Molecular mechanisms of transcriptional regulation in eukaryotes
Crystal structure of 14-subunit yeast RNA polymerase I. The background shows an electron micrograph of Miller chromatin spreads where nascent pre-rRNA transcripts form tree-like structures (Fernandez-Tornero et al., 2013).
The Müller group uses integrated structural biology, biophysical and biochemical approaches to learn about the molecular mechanisms of transcription regulation in eukaryotes, where DNA is packaged into chromatin.
Previous and current research
In the context of chromatin, we are interested how sequence-specific transcription factors assemble on DNA and how these factors interact with co-activators and general transcription factors to recruit RNA polymerases to the transcription start site. We are also studying the overall structure, architecture and inner workings of large molecular machines like RNA polymerases or chromatin modifying complexes involved in the transcription process. Finally, we would like to gain insight into how DNA sequence information and epigenetic modifications work together to regulate gene transcription.
To achieve these goals, we use structural information mainly obtained by X-ray crystallography and electron microscopy combined with other biophysical and biochemical approaches. Systems currently under investigation include multi-protein complexes involved in chromatin targeting, remodelling and histone modifications, yeast RNA polymerase I and III, and the Elongator complex.
Chromatin modifying complexes: The accessibility of chromatin in eukaryotes is regulated by ATP-dependent chromatin remodelling factors and histone modifying enzymes. Both classes of enzymes use similar domains like bromodomains, chromodomains, MBT domains, PHD fingers and SANT domains for the controlled access to defined genomic regions. We try to understand the molecular architecture of large chromatin modifying complexes, such as polycomb repressive complexes (PRCs), by which mechanisms they are recruited, how they interact with the nucleosome, and how their activities are regulated.
RNA polymerase I and III transcription: RNA polymerase I (Pol I) and III (Pol III) consist of 14 and 17 subunits, respectively. Whereas Pol I is responsible for the biosynthesis of ribosomal RNA, Pol III synthesises small RNAs like tRNA and 5S RNA. Misregulation of Pol I and Pol III has been associated with different types of cancer. Our research aims to understand the overall architecture of the Pol I and Pol III enzymes and the architecture of their pre-initiation machineries using a broad and interdisciplinary approach that combines integrated structural biology with in vitro and in vivo functional analysis.
Elongator: The 6-subunit Elongator complex was initially identified as a transcriptional regulator associated with elongating RNA polymerase II. However, recent results suggest that Elongator is involved in the specific modification of uridines at the wobble base position of tRNAs. Our group recently solved the Elp456 subcomplex that forms a ring-like heterohexameric structure resembling hexameric RecA-like ATPases. We are now pursuing the structural and functional analysis of the entire Elongator complex to gain further insight into its molecular function.
Future projects and goals
- Molecular insights into the recruitment of transcriptional regulators through the combination of DNA sequence-specific recognition and epigenetic modifications.
- Structural and functional analysis of macromolecular machines involved in transcription regulation, chromatin remodelling and chromatin modification.
- Contributing to a better mechanistic understanding of eukaryotic transcription and epigenetics using integrated structural biology combined with biochemical and cell biology approaches.