Skip Navigation



Nucleic Acids Research Advance Access published online on April 13, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn158
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (5132K) Freely available
Right arrow Screen PDF (898K) Freely available
Right arrow Supplementary Data
Right arrowOA All Versions of this Article:
36/9/3150    most recent
gkn158v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Shen, Y.
Right arrow Articles by Li, Q. Q.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Shen, Y.
Right arrow Articles by Li, Q. Q.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 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


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Genome ResHome page
H. Kuang, C. Padmanabhan, F. Li, A. Kamei, P. B. Bhaskar, S. Ouyang, J. Jiang, C. R. Buell, and B. Baker
Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: New functional implications for MITEs
Genome Res., January 1, 2009; 19(1): 42 - 56.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.