Skip Navigation



Bioinformatics Advance Access published online on January 26, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti180
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
21/8/1358    most recent
bti180v2
bti180v1
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 arrowRequest Permissions
Google Scholar
Right arrow Articles by Lian, Y.
Right arrow Articles by Garner, H. R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Lian, Y.
Right arrow Articles by Garner, H. R.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics © Oxford University Press 2004; all rights reserved.
Received July 13, 2004
Revised November 8, 2004
Accepted November 23, 2004

Article

Evidence for the regulation of alternative splicing via complementary DNA sequence repeats

Yun Lian 1 and Harold R. Garner 1*

1 Department of Biochemistry, McDermott Center for Human Growth and Development and Center for Biomedical Inventions, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA; Department of Internal Medicine, McDermott Center for Human Growth and Development and Center for Biomedical Inventions, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA

* To whom correspondence should be addressed.
Harold R. Garner, E-mail: garner{at}swmed.edu


  Abstract

Motivation: While the mechanism for regulating alternative splicing is poorly understood, secondary structure has been shown to be integral to this process. Due to their propensity for forming complementary hairpin loops and their elevated mutation rates, tandem repeated sequences have the potential to influence splicing regulation. Results: An analysis of human intronic sequences reveals a strong correlation between alternative splicing and the prevalence of mono- through hexanucleotide tandem repeats that may engage in complementary pairing in introns that flank alternatively spliced exons. While only 44% of the 18,173 genes in the Human Alternative Splicing Database are known to be alternatively spliced, they contain 84% of the 694,237 intronic complementary repeat pairs. Significantly, the normalized frequency and distribution of repeat sequences, independent of their potential for pairing, is indistinguishable between alternatively spliced and non-alternatively spliced genes. Thus, the increased prevalence of repeats with pairing potential in alternatively spliced genes is not merely a consequence of more repeats or repeat composition bias. These results suggest that complementary repeats may play a role in the regulation of alternative splicing.


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
 Nucleic Acids ResHome page
E. Buratti, A. Dhir, M. A. Lewandowska, and F. E. Baralle
RNA structure is a key regulatory element in pathological ATM and CFTR pseudoexon inclusion events
Nucleic Acids Res., July 26, 2007; 35(13): 4369 - 4383.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
N. Kim, A. V. Alekseyenko, M. Roy, and C. Lee
The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D93 - D98.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
D.-S. KIM, V. GUSTI, S. G. PILLAI, and R. K. GAUR
An artificial riboswitch for controlling pre-mRNA splicing
RNA, November 1, 2005; 11(11): 1667 - 1677.
[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.