Dr. Prokop got his start in studying SRY and how the gene duplicated on the rat Y-chromosome. From then on, he has maintaned an interested in transcriptional control in hopes of developing better tools for characterizing noncoding variants.
Transcription Factor Structure Database
The largest undertaking by the lab is to take ENCODE ChIP-Seq datasets and build the binding into structural models. Below represents the breakdown of models generated.
Transcription Factor Dynamics Database
With the structures we then run molecular dynamic simulations to begin developing a systematic knowledge of molecular DNA contact.
DNA Methylation Changes to binding
Further we can study how changes to DNA states alter the transcription factor interactions.
Understand difficult TFs binding in cells
Finally, working with ENCODE we are using CETCh-Seq in iPSCs and NPCs to tag factors and do ChIP-Seq in differentiated cells. The binding sites are compared to ENCODE generated ChIP-Seq to impute further transcriptional mechanisms.