases multiplicatively (i.e., log-additively) with seed match count. We integrated these features into a target scoring scheme, TargetRank, and demonstrated the effectiveness of our rankings in predicting in vivo target responses. Mammalian genes frequently have multiple, competing poly(A) sites, and the features influencing site selection remain poorly understood. Poly(A) site recognition occurs co-transcriptionally and given that transcription is highly influenced by the tight packaging of genomic DNA into chromatin, we investigated the potential impact of nucleosome positioning on poly(A) site usage. Using recent, public, Illumina sequencing data from human nucleosome boundaries, we found evidence that greater nucleosome density in regions flanking but not overlapping poly(A) sites is associated with more frequent usage.