Genome-wide determination of poly(A) sites in Medicago truncatula: evolutionary conservation of alternative poly(A) site choice

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.

Noncanonical Alternative Polyadenylation Contributes to Gene Regulation in Response to Hypoxia

“…In plants, a majority of genes that possess multiple poly(A) sites have at least one site situated upstream of the 39-UTR, proximal to the associated promoter (Shen et al, 2011;Wu et al, 2011Wu et al, , 2014Fu et al, 2016). The results presented in this study indicate that the products of proximal poly(A) site choice (collectively, noncanonical mRNA isoforms) may be differentiated according to the location of the poly(A) site within the transcriptional unit.…”

“…In Arabidopsis, the set of genes that encode mRNAs with polyadenylation sites occurring within proteincoding regions and introns is enriched in those that are associated with stress responses and those that encode putative receptor proteins . In addition, there is a modest evolutionary conservation of APA events that lead to noncanonical mRNA isoforms in Arabidopsis and Medicago truncatula (Wu et al, 2014). These reports indicate that noncanonical polyadenylated mRNA isoforms are a standard component of the transcriptional output in plants.…”

“…The results presented here suggest a similar role for APA in plants, especially for events that lead to polyadenylation within protein-coding regions. In plants, genes that encode NBS-LRR (nucleotide binding site-leucine-rich repeat) receptors are subject to APA (Tan et al, 2007), and genes in this set are often affected by polyadenylation within protein coding regions (Thomas et al, 2012;Wu et al, 2014). Many such genes are among those affected by APA in response to hypoxia ( Figure 2D).…”

“…In plants, as in other eukaryotes, alternative polyadenylation is a widespread and pervasive process, potentially affecting a large majority of genes for a given species (Shen et al, 2011;Wu et al, 2011Wu et al, , 2014Sherstnev et al, 2012). In plants, a majority of genes that possess multiple poly(A) sites have at least one site situated upstream of the 39-UTR, proximal to the associated promoter (Shen et al, 2011;Wu et al, 2011Wu et al, , 2014Fu et al, 2016).…”

“…In Arabidopsis thaliana, intronic-APA regulates the balance of non/ functional mRNA isoforms encoded by the FCA gene, a central flowering time regulator (Simpson et al, 2003;Duc et al, 2013) and by the gene that encodes RPP7, a receptor involved in defense responses (Tsuchiya and Eulgem, 2013). Using genome-scale approaches, numerous noncanonical mRNA isoforms with polyadenylated 39 ends that lie within intronic, 59-UTR, and proteincoding regions have been described in plants (Shen et al, 2011;Wu et al, 2011Wu et al, , 2014. In Arabidopsis, the set of genes that encode mRNAs with polyadenylation sites occurring within proteincoding regions and introns is enriched in those that are associated with stress responses and those that encode putative receptor proteins .…”