Retained introns increase putative microRNA targets within 3′ UTRs of human mRNA

MicroRNAs (miRNAs) are a class of non-coding RNA that post-transcriptionally regulates the expression of target genes by binding to mRNAs. As one form of alternative splicing, intron retention has influence upon mRNA modification and protein encoding. The effect of miRNA on mRNA containing retained intron within 3' UTR, however, has not been systematically elucidated. Here, we examined a total of 2864 human genes which contain at least one retained intron from the MAASE and ASD databases and found 387 genes having contained retained introns within 3' UTR. The effect of retained introns upon miRNA targets was explored with three web-based programs for miRNA prediction including miRanda, TargetScanS and PicTar. The results showed that retained introns can increase putative miRNA targets in human mRNA. Retained introns have higher chances than other regions of 3' UTR in involving the site of miRNAs targets of most genes which contain putative miRNA targets within it. Furthermore, some transcripts contain miRNA targets solely because of the retained introns in 3' UTR. In addition, we examined those 'Ignored' retained introns by miRanda software and the results indicated that miRNAs may contain many more putative targets. (c) 2007 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.