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Quail Group

Principles of genome self-organisation

At EMBL from November 2022.

The Quail group investigates the physical and biochemical principles of genome self-organisation.

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The Quail group investigates the physical and biochemical principles of genome self-organisation.

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Previous and current research

How the cell organises its contents represents a remarkable example of collective behaviour in which thousands of factors — such as proteins, nucleic acids, and lipids — self-organise to compartmentalise biochemical reactions, build intracellular structures, and perform mechanical work. One striking example of collective behaviour in the cell is the organisation of the genome. In every eukaryotic cell, two meters of DNA are packaged into the cell nucleus, a subcellular organelle with a diameter of roughly 5-10 μm. Proteins drive this process, generating forces that compartmentalise the genome into nucleosomal arrays, topologically associated domains, chromatin domains, and chromosomal territories. Genetic, proteomic, and structural studies have revealed the identity of many of these force-generating proteins, and techniques such as chromosome conformation capture have generated static pictures that have demonstrated the genome’s non-random organisation. However, how these proteins work collectively together to coordinate this organisation remains unclear and raises many questions. What physical mechanisms drive genome organisation? How does the biochemistry of individual factors regulate this organisation? How do these physical mechanisms regulate processes in the nucleus such as transcription, DNA damage repair, and DNA replication?

To address these questions, we adopt a broad, interdisciplinary, and quantitative approach, combining in vitro biochemistry, quantitative microscopy, single-molecule biophysics, Xenopus egg extracts, and theory. We focus on how the condensation of proteins can generate forces that bridge distally located DNA (Quail et al., 2021) and how these condensates compete with energy-consuming motors that drive genome organisation (Golfier et al., 2020). To make progress on these problems, we directly image how proteins drive genome organisation at different length scales (from single molecules to intact nuclei), extract quantitative data from these experiments, and then develop theoretical models that generate testable experimental predictions.

Future projects and goals

We have just started understanding how proteins drive genome self-organisation across different length scales and have many open research goals and directions.  

  • Obtaining a quantitative picture of how protein condensation drives genome organisation in intact nuclei and dissecting how this regulates diverse processes such as transcription, DNA damage repair, and DNA replication. 
  • Dissecting the physical interplay between protein condensation and energy-consuming motors that extrude DNA loops in physiological contexts.
  • Understanding how single molecules navigate chemically distinct environments in the nucleus and how this controls protein search dynamics. 
  • Developing methods to measure the material properties of physiological chromatin and investigating how protein activity governs the nature of the material.

We are an inclusive and curiosity-driven lab, tackling the problem of genome self-organisation using a wide range of backgrounds, tools, and expertise that span biochemistry, cell biology, and physics. We foster an open lab environment focused on scientific exploration and growth. New ideas, approaches, model systems, and interdisciplinarity in any form is encouraged — reach out if you are interested in joining!

Assemblies of the transcription factor FoxA1
Figure 1: Top: Assemblies of the transcription factor FoxA1 condense single molecules of DNA in a mechanosensitive fashion. Scale bar, 2 μm. Bottom: The key physical ingredients that drive protein-DNA co-condensation. Adapted from Quail et al. (2021).
Video 1: Dynamics of the transcription factor FoxA1 in a pair of nuclei reconstituted in Xenopus egg extracts. Scale bar, 5 μm.
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