Pöpsel, Simon - JRG 11

About

We are interested in the molecular mechanisms that orchestrate gene expression, cellular differentiation and many other processes, on the level of chromatin, the physical and functional state of eukaryotic genomes. Our biochemical understanding of the multi-protein complexes that regulate chromatin structure and function is still limited. Therefore, we aim to define aspects of their context dependent, local activity regulation using an integrative structural biology approach of single-particle cryo-electron microscopy (cryo-EM), cross-linking mass spectrometry (XL-MS) and molecular modelling, complemented by biochemical and cell biological methods.

Introduction

The many different cell types of our bodies share essentially the same genetic information, yet they differ dramatically in shape, behavior and function. A fundamental basis of these differences are the sets of genes that are transcribed (active) or repressed (inactive). Importantly, gene expression patterns, once set, can be passed on to daughter cells, thus allowing for stable cell identities within tissues and organs.

Transcriptional activity and many other DNA associated processes are controlled through mechanisms that affect the chromatin structure. Histone proteins form the core of nucleosomes, the basic structural and functional unit of chromatin. Nucleosomes facilitate DNA compaction and organization, but are also essential hubs for transcriptional regulation. For example, histone proteins are chemically changed by enzymes that reside in chromatin modifying complexes. As a result, histone that carry such chemical modifications serve as recognition sites for regulatory factors that mediate, for example, transcriptional activation or repression. Transcription factors that recognize specific DNA sequences in the genome rely on their interactions with chromatin regulator complexes to fulfill their function and are therefore also dependent on chromatin-based mechanisms. 

In cancer, chromatin modifiers are frequently dysfunctional because of mutations, chromosomal fusions or changes of their abundance, leading to a loss of transcriptional control and, consequently, pathological cellular phenotypes such as uncontrolled proliferation and tissue invasion. 

In order to understand the function of chromatin regulator complexes in health and disease, we identify the molecular mechanisms that guide them to their targets within the genome and locally regulate their dynamic interactions and enzymatic activities. With such knowledge, we hope to better understand mechanisms of chromatin regulation and how the dysfunction of chromatin regulator complexes contributes to disease processes.

Structure and Regulation of Human Histone Methyltransferase and Demethylase Complexes

Histone methyltransferases (HMTases) and demethylases are enzymes that attach and remove methyl groups from lysine or arginine residues. Like all chromatin modifying enzymes, they are typically active as parts of multi-protein complexes. Subunits of these complexes engage in dynamic interactions with other regulatory factors to recognize and respond to distinct features of their local chromatin environment.

In our group, we isolate native chromatin modifying complexes from cultured human cells or reconstitute defined protein complexes and their chromatin substrates from recombinant sources. We are using a variety of cell biological, biochemistry and integrative structural biology approaches to unravel the mechanisms that control the assembly and function of chromatin regulator complexes. As important methods, we use single-particle cryo-electron microscopy (cryo-EM) and cross-linking mass spectrometry (XL-MS) to visualize the three-dimensional structure of these molecular assemblies. With the help of biochemical and biophysical assays, we monitor the interactions, stability and activity of the investigated complexes to derive conclusions regarding the functional implications of our structural insights. 

For example, we are studying how the human histone methyltransferase complex Polycomb Repressive Complex 2 (PRC2) engages with regulatory or substrate chromatin elements to control its catalytic activity. We have discovered a dimeric state of PRC2 while bound to a substrate nucleosome that enables an allosteric activation of one PRC2 complex by its interaction partner within the dimer. Interestingly, this stimulatory dimer is dependent on the auto-methylation of EZH2, the catalytically active subunit of PRC2.