Published online 8 September 2004
Nucleic Acids Research, Vol. 32 No. 16 © Oxford University Press 2004; all rights reserved
Over 20% of human transcripts might form sense–antisense pairs
Department of Medicine, University of Chicago, 5841 S. Maryland Avenue, MC2115, Chicago, IL 60637, USA, 1 Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA, 2 Department of Computer Science, Iowa State University, 226 Atanasoff Hall, Ames, IA 50011, USA, 3 Synatom Research Inc., PO Box 0699, Ringoes, NJ 08551-0699, USA and 4 Biostatistics and Bioinformatics Unit, Comprehensive Cancer Center, University of Alabama at Birmingham, 1824 6th Avenue South, WTI 153, Birmingham, AL 35294, USA
* To whom correspondence should be addressed. Tel: +1 773 795 5474; Fax: +1 773 702 3002; Email: jchen{at}medicine.bsd.uchicago.edu
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
Received July 29, 2004; Revised and Accepted August 23, 2004
The major challenge to identifying natural sense– antisense (SA) transcripts from public databases is how to determine the correct orientation for an expressed sequence, especially an expressed sequence tag sequence. In this study, we established a set of very stringent criteria to identify the correct orientation of each human transcript. We used these orientation-reliable transcripts to create 26 741 transcription clusters in the human genome. Our analysis shows that 22% (5880) of the human transcription clusters form SA pairs, higher than any previous estimates. Our orientation-specific RT–PCR results along with the comparison of experimental data from previous studies confirm that our SA data set is reliable. This study not only demonstrates that our criteria for the prediction of SA transcripts are efficient, but also provides additional convincing data to support the view that antisense transcription is quite pervasive in the human genome. In-depth analyses show that SA transcripts have some significant differences compared with other types of transcripts, with regard to chromosomal distribution and Gene Ontology-annotated categories of physiological roles, functions and spatial localizations of gene products.
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