Investigating Molecular Mechanisms of Transcription

Investigating the molecular basis for activation and short-range repression in eukaryotic organisms through quantitative modeling approaches

modeling
 
In the field of gene regulation, the most popular static model of transcriptional regulation for incorporating DNA level information is a thermodynamic-based (or fractional occupancy) model. Thermodynamic models can be used to predict quantitative levels of gene expression given the DNA sequence and concentration gradients of the transcription factors (TFs) involved in regulation. They do this using techniques derived from statistical physics which involve computing all possible states of TFs binding to a cis-regulatory module (CRM) and relating these states to gene expression.We are currently applying thermodynamic models of gene regulation to synthetic CRMs designed to investigate the binding strength of specific TFs and the role of certain TF interactions, such as quenching and competition, on short-range repression during early Drosophila development. The use of synthetic constructs with a small number of binding sites decreases the complexity of TF interactions, thus increasing parameter identifiability and model reproducibility.This will allow us to fit the model, with a high level of confidence, to quantitative expression data obtained from in situ hybridization of reporter genes under the control of these synthetic CRMs, and begin to uncover the nature of TF-induced regulation of gene expression.