Figure 1: Interaction between the Polycomb group protein Sfmbt 4MBT domain and the Pho spacer region (Alfieri et al., 2013).

Figure 1: Interaction between the Polycomb group protein Sfmbt 4MBT domain and the Pho spacer region (Alfieri et al., 2013).

Figure 2: 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).

Figure 2: 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

We study how sequence-specific transcription factors assemble on DNA and how they interact with co-activators and general transcription factors to recruit RNA polymerases to the transcription start site. We also study the overall structure, architecture and inner-working 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. We study the molecular architecture of chromatin modifying complexes – i.e.: Polycomb group (PcG) protein complexes, how they are recruited, interact with nucleosome, and 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. We are studying the overall architecture of the Pol I and Pol III enzymes and of their pre-initiation machineries using a broad and interdisciplinary approach, combining integrated structural biology with in vitro and in vivo functional analysis. Ultimately, we would like to understand what features make Pol I and Pol III particularly suitable to fulfil their respective tasks.

Elongator

The 6-subunit Elongator complex is involved in the specific modification of uridines at the wobble base position of tRNAs. Our group recently solved the structure of the Elp456 subcomplex: a ring-like heterohexameric structure resembling hexameric RecA-like ATPases, as well as that of the Kti11/Kti13 heterodimer involved in the regulation of Elongator. We are now pursuing the structural and functional analysis of the entire Elongator complex.

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.
ERC ADVANCED INVESTIGATOR