An Interaction-Dependent Model for Transcription Factor Binding

Transcriptional regulation is accomplished by several transcription factor proteins that bind to specific DNA elements in the relative vicinity of the gene, and interact with each other and with Polymerase enzyme. Thus the determination of transcription factor-DNA binding is an important step toward understanding transcriptional regulation. An effective way to experimentally determine the genomic regions bound by a transcription factor is by a ChIP-onchip assay. Then, given the putative genomic regions, computational motif finding algorithms are applied to estimate the DNA binding motif or positional weight matrix for the TF. The a priori expectation is that the presence or absence of the estimated motif in a promoter should be a good indicator of the binding of the TF to that promoter. This association between the presence of the transcription factor motif and its binding is however weak in a majority of cases where the whole genome ChIP experiments have been performed. One possible r...

• Type: Conference
• Year: 2005
• Where: RECOMB
• Authors: Li-San Wang, Shane T. Jensen, Sridhar Hannenhalli
• Keywords: Computational Biology, Positional Weight Matrix, RECOMB 2005, Transcription Factor, Transcriptional Regulation