Abstract
Alternative polyadenylation sites produce transcript isoforms with 3′ untranslated regions (UTRs) of different lengths. If a microRNA (miRNA) target is present in the UTR, then only those target-containing isoforms should be sensitive to control by a cognate miRNA. We carried out a systematic examination of 3′ UTRs containing multiple poly(A) sites and putative miRNA targets. Based on expressed sequence tag (EST) counts and EST library information, we observed that levels of isoforms containing targets for miR-1 or miR-124, two miRNAs causing downregulation of transcript levels, were reduced in tissues expressing the corresponding miRNA. This analysis was repeated for all conserved 7-mers in 3′ UTRs, resulting in a selection of 312 motifs. We show that this set is significantly enriched in known miRNA targets and mRNA-destabilizing elements, which validates our initial hypothesis. We scanned the human genome for possible cognate miRNAs and identified phylogenetically conserved precursors matching our motifs. This analysis can help identify target-miRNA couples that went undetected in previous screens, but it may also reveal targets for other types of regulatory factors.
Highlights
The current model of animal microRNA function posits that part of the 21–22nt miRNA sequence binds to the 39 untranslated region (UTR) of a target mRNA, causing a downregulation of gene expression [1]
After clustering expressed sequence tag (EST)/cDNA hits, we identified putative poly(A) sites based on several stringent criteria, including presence of at least three 39 ESTs/cDNA from distinct libraries ending at each site, lack of potential internal priming, and presence of a poly(A) signal near the 39 end of match
Our initial observation that transcript isoforms containing miRNA targets were generally not underexpressed compared to target-free isoforms (Figure 3) was at a first glance discouraging
Summary
The current model of animal microRNA (miRNA) function posits that part of the 21–22nt miRNA sequence binds to the 39 untranslated region (UTR) of a target mRNA, causing a downregulation of gene expression [1]. Most animal miRNAs were believed to act by repressing translation, rather than by mRNA cleavage as observed in plants [6]. MiRNA may induce a largescale transcriptional shift towards a tissue-specific expression pattern. It is not clear yet whether messenger levels are reduced through a specific mechanism or as a consequence of translational repression, but this observation opens new avenues for monitoring and understanding miRNA-based gene regulation
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