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ISSN 0582-9879 Acta Biochim et Biophysica Sinica 2004, 36(4):250-258 CN 31-1300/Q
Predicting
Polymerase II Core Promoters by Cooperating Transcription Factor
Binding Sites in Eukaryotic Genes
Xiao-Tu MA, Min-Ping
QIAN*, and Hai-Xu TANG1
( School of Mathematical Sciences, Peking University and Center for Theoretical
Biology, Peking University, Beijing 100871, China;
1Department of Computer Science and Engineering, University of California, San
Diego, La Jolla CA 92093-0114, USA)
Abstract Several discriminate
functions for predicting core promoters that based on the potential cooperation
between transcription factor binding sites (TFBSs) are discussed. It is demonstrated
that the promoter predicting accuracy is improved when the cooperation among
TFBSs is taken into consideration. The core promoter region of a newly discovered
gene CKLFSF1 is predicted to locate more than 1.5 kb far away from the
5′ end of the transcript and in the last intron of its upstream gene, which
is experimentally confirmed later. The core promoters of 3402 human RefSeq sequences,
obtained by extending the mRNAs in
human genome sequences, are predicted by our algorithm, and there are about
60% of the predicted core promoters locating within the ± 500 bp region relative
to the annotated transcription start site.
Key words promoter; transcription
factor binding site; transcription start site; gene finding
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Received: December 8, 2003 Accepted:
February 5, 2004
This work is supported by the grants from National Natural Science Foundation
of China (No. 90208022), and the National High Technology Research and Development
Program of China (No. 2002AA234011)
*Corresponding author: Tel, 86-10-62759666; E-mail, [email protected]