Molecular mechanisms of transcriptional regulation in eukaryotes
Elongator subunits Elp4 (green), Elp5 (blue) and Elp6 (green) form a ring-like structure resembling hexameric RecA-like ATPases that specifically binds tRNA (Glatt et al., 2012).
The Müller group uses 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 overall structure, architecture and inner-working of large molecular machines, such as RNA polymerases or chromatin modifying complexes, involved in transcription. We would also 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 obtained by X-ray crystallography and electron microscopy combined with other biophysical and biochemical approaches. Systems currently under investigation include transcription factor/DNA complexes, yeast RNA polymerase III, Elongator, and multi-protein complexes involved in chromatin targeting, remodelling and histone modifications.
RNA polymerase III transcription: RNA polymerase III (Pol III) consists of 17 subunits and is responsible for the transcription of small RNAs, such as tRNA and 5S RNA. Recruitment of the enzyme requires binding of the general transcription factor TFIIIC (composed of six subunits) to internal promoter sites, followed by the binding of TFIIIB (composed of three subunits). We aim to understand the overall architecture of the Pol III pre-initiation complex and the interaction between Pol III, TFIIIB and TFIIIC during Pol III recruitment, transcriptional elongation and termination.
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 analysis of the entire Elongator complex to gain further insight into its function.
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 chromatin modifying and remodelling complexes, by which mechanisms they are recruited, how they interact with nucleosomes and larger chromatin templates, and how their activities are regulated.
Future projects and goals
- Gaining molecular insights into the recruitment of transcriptional regulators through DNA sequence-specific recognition and epigenetic modifications.
- Structural and functional analysis of macromolecular machines involved in transcription regulation and chromatin remodelling and modification.
- Contributing to a better mechanistic understanding of eukaryotic transcription and epigenetics using integrated structural biology combined with biochemical and cell biology approaches.