title: Genome level analysis of rice mRNA 3'-end processing signals and alternative polyadenylation.
abstract: The position of a poly(A) site of eukaryotic mRNA is determined by sequence signals in pre-mRNA and a group of polyadenylation factors. To reveal rice poly(A) signals at a genome level, we constructed a dataset of 55 742 authenticated poly(A) sites and characterized the poly(A) signals. This resulted in identifying the typical tripartite cis-elements, including FUE, NUE and CE, as previously observed in Arabidopsis. The average size of the 3'-UTR was 289 nucleotides. When mapped to the genome, however, 15% of these poly(A) sites were found to be located in the currently annotated intergenic regions. Moreover, an extensive alternative polyadenylation profile was evident where 50% of the genes analyzed had more than one unique poly(A) site (excluding microheterogeneity sites), and 13% had four or more poly(A) sites. About 4% of the analyzed genes possessed alternative poly(A) sites at their introns, 5'-UTRs, or protein coding regions. The authenticity of these alternative poly(A) sites was partially confirmed using MPSS data. Analysis of nucleotide profile and signal patterns indicated that there may be a different set of poly(A) signals for those poly(A) sites found in the coding regions. Based on the features of rice poly(A) signals, an updated algorithm termed PASS-Rice was designed to predict poly(A) sites.
authors.affiliation: Department of Botany, Miami University, Oxford, OH 45056, USA.
authors.forename: Yingjia
authors.initials: Y
authors.lastname: Shen
authors.forename: Guoli
authors.initials: G
authors.lastname: Ji
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Haas
authors.forename: Xiaohui
authors.initials: X
authors.lastname: Wu
authors.forename: Jianti
authors.initials: J
authors.lastname: Zheng
authors.forename: Greg J
authors.initials: GJ
authors.lastname: Reese
authors.forename: Qingshun Quinn
authors.initials: QQ
authors.lastname: Li
mesh_terms: D020413:3' Untranslated Regions / Q000737:chemistry*; D000465:Algorithms; D017343:Genes, Plant; D018745:Genome, Plant; D023281:Genomics; D012275:Oryza / Q000235:genetics* / Q000378:metabolism; D011061:Poly A / Q000032:analysis; D026723:Polyadenylation; D038621:Regulatory Sequences, Ribonucleic Acid
chemical_list: D020413:3' Untranslated Regions; D038621:Regulatory Sequences, Ribonucleic Acid; D011061:Poly A