Project (Christian Dienemann)
Structural biology of transcription regulation

We are investigating the molecular mechanisms and systemic principles of genome transcription and regulation using a combination of structural biology with functional genomics and bioinformatics in human cells (http://www.mpinat.mpg.de/cramer). We offer several exciting projects in these areas and will recruit highly motivated and talented PhD students with experimental or computational backgrounds. As part of the IMPRS-GS, our laboratory offers PhD projects in structural biology of gene transcription using cryo-electron microscopy (cryo-EM). Please find below additional information regarding our recent and ongoing work relating to the PhD projects.

Transcription by RNA polymerase II (Pol II) is regulated at many steps throughout the transcription cycle of a gene. We aim to understand the molecular mechanisms behind transcription regulation by reconstituting transcription complexes at different stages of the cycle in vitro, and determine their three-dimensional structures by cryo-EM. The processes of pre-initiation complex assembly, promoter-proximal Pol II pausing and transcription through a nucleosome are of particular interest as these steps are major regulatory events during gene transcription (1). In the future, we will further extend our research to investigate the interfaces of transcription with other processes in the nucleus such as DNA replication. To investigate transcription complexes at various stages, we purify all components of the human transcription machinery and reconstitute transcription in the test tube, either in a promoter-dependent manner or by extension of an existing RNA primer. Alternatively, we develop methods to purify endogenous transcription complexes from cells directly. These samples can then be used for structural and biochemical analyses.
A typical project may involve protein expression in bacteria and insect cells, protein purification by various chromatography methods as well as gradient-based complex preparation methods. Further, we use gel-based assays for monitoring RNA production by Pol II-containing transcription complexes and eventually cryo-electron microscopy and single-particle image analysis to determine atomic structures of transcription complexes. Therefore, a strong background in protein biochemistry and/or structural biology (X-ray crystallography or cryo-EM) is of advantage.

In our research group we also offer PhD projects in computational and systems biology:
https://www.uni-goettingen.de/de/application/558700.html





Homepage Research Group
http://www.mpinat.mpg.de/cramer



Publications:

1) Osman and Cramer. Structural Biology of RNA Polymerase II Transcription: 20 Years On. Annu Rev Cell Dev Biol. 2020

Full publication list: https://www.mpinat.mpg.de/635004/publications