An information transmission model for transcription factor binding at regulatory DNA sites.
BACKGROUND
Computational identification of transcription factor binding sites (TFBSs) is a rapid, cost-efficient way to locate unknown regulatory elements. With increased potential for high-throughput genome sequencing, the availability of accurate computational methods for TFBS prediction has never been as important as it currently is. To date, identifying TFBSs with high sensitivity and specificity is still an open challenge, necessitating the development of novel models for predicting transcription factor-binding regulatory DNA elements.


RESULTS
Based on the information theory, we propose a model for transcription factor binding of regulatory DNA sites. Our model incorporates position interdependencies in effective ways. The model computes the information transferred (TI) between the transcription factor and the TFBS during the binding process and uses TI as the criterion to determine whether the sequence motif is a possible TFBS. Based on this model, we developed a computational method to identify TFBSs. By theoretically proving and testing our model using both real and artificial data, we found that our model provides highly accurate predictive results.


CONCLUSIONS
In this study, we present a novel model for transcription factor binding regulatory DNA sites. The model can provide an increased ability to detect TFBSs.
Beijing Institute of Biotechnology, Beijing 100071, China.
Mingfeng
M
Tan
Dong
D
Yu
Yuan
Y
Jin
Lei
L
Dou
Beiping
B
Li
Yuelan
Y
Wang
Junjie
J
Yue
Long
L
Liang
D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D004247:DNA / Q000235:genetics*; D030541:Databases, Genetic; D008957:Models, Genetic; D011401:Promoter Regions, Genetic / Q000235:genetics; D011485:Protein Binding / Q000235:genetics; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D014157:Transcription Factors / Q000378:metabolism*
D014157:Transcription Factors; D004247:DNA