Title: Elucidating the sequence and structural specificities of DNA-binding factors
Description: Characterizing the binding preferences of transcription factors is a major objective in molecular biology. Important processes such as development and responses to environmental stresses are regulated by the interactions between transcription factors and DNA. In this thesis, we address three key issues in the analysis of protein-DNA interactions. First, we demonstrate how transcription factor binding motifs can be inferred from ChIP-seq data by integrating a peak-calling algorithm and a biophysical model of transcription factor specificity. Next, we show that high-resolution DNase I cleavage profiles can provide detailed information about the role that DNA shape plays in protein- DNA recognition. Our analysis reveals the interplay between DNA sequence, methylation status, DNA geometry, and DNase I cleavage. Finally, we construct a model of transcription factor-DNA interaction that allows multiple transcription factors to bind co- operatively and competitively. In addition, the model can also infer transcription factor concentration.

As the binding preferences of transcription factors continue to be characterized with a high degree of precision, we anticipate that use of these more realistic models will become more prevalent.