Genome-Wide Landscape of Alternative Polyadenylation: Impact on Developmental Gene Expression Regulation in Rice

Effective gene expression of a complex genome requires precise regulation.  Alternative polyadenylation (APA), a phenomenon that a gene may use any of its poly(A) sites to produce a defined 3’-end and a poly(A) tail for each transcript, has been recognized as a regulatory mechanism in eukaryotic gene expression.  To elucidate such a machanism in important crop rice, we have begun to reveal the whole genome APA profiles.  Using a protocol that we developed to tally the junctions of poly(A) tails and their attached 3’-UTR, poly(A)-tag sequencing (PAT-seq), we have finished the analysis of the most poly(A) sites in the rice genome.  Comparison of 15 different tissues/developmental stages of rice, including different stages of the root and leaf, and different tissues like flower parts (glume, caryopsis, mature pollen, anther, pistil), embryo, endosperm, and imbibed seeds, distinct profiles of APA have emerged.  Some genes have numerous poly(A) sites that are used in different tissue types and developmental stages.  Their roles in gene expression can be drawn from their APA patterns, result in truncated proteins to altered mRNA length to attract or avoid miRNA targeting etc.  Poly(A) sites located in the intergenic regions are also potentially indicative of differential transcription activities.  GO analyses revealed that particular groups of genes responsive to environmental stimuli, biotic and abiotic stresses are more prone to have APA, indicative of their potential functions.  The poly(A) site information of the rice genes is also useful to annotate the ends of genes in the rice genome.