Eustermann Group

Exploring the chromatin landscape by cryo-electron microscopy

The Eustermann group explores the molecular landscape of chromatin to understand at an atomic level the principles underlying expression and maintenance of genomic information in eukaryotes.

Inside the nucleus of a eukaryotic cell, genomic DNA, proteins and RNA are packaged into a highly condensed, supra-molecular assembly known as chromatin. Given its fundamental role in the control of gene expression and genome maintenance, we are interested in the molecular machinery that actively reconfigures the composition and 3D architecture of chromatin.

The nucleosome is the basic subunit of chromatin, comprising approximately 147 bp of DNA wrapped around a histone octamer. Since its discovery and first structural analysis, fascinating insights into chromatin have been derived from advances in DNA sequencing-based mapping and light microscopy imaging. The genome of a typical human cell, for example, is tightly packed with an estimated 22 million nucleosomes. Coordinated changes in their organisation regulate access to the genetic information and have thus been proposed to control gene expression, by which cells differentiate and maintain their identity. Aberrant nucleosome organisation is closely linked to human diseases such as cancer.

Previous and current research

How the tertiary fold and structural dynamics of chromatin underlies its fundamental function remains largely unexplored at a molecular level, even in light of progress in the post-genomic era. Atomic structures have started to emerge that show interactions between individual chromatin factors and parts of the transcriptional machinery. However, the cooperative interplay of such factors in concert with the precise 3D-packing arrangement of nucleosomes, across the vast sequence space of the genome, presents an outstanding challenge for modern structural molecular biology. Our research tackles this challenge by developing system-based approaches to reconstitute the chromosomal landscape in order to visualise its atomic structure and dynamics by advanced methods in cryo-electron microscopy (cryo-EM).

Recently, we determined by single-particle cryo-EM the first high-resolution structure of a multi-subunit ATP-dependent chromatin remodeller and revealed unifying principles by which these enigmatic, megadalton molecular machines govern the genomic position and composition of nucleosomes. In a close collaboration with the Korber group (LMU Munich), we are currently exploiting this remarkable activity to establish whole genome reconstitutions. Rebuilding the chromosomal landscape, including hallmark features around gene promoter regions, enables us to directly probe the principles by which its tertiary structure is generated and reconfigured for transcriptional control, while also providing a powerful approach towards structural studies of the underlying mechanism.

Future projects and goals

  • Integrating cryo-EM methods and system-based reconstitution approaches to elucidate the compositional and structural complexity of chromatin hallmark regions.
  • Developing cryo-EM sample preparation and single particle image analysis to characterise the structural dynamics by which macromolecular machines reconfigure chromatin.
  • Identifying allosteric networks within the tertiary structure of chromatin, and associated factors by which transcriptional control is epigenetically encoded.
Video: Atomic model of the multi-subunit chromatin remodeller INO80 in complex with a nucleosomal substrate (based on Eustermann et al., Nature, 2018 & Knoll et al., Nature SMB, 2018).
Pioneering electron micrograph of a chromatin preparation. Credit: From Olins AL, Olins DE. Spheroid chromatin units (v bodies). Science. 1974;183(4122):330-2. Reproduced with permission from AAAS (This image is subject to copyright restrictions*).

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Artistic view of non-canonical nucleosome remodeling. Our structural and biochemical study of the hexasome-INO80 complex revealed the underlying mechanism (Zhang et al. Science 2023). Image credit: Luis Hauptmann (EMBL Eustermann Group)
Artistic view of condensin folding DNA into loops to build a mitotic chromosome. In collaboration with the Häring group we determined the cryoEM structure 
of DNA-bound structure condensin revealing intriguing insights into the underlying mechanism of DNA loop extrusion (Shaltiel et al. Science 2022). Image credit: Illustratoren.de/TobiasWuestefeld 
We are part of multi-lab collaboration headed by the Papp Team (Robotics and Automation, EMBL Grenoble ) developing cryoEM sample preparation technologies for advanced applications.