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Nucleic Acids Research Advance Access published online on April 13, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn158
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Computational Biology

Genome level analysis of rice mRNA 3'-end processing signals and alternative polyadenylation

Yingjia Shen1, Guoli Ji2, Brian J. Haas3, Xiaohui Wu2, Jianti Zheng2, Greg J. Reese4 and Qingshun Quinn Li1,*

1Department of Botany, Miami University, Oxford, OH 45056, USA, 2Department of Automation, Xiamen University, Xiamen, Fujian, China 361005, 3The Genome Research Institute, Rockville, MD 20850 and 4IT Research Computing Support Group, Miami University, Oxford, OH 45056, USA

*To whom correspondence should be addressed. Tel: +1 513 529 4256; Fax: +1 513 529 4243; Email: liq{at}muohio.edu

Received December 31, 2007. Revised March 18, 2008. Accepted March 19, 2008.

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.

Present address: Brian J. Haas, The Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA


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