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DNA shape readout is an important mechanism of target site recognition bytranscription factors, in addition to the sequence readout. Several models oftranscription factor-DNA binding which consider DNA shape have been developedin recent years. We present a new biophysical model of protein-DNA interactionby considering the DNA shape features, which is based on a neighbourdinucleotide dependency model BayesPI2. The parameters of the new model arerestricted to a subspace spanned by the 2-mer DNA shape features, whichallowing a biophysical interpretation of the new parameters asposition-dependent preferences towards certain values of the features. Usingthe new model, we explore the variation of DNA shape preferences in severaltranscription factors across cancer cell lines and cellular conditions. We findevidence of DNA shape variations at FOXA1 binding sites in MCF7 cells aftertreatment with steroids. The new model is useful for elucidating finer detailsof transcription factor-DNA interaction. It may be used to improve theprediction of cancer mutation effects in the future.

Predicting variation of DNA shape preferences in protein-DNA interaction in cancer cells with a new biophysical model