Patrick Heun

Wellcome Senior Research Fellow

Patrick Heun is a senior researcher at the Wellcome Centre for Cell Biology, University of Edinburgh. His group is studying the epigenetic inheritance and organisation of centromeres using cultured Drosophila and human cells as a model. This involves the general tools of molecular biology combined with biochemistry and microscopy. Patrick Heun obtained his Ph.D. at the University of Lausanne in the laboratory of Susan Gasser. In 2001, he moved to the Salk Institute, San Diego followed by the Lawrence Berkeley National labs as a postdoctoral fellow with Gary Karpen. In 2005, he started his own lab as a junior group leader at the Max-Planck Institute for Immunobiology and Epigenetics in Freiburg, Germany and moved to the University of Edinburgh as a Wellcome Senior Research Fellow in 2014.

Lab members

Mathilde Fabe, Meena Krishnan, Alessandro Stirpe, George Yankson, Hwei Ling Tan

Establishment and maintenance of chromatin identity

Our lab is interested in the organisation, establishment, and maintenance of specialised chromatin states. Epigenetic transmission of centromere identity through many cell generations is required for proper centromere function and when perturbed can lead to genome instability and cellular malfunction. We use Drosophila and human tissue culture cells as model organisms to address the following questions:

What is the role of transcription at the centromere?

Loading of CENP-A at the centromere occurs outside of S-phase and requires the removal of H3 “placeholder" nucleosomes. Transcription at centromeres has been linked to the deposition of new CENP-A, although the molecular mechanism is not understood. Using fast acting transcriptional inhibitors in combination with a newly developed CENP-A loading system, we demonstrate that centromeric transcription is required for loading of new dCENP-A by removing placeholder nucleosomes and promoting dCENP-A transition from chromatin association to nucleosome incorporation (Bobkov et al., 2020). Unlike placeholder nucleosomes, previously deposited CENP-A is specifically retained by Spt6 both in human and Drosophila cells, identifying Spt6 as a CENP-A maintenance factor that ensures the stability of epigenetic centromere identity (Figure 1). We are currently investigating the molecular mechanism how some histones like CENP-A are maintained while others like H3.3 placeholders are evicted to preserve epigenetic centromere identity.

How is the centromeric chromatin fiber organised?

To map centromere proteins on the linear centromeric chromatin fiber, we have recently developed a novel approach where proteins-of-interest fused to Biotin ligases or DNA methyltransferases leave a “footprint” on the underlying nucleosomes through proximity-labelling. With this methodology we have described novel localization patterns of a subset of centromere proteins at human centromeres (Kyriacou and Heun, 2018). We are extending this approach to proteins localising to all layers of the centromere using different technologies like stretched chromatin fibers and long read-DNA sequencing.

How does Su(var)2-10/PIAS contribute to heterochromatin organisation?

The Su(var)2-10 gene has been originally identified in position-effect-variegation (PEV) assays designed to uncover proteins involved in heterochromatin formation. Cloning of the gene revealed its homology to the protein family SUMO E3-ligase PIAS (Protein Inhibitor of activated STAT), but how sumoylation promotes heterochromatin formation remains unknown. While PIAS does not localise to pericentric heterochromatin in somatic cells, it is enriched next to centromeres in early fly embryogenesis, suggesting a role in heterochromatin establishment (Figure 2). We are specifically depleting PIAS at this point of development to shed light on the link between PIAS’ SUMO targets and chromatin organisation.

Selected publications:

Bobkov, G.O.M., Huang, A., van den Berg, S.J.W., Mitra, S., Anselm, E., Lazou, V., Schunter, S., Feederle, R., Imhof, A., Lusser, A., et al. (2020). Spt6 is a maintenance factor for centromeric CENP-A. Nature communications 11, 2919.

Logsdon, G.A., Gambogi, C.W., Liskovykh, M.A., Barrey, E.J., Larionov, V., Miga, K.H., Heun, P., and Black, B.E. (2019). Human Artificial Chromosomes that Bypass Centromeric DNA. Cell 178, 624-639 e619. PMC6657561

Roure, V., Medina-Pritchard, B., Lazou, V., Rago, L., Anselm, E., Venegas, D., Jeyaprakash, A.A., and Heun, P. (2019). Reconstituting Drosophila Centromere Identity in Human Cells. Cell Rep 29, 464-479 e465.
 

Figure 1. Model for the role of transcription at centromeres: Transcription remodels centromere chromatin and evicts H3-nucleosomes (green) to allow new CENP-A (orange) loading. Evicted old CENP-A (red) is maintained by the transcription elongation factor Spt6. 
Figure 2. The SUMO E3 Ligase PIAS is required for heterochromatin formation. 
A. Embryonic cycle 1-14 (image William Sullivan)
B. Fixed cycle 13 embryos showing αPIAS and heterochromatin marker αH3K9me3 in apical heterochromatin in wildtype and PIAS RNAi.   
C. Proposed role of PIAS in chromosome organisation.