RNA regulatory elements and polyadenylation in plants

Abstract

Alternative poly(A) site choice (also known as alternative polyadenylation, or APA) has the potential to affect gene expression in qualitative and quantitative ways. APA may affect as many as 82% of all expressed genes in a plant. The consequences of APA include the generation of transcripts with differing 3'-UTRs (and thus differing regulatory potential) and of transcripts with differing protein-coding potential. Genome-wide studies of possible APA suggest a linkage with pre-mRNA splicing, and indicate a coincidence of and perhaps cooperation between RNA regulatory elements that affect splicing efficiency and the recognition of novel intronic poly(A) sites. These studies also raise the possibility of the existence of a novel class of polyadenylation-related cis elements that are distinct from the well-characterized plant polyadenylation signal. Many potential APA events, however, have not been associated with identifiable cis elements. The present state of the field reveals a broad scope of APA, and also numerous opportunities for research into mechanisms that govern both choice and regulation of poly(A) sites in plants.

Keywords: UTRs; alternative polyadenylation; exons; introns; splicing.

Figure 1

Alternative poly(A) site choice in the gene encoding TAS3a (At3g17185). The bar with the colored vertical lines represents the DNA sequence of the locus, color-coded using the default settings from the Integrated Genomics Viewer (IGV2.0). The extent of the RNA coding region is represented as the solid blue line beneath the sequence. Beneath this are shown the directions of transcription, locations of the two principal poly(A) sites, and the miR390 target site (Allen et al., 2005). Finally, the numerous blue lines below the gray separator represent individual poly(A) tags (taken from the Arabidopsis leaf set from Wu et al., 2011) that map to the At3g17185 locus. Colored tics within the tag representations signify differences in sequence from the known TAS3a sequence; these differences provide an illustration of the error rate inherent in the high-throughput PAT sequencing. The right-most extremity of each tag represents the 3′-end of the tag, and hence the mRNA–poly(A) junction. These tags were mapped to the Arabidopsis genome using CLC Genomics Workbench and displayed using the Integrated Genomics Viewer 2.0 (Robinson et al., 2011).