Genome-wide determination of poly(A) sites in Medicago truncatula: evolutionary conservation of alternative poly(A) site choice
文献类型： 外文期刊
作者： Wu, Xiaohui 1 ; Gaffney, Bobby 2 ; Hunt, Arthur G. 2 ; Li, Qingshun Q. 3 ;
作者机构： 1.Xiamen Univ, Dept Automat, Xiamen, Peoples R China
2.Univ Kentucky, Dept Plant & Soil Sci, Lexington, KY 40506 USA
3.Xiamen Univ, Coll Environm & Ecol, Key Lab Minist Educ Costal Wetland Ecosyst, Xiamen, Peoples R China
4.Miami Univ, Dept Biol, Oxford, OH 45056 USA
5.Fujian Acad Agr Sci, Rice Res Inst, Fuzhou, Fujian, Peoples R China
关键词： Alternative polyadenylation;RNA processing;Antisense;Evolutionary conservation;Legume;Medicago truncatula
期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）
ISSN： 1471-2164
年卷期： 2014 年 15 卷
页码：
收录情况： SCI
摘要： Background: 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. 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. Results: The 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. Conclusions: Our 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.
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