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Nucleic Acids Research 2005 33(16):5034-5044; doi:10.1093/nar/gki804
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Published online 7 September 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

Open reading frames provide a rich pool of potential natural antisense transcripts in fungal genomes

Stephan Steigele and Kay Nieselt*

Wilhelm-Schickard-Institut f. Informatik, ZBIT–Center for Bioinformatics, Tübingen, University of Tübingen Germany

*To whom correspondence should be addressed. Tel: +49 7071 2970443; Fax: +49 7071 295147; Email: nieselt{at}informatik.uni-tuebingen.de

Received July 29, 2005. Revised August 15, 2005. Accepted August 15, 2005.

Natural antisense transcripts are reported from all kingdoms of life and several recent reports of genomewide screens indicate that they are widely distributed. These transcripts seem to be involved in various biological functions and may govern the expression of their respective sense partner. Very little, however, is known about the degree of evolutionary conservation of antisense transcripts. Furthermore, none of the earlier analyses has studied whether antisense relationships are solely dual or involved in more complex relationships. Here we present a systematic screen for cis- and trans-located antisense transcripts based on open reading frames (ORFs) from five fungal species. The relative number of ORFs involved in antisense relationships varies greatly between the five species. In addition, other significant differences are found between the species, such as the mean length of the antisense region. The majority of trans-located antisense transcripts is found to be involved in complex relationships, resulting in highly connected networks. The analysis of the degree of evolutionary conservation of antisense transcripts shows that most antisense transcripts have no ortholog in any other species. An annotation of antisense transcripts based on Gene Ontology directs to common terms and shows that proteins of genes involved in antisense relationships preferentially localize to the nucleus with common functions in the regulation or maintenance of nucleic acids.

Correspondence may also be addressed to Stephan Steigele, Email: steigele{at}informatik.uni-tuebingen.de


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Y. Zhang, X. S. Liu, Q.-R. Liu, and L. Wei
Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species
Nucleic Acids Res., July 18, 2006; 34(12): 3465 - 3475.
[Abstract] [Full Text] [PDF]


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