Two important measures of the in vivo interaction of transcription factors with chromatin are the search time and the residence time. The former refers to the time it takes a factor to find its binding location, while the latter is the time the factor physically attaches to the chromatin. By quantifying the interaction dynamics of transcription factors, researchers hope to understand the role of these factors in basic cellular processes such as transcription and gene regulation. The RC team is working with collaborators from UVA and the NIH to understand the dynamics of the Gal4 protein in yeast. The project involves quantitatively analyzing ChIP-qPCR data, writing and running non-linear regression and statistical routines in Mathematica, and developing numerical simulations to determine the error bounds on the kinetic parameters.
PI: Stefan Bekiranov (Biochemistry and Molecular Genetics)