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3D genome folding and its role in DNA-based processes

   Molecular and Cell Biology

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  Prof D Panne, Prof Peijun Zhang, Dr T Schalch  Applications accepted all year round  Self-Funded PhD Students Only

About the Project

The organization of genomic DNA into chromatin fibres and nucleosomes and their regulation by histone modifications is well understood, as is the relevance of these mechanisms for gene regulation. However, chromatin fibres also fold over large distances, often spanning hundreds of kilo-base pairs of DNA. Recent chromosome capture experiments, imaging data and genetic perturbation has led to the identification of two major mechanisms that are behind such large-scale chromosome organisation: (1) at shorter genomic distances, genomes are organized into topologically associating domains (TADs) which arise through the process of loop extrusion by complexes such as cohesin; (2) at longer-range genomic distances, genomes are spatially compartmentalized into active, euchromatic and inactive, heterochromatic regions. In this project we address these two key aspects of chromosome folding.

(1) Current models suggest that the formation of TADs occurs through a process called ‘loop extrusion’. This process is carried out by SMC ATPases including cohesin that are conserved across all domains of life. By reeling genomic DNA into loops, cohesin brings distant loci into proximity, and hereby plays important structural and regulatory roles in processes such as replication, transcription, recombination and repair. Cohesin also holds together sister DNAs to enable faithful chromosome segregation. How cohesin can control all these different chromosomal processes remains mysterious.

(2) We also aim to understand the molecular mechanism driving longer-range genome compartmentalization. Heterochromatic regions typically contain methylated histone while euchromatic and transcriptionally active regions are typically enriched for acetylation. One hypothesis is that this compartmentalisation is driven by condensation reactions of proteins that specifically associate with inactive and active chromatin. One model is that the key driver event that shapes both eu-and heterochromatic genome organization both locally and globally is actually active transcription.

It is important to understand these key control processes as their dysregulation is invariably associated with cancer. We will use a multi-disciplinary approach that includes preparative biochemistry of multi-protein complexes and determine the underlying molecular mechanism using structural biology (cryoEM/Xray) and biochemical methods. We work in a highly collegial environment at the Leicester Institute of Structural and Chemical Biology and have excellent access to state-of-the-art structural biology technologies.

To visualise the impact on chromosome conformation in cells we will use our cryoFIB-SEM pipeline in collaboration with Peijun Zhang (Oxford University). These methods will allow us to study the impact on large-scale chromosomal features at supra-molecular detail. The project will provide fundamental insights into the mechanisms that control chromosome structure in cells. We anticipate that our work may also provide insights into the aetiology of human disorders such as cancer caused by dysregulation of large-scale genome architecture. A molecular understanding of the underlying processes opens up the opportunity to develop new drug targeting approaches.

This project will lead to a PhD in Biochemistry.


1. Li Y., Haarhuis J., Cacciatore A.S., Willems L., TeunissenH., Muir K.W., de Wit E., Rowland, B.D. & Panne D. Nature (2020)
2. Muir K.W., Li Y., Weiss F., Panne D. (2020) The structure of the cohesin ATPase elucidates the mechanism of SMC-kleisin ring opening. Nature Struct Mol Biol 27: 233-239.
3. Ortega E., Rengachari S., Ibrahim Z., Hoghoughi N., Gaucher J., Holehouse A.S., Khochbin S., Panne D. (2018) Transcription factor dimerization activates the p300 acetyltransferase. Nature 562: 538–544.
4. Li Y., Muir K.W., Bowler M.W., Metz J., Haering C.H., Panne D. (2018) Structural basis for Scc3-dependent cohesin recruitment to chromatin eLife 7: e38356
5. Rengachari S., Groiss S., Devos J., Caron E., Grandvaux N., Panne D. (2018) Structural Basis of STAT2 Recognition by IRF9 Reveals Molecular Insights Into ISGF3 Function. PNAS; 115 (4) E601-E609 doi: 10.1073/pnas.1718426115
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