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Genome-wide characterization of intergenic polyadenylation sites redefines gene spaces in Arabidopsis thaliana

文献类型： 外文期刊

作者： Wu, Xiaohui 1 ; Zeng, Yong 1 ; Guan, Jinting 1 ; Ji, Guoli 1 ; Huang, Rongting 1 ; Li, Qingshun Q. 2 ;

作者机构： 1.Xiamen Univ, Dept Automat, Xiamen, Fujian, Peoples R China

2.Xiamen Univ, Coll Environm & Ecol, Key Lab Minist Educ Costal Wetland Ecosyst, Xiamen, Fujian, Peoples R China

3.Western Univ Hlth Sci, Grad Coll Biomed Sci, Pomona, CA USA

4.Fujian Acad Agr Sci, Rice Res Inst, Fuzhou, Fujian, Peoples R China

5.Xiamen Univ, Innovat Ctr Cell Signaling Network, Xiamen, Fujian, Peoples R China

关键词： Alternative polyadenylation;RNA processing;Genome annotation;Intergenic region;3 '-UTR

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： 2015 年 16 卷

页码：

收录情况： SCI

摘要： Background: Messenger RNA polyadenylation is an essential step for the maturation of most eukaryotic mRNAs. Accurate determination of poly(A) sites helps define the 3'-ends of genes, which is important for genome annotation and gene function research. Genomic studies have revealed the presence of poly(A) sites in intergenic regions, which may be attributed to 3'-UTR extensions and novel transcript units. However, there is no systematically evaluation of intergenic poly(A) sites in plants. Results: Approximately 16,000 intergenic poly(A) site clusters (IPAC) in Arabidopsis thaliana were discovered and evaluated at the whole genome level. Based on the distributions of distance from IPACs to nearby sense and antisense genes, these IPACs were classified into three categories. About 70 % of them were from previously unannotated 3'-UTR extensions to known genes, which would extend 6985 transcripts of TAIR10 genome annotation beyond their 3'-ends, with a mean extension of 134 nucleotides. 1317 IPACs were originated from novel intergenic transcripts, 37 of which were likely to be associated with protein coding transcripts. 2957 IPACs corresponded to antisense transcripts for genes on the reverse strand, which might affect 2265 protein coding genes and 39 non-protein-coding genes, including long non-coding RNA genes. The rest of IPACs could be originated from transcriptional read-through or gene mis-annotations. Conclusions: The identified IPACs corresponding to novel transcripts, 3'-UTR extensions, and antisense transcription should be incorporated into current Arabidopsis genome annotation. Comprehensive characterization of IPACs from this study provides insights of alternative polyadenylation and antisense transcription in plants.

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[1]Genome-wide determination of poly(A) sites in Medicago truncatula: evolutionary conservation of alternative poly(A) site choice. Wu, Xiaohui,Gaffney, Bobby,Hunt, Arthur G.,Li, Qingshun Q.,Li, Qingshun Q.,Li, Qingshun Q.. 2014

[2]Plant polyadenylation factors: conservation and variety in the polyadenylation complex in plants. Hunt, Arthur G.,Xing, Denghui,Li, Qingshun Q.,Li, Qingshun Q.,Li, Qingshun Q.. 2012

[3]The regulatory role of Pcf11-similar-4 (PCFS4) in Arabidopsis development by genome-wide physical interactions with target loci. Xing, Denghui,Wang, Yajun,Xu, Ruqiang,Li, Qingshun Q.,Ye, Xinfu,Yang, Dewei,Li, Qingshun Q.,Li, Qingshun Q.,Li, Qingshun Q.. 2013

[4]Bioinformatics Analysis of Alternative Polyadenylation in Green Alga Chlamydomonas reinhardtii Using Transcriptome Sequences from Three Different Sequencing Platforms. Zhao, Zhixin,Wu, Xiaohui,Kumar, Praveen Kumar Raj,Dong, Min,Li, Qingshun Quinn,Liang, Chun,Wu, Xiaohui,Dong, Min,Ji, Guoli,Li, Qingshun Quinn,Li, Qingshun Quinn,Li, Qingshun Quinn. 2014

[5]Genome-wide identification and predictive modeling of polyadenylation sites in eukaryotes. Ji, Guoli,Guan, Jinting,Zeng, Yong,Wu, Xiaohui,Ji, Guoli,Li, Qingshun Q.,Li, Qingshun Q.,Li, Qingshun Q..

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