title: Genome-wide characterization of intergenic polyadenylation sites redefines gene spaces in Arabidopsis thaliana.
abstract: 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.
authors.affiliation: Department of Automation, Xiamen University, Xiamen, Fujian, China. xhuister@xmu.edu.cn.
authors.forename: Xiaohui
authors.initials: X
authors.lastname: Wu
authors.affiliation: Department of Automation, Xiamen University, Xiamen, Fujian, China. zy_lol@163.com.
authors.forename: Yong
authors.initials: Y
authors.lastname: Zeng
authors.affiliation: Department of Automation, Xiamen University, Xiamen, Fujian, China. jintingguan@gmail.com.
authors.forename: Jinting
authors.initials: J
authors.lastname: Guan
authors.affiliation: Department of Automation, Xiamen University, Xiamen, Fujian, China. glji@xmu.edu.cn.|Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, Fujian, China. glji@xmu.edu.cn.
authors.forename: Guoli
authors.initials: G
authors.lastname: Ji
authors.affiliation: Department of Automation, Xiamen University, Xiamen, Fujian, China. trhuang@stu.xmu.edu.cn.
authors.forename: Rongting
authors.initials: R
authors.lastname: Huang
authors.affiliation: Key Laboratory of the Ministry of Education on Costal Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China. liqq@xmu.edu.cn.|Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, USA. liqq@xmu.edu.cn.|Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China. liqq@xmu.edu.cn.
authors.forename: Qingshun Q
authors.initials: QQ
authors.lastname: Li
mesh_terms: D020413:3' Untranslated Regions; D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D011061:Poly A / Q000032:analysis*; D016372:RNA, Antisense / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics
chemical_list: D020413:3' Untranslated Regions; D029681:Arabidopsis Proteins; D016372:RNA, Antisense; D018749:RNA, Plant; D011061:Poly A