title: An exploration of 3'-end processing signals and their tissue distribution in Oryza sativa.
abstract: The 3' untranslated regions deeply affect many properties of eukaryotic mRNA. In plants, the polyadenine control signals contained in these regions seem to be more variable than of mammals. Three cDNA libraries derived from the leaf, endosperm and stem tissues of rice were sequenced from the 3'-end. Of the 9911 transcripts analyzed, 5723 unique transcripts were identified from the leaf sequences, 2934 from the endosperm and 1254 from the stem. The information entropy and two statistical methods were used to compile a list of rice poly(A) control signals. Based on their distribution, these signals can be roughly grouped into far-upstream element (FUE), near-upstream element (NUE), T-rich region (TRE) and downstream element (DE). The distribution of rice conserved regions is similar to the previous model from Arabidopsis and yeast, with a few differences in word constructions. Interestingly, we also found the word distributions were diverse in the cleavage site of downstream sequences of different rice tissues. The signal bias in downstream sequences may lead mRNA to be differently cleaved in different rice tissues.
authors.affiliation: Bioinformatics and Gene Network Research Group, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China. htdong@zjuem.zju.edu.cn
authors.forename: Haitao
authors.initials: H
authors.lastname: Dong
authors.forename: Ye
authors.initials: Y
authors.lastname: Deng
authors.forename: Jack
authors.initials: J
authors.lastname: Chen
authors.forename: Sheng
authors.initials: S
authors.lastname: Wang
authors.forename: Sihua
authors.initials: S
authors.lastname: Peng
authors.forename: Cheng'en
authors.initials: C
authors.lastname: Dai
authors.forename: Yongqi
authors.initials: Y
authors.lastname: Fang
authors.forename: Jing
authors.initials: J
authors.lastname: Shao
authors.forename: Yichun
authors.initials: Y
authors.lastname: Lou
authors.forename: Debao
authors.initials: D
authors.lastname: Li
mesh_terms: D020413:3' Untranslated Regions; D019295:Computational Biology; D018076:DNA, Complementary; D020224:Expressed Sequence Tags; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D012275:Oryza / Q000235:genetics*; D018515:Plant Leaves / Q000235:genetics; D018547:Plant Stems / Q000235:genetics; D039104:RNA 3' Polyadenylation Signals; D012323:RNA Processing, Post-Transcriptional; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics* / Q000378:metabolism; D012639:Seeds / Q000235:genetics
chemical_list: D020413:3' Untranslated Regions; D018076:DNA, Complementary; D012333:RNA, Messenger; D018749:RNA, Plant