Methodology article
BayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors
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* Corresponding author: Junbai Wang junbai.wang@rr-research.no
1 Division of Pathology, The Norwegian Radium Hospital, Rikshospitalet University Hospital, Montebello 0310 Oslo, Norway
2 Department of Cell Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Rikshospitalet University Hospital, Montebello 0310 Oslo, Norway
BMC Bioinformatics 2009, 10:345 doi:10.1186/1471-2105-10-345
Published: 20 October 2009Abstract
Background
We have incorporated Bayesian model regularization with biophysical modeling of protein-DNA interactions, and of genome-wide nucleosome positioning to study protein-DNA interactions, using a high-throughput dataset. The newly developed method (BayesPI) includes the estimation of a transcription factor (TF) binding energy matrices, the computation of binding affinity of a TF target site and the corresponding chemical potential.
Results
The method was successfully tested on synthetic ChIP-chip datasets, real yeast ChIP-chip experiments. Subsequently, it was used to estimate condition-specific and species-specific protein-DNA interaction for several yeast TFs.
Conclusion
The results revealed that the modification of the protein binding parameters and the variation of the individual nucleotide affinity in either recognition or flanking sequences occurred under different stresses and in different species. The findings suggest that such modifications may be adaptive and play roles in the formation of the environment-specific binding patterns of yeast TFs and in the divergence of TF binding sites across the related yeast species.