Abstract
BackgroundAlternative polyadenylation (APA) plays an important role in the post-transcriptional regulation of gene expression. Little is known about how APA sites may evolve in homologous genes in different plant species. To this end, comparative studies of APA sites in different organisms are needed. In this study, a collection of poly(A) sites in Medicago truncatula, a model system for legume plants, has been generated and compared with APA sites in Arabidopsis thaliana.ResultsThe poly(A) tags from a deep-sequencing protocol were mapped to the annotated M. truncatula genome, and the identified poly(A) sites used to update the annotations of 14,203 genes. The results show that 64% of M. truncatula genes possess more than one poly(A) site, comparable to the percentages reported for Arabidopsis and rice. In addition, the poly(A) signals associated with M. truncatula genes were similar to those seen in Arabidopsis and other plants. The 3′-UTR lengths are correlated in pairs of orthologous genes between M. truncatula and Arabidopsis. Very little conservation of intronic poly(A) sites was found between Arabidopsis and M. truncatula, which suggests that such sites are likely to be species-specific in plants. In contrast, there is a greater conservation of CDS-localized poly(A) sites in these two species. A sizeable number of M. truncatula antisense poly(A) sites were found. A high percentage of the associated target genes possess Arabidopsis orthologs that are also associated with antisense sites. This is suggestive of important roles for antisense regulation of these target genes.ConclusionsOur results reveal some distinct patterns of sense and antisense poly(A) sites in Arabidopsis and M. truncatula. In so doing, this study lends insight into general evolutionary trends of alternative polyadenylation in plants.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-615) contains supplementary material, which is available to authorized users.
Highlights
Alternative polyadenylation (APA) plays an important role in the post-transcriptional regulation of gene expression
Our results show that poly(A) signals in M. truncatula are similar to those seen in other plants, and that the scope of possible alternative polyadenylation (APA) is similar to that reported for other plants
High throughput determination of poly(A) sites in M. truncatula To determine poly(A) sites encoded in the M. truncatula genome, the poly(A)-tag-seq (PAT-seq) approach described by Wu et al [7] was used
Summary
Alternative polyadenylation (APA) plays an important role in the post-transcriptional regulation of gene expression. Little is known about how APA sites may evolve in homologous genes in different plant species. To this end, comparative studies of APA sites in different organisms are needed. Polyadenylation is a key process during eukaryotic gene expression, playing an important role in mRNA stability, translation and transport [1]. If a gene possesses more than one poly(A) site, it undergoes alternative polyadenylation (APA). Recent studies have shown extensive networks of potential APA in different species and have linked APA to epigenetic regulation and many biological processes [1,2]. In higher plants (Arabidopsis and rice), more than 70% of expressed genes possess more than one poly(A)
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