The active miniature inverted-repeat transposable element mPing posttranscriptionally produces new transcriptional variants in the rice genome

Abstract

Posttranscriptional RNA processing inclusive of alternative splicing and alternative polyadenylation, as well as transcriptional regulation, plays important regulatory roles in eukaryotic gene expression. In eukaryotic genomes, transposable elements can alter gene expression at both transcriptional and posttranscriptional levels. Miniature Ping (mPing) is an active miniature inverted-repeat TE discovered in the rice genome, and its insertion renders adjacent genes stress inducible. In this study, we examined the effect of mPing insertion into coding sequences on RNA processing. The 3′ RACE (rapid amplification of cDNA ends) analysis of mutant alleles, each harboring an mPing insertion, revealed that mPing induced various alternative splicing events. Furthermore, it was found that mPing induced alternative polyadenylation within its sequence. In the mutant allele, the body region of mPing was heavily methylated, whereas the mPing-flanking regions were moderately methylated. These results indicate that mPing alters transcript structures posttranscriptionally via induction of alternative splicing that most likely depends on DNA methylation. Based on these results, we discuss the availability of mPing as an insertional mutagen in rice.