Exploring transcription factor interactions using cell-free genomics

Transcription factors (TF) need to identify their physiological targets from a large pool of similar but ultimately nonfunctional sites. Additionally, they need to compete with nucleosomes and other TFs for their binding sites on DNA. We employ a genome-wide in vitro chromatin reconstitution system based on pre-blastoderm embryonal extracts (DREX) to understand the fundamental principles of TF cooperativity and binding site selection in a tightly controlled cell-free system. As a model we are using the components of the Drosophila Dosage Compensation complex (DCC). The binding sites of MSL2, the DNA binding subunit of the DCC, are known. However, the mechanisms by which they are chosen remain unresolved. By titration of additional factors and competitors we were able to establish certain DNA-shape features that help to exclude other factors from MSL2`s physiological binding sites aiding in complex targeting. Additionally, we used the DREX system to illustrate how certain TFs can interact with nucleosomes and position them to distinct positions around their binding sites.

Bio:
Nikolas obtained his Bachelor's and Masters's degree in Biochemsitry from the University of Tuebingen. He then obtained a PhD in Peter B. Beckers lab at the Ludwig-Maximilians-University in Munich, where he assayed the targeting of transcription factors to chromatin using an in vitro chromatin reconstitution system. Nikolas is now working as a Post-Doc in Peter B. Beckers lab, again working on transcription factor targeting, nucleosome interaction and other chromatin related topics.