Looking for a motivated student holding a Master degree in Genetics, Molecular & Cellular Biology, or Biochemistry to start next fall. Skills in genomics and/or bioinformatics are an asset. Position is open until filled.
Project:
Transcription involves the coordinated activities of a multitude of regulatory factors. An important class of regulators has chromatin-modifying or –remodeling activities and function as co-activators during transcription initiation. Co-activators are typically multifunctional complexes that integrate regulatory information from promoter elements, transcription factors, and chromatin marks. Despite the advent of functional genomics, understanding how these factors establish specific gene expression programs remains challenging, likely because our view of their function is static. Here we propose a systems biology approach combining kinetic analyses, innovative transcriptomic approaches, and computational modelling to address this issue. The PhD student will measure the effects of co-activators on the temporal dynamics of transcription, nucleosome modifications, and general transcription factor assembly, allowing the ordering of mechanistic events. In collaboration with a team of physicists in Strasbourg, we will integrate these data into a stochastic biophysical model of transcription regulation by co-activators, which predictions will be tested experimentally. Overall, we expect this PhD project to make an important contribution in the transcription field, by identifying the principles governing the gene-specific effects of co-activators and better understanding how these properties sustain both robustness and plasticity of gene expression in response to perturbations.
This project will be performed in close collaboration with another PhD student in biophysics/statistics who will start around the same time in the group of Nacho Molina at IGBMC (Strasbourg ,France).
Keywords: Transcription, Chromatin, Systems Biology, Functional Genomics.
References:
Fischer V et al. Transcription (2019) 1:29-36.
Helmlinger D & Tora L TiBS (2017) 42:850-61.
Helmlinger D et al. The EMBO J. (2011) 30:2843-52.
Timmers HTM & Tora L Mol. Cell (2018) 72:10-7.
Baptista T et al. Mol. Cell (2017) 68:130-43.
Elias-Villalobos A et al., Nat. Commun. 10(1):5237.
Suter D*, Molina N* et al., Science (2011) 332:472-4.
Molina N*, Suter D* et al., PNAS (2013) 110:20563-8.
Mentoring:
Weekly one-on-one meetings with myself and co-supervisor (Peggy Raynaud). Monthly presentation at group labmeeting. Yearly internal seminar at CRBM and CBS2 meeting. Yearly thesis committee. Writing peer-reviewed publications. Presentation at international conferences.