Mechanism of transcription repression by the Polycomb complex PRC1

Project Description: Single molecule analysis of transcription repression by PRC1.

Polycomb Group proteins have essential developmental functions in maintaining gene repression through chromatin based mechanisms. Polycomb proteins assemble into multiprotein complexes (PRC1 and PRC2), both of which modify chromatin. PRC1 is also directly implicated in transcription repression. Despite decades of study, we still do not know how PRC1 prevents transcription by RNA Polymerase II—which step(s) does it act on, and through which mechanism(s)? Two models for repression are: A) PRC1 OR transcription, in which genes exist in two states—OFF, with PRC1 bound and chromatin altered, and ON, in which PRC1/chromatin modifications are absent. The degree of repression is determined by how long the gene spends in each state, but in the ON state, transcription parameters are unaffected by PRC1. B) PRC1 AND transcription, in which cPRC1/chromatin modifications co-occur with the transcription machinery and impair its action, resulting in altered transcription parameters. A mixture of two states (OR) vs. intermediate states (AND) cannot be distinguished in bulk, steady-state measurements but they have distinct underlying biochemical and kinetic mechanisms at the level of individual transcription events and single molecules. To understand how cPRC1 affects transcription bursting and to relate this kinetic control to molecular states, we will analyze transcription, chromatin organization and factor binding at the single molecule level. We will use live imaging of transcription reporters (using the MS2 system) and single molecule FISH of endogenous genes to determine how PRC1 affects transcription in Drosophila cells. To relate kinetic parameters to molecular events, we will use DNA methylation based single molecule footprinting coupled to long read sequencing. We will finally develop a mathematical model integrating kinetic and molecular promoter states to define transcription repression by PRC1. This project will be conducted in collaboration with the lab of Daniel Zenklusen at l’Université de Montréal.

Your profile

We are open to candidates with different experience, and to adapting training and projects to the student. We encourage you to apply if you have:

• A degree (MSc level) in biochemistry, biophysics or related discipline, or in chemistry, engineering, physics or related fields with a strong interest in learning biology
• An interest in and/or experience with quantitative approaches
• A high level of motivation and curiosity
• A collaborative nature and ability to work independently and in a team

What we offer:

• A chance to work at the IRCM, a diverse internationally recognized research institute affiliated with the University of Montreal
• A chance to live in Montreal, a vibrant, cosmopolitan city with a thriving research and cultural environment
• An opportunity to work in a bilingual environment—we are a French-speaking institute, but interactions in the Francis lab occur mainly in English
• The chance to work labs that values diversity, technical skill, intellectual engagement, collaboration and curiosity, and is committed to scientific excellence and personal development of all members
• The chance to work across disciplines and integrate cutting edge genomics methodologies and analysis as part of a small team, and to have co-supervision.

About the Francis lab:

Our lab is interested in epigenetic mechanisms, with a particular focus on transcription memory and how chromatin-based information is passed through the cell cycle. Some of our recent publications are below, and more information can be found on our website https://www.francis-lab-epigenetics.ca/:

1. Gemeinhardt, T.M.*, Regy, R.M.*, Phan, T.M.*, Pal, N., Sharma, J., Senkovich, O., Mendiola, A.J., Ledterman, H.J., Henrickson, A., Lopes, D., Kapoor, U., Bihani, A., SIhou, D., Kim, Y.C., Jeruzalmi, D., Demeler, B., Kim, C.A., Mittal, J.# & Francis, N.J.# (2025) A disordered linker in the Polycomb protein Polyhomeotic tunes phase separation and oligomerization. Molecular Cell 85: 2128-2146. https://doi.org/10.1016/j.molcel.2025.05.008
2. Seif, E., Kang, J.J., Sasseville, C., Senkovich, O., Kaltashov, A., Boulier, E.L., Kapur, I., Kim, C.A., and Francis, N.J. (2020) Phase separation by the Sterile Alpha Motif of Polyhomeotic compartmentalizes Polycomb Group proteins and enhances their activity. Nat Commun 11, 5609. https://rdcu.be/b9L1P
3. Alecki, C., Chiwara, V., Sanz, L. A., Grau, D., Pérez, O. A., Boulier, E. L., Armache, K.-J., Chédin, F., & Francis, N. J. (2020). RNA-DNA strand exchange by the Drosophila Polycomb complex PRC2. Nature Commun., 11(1), 1–14. https://rdcu.be/b3y5P

About the Zenklusen lab:

The Zenklusen lab (zenklusenlab.org) studies how gene expression is regulated at the level of individual molecules, from transcription and RNA processing to mRNA packaging and nuclear export. We develop and apply quantitative single-molecule approaches, including single-molecule FISH, MS2/PP7 live-cell imaging of transcription, and single-particle tracking, and combine them with mathematical modeling to extract kinetic information from individual cells.

1. Bensidoun, P., Reiter, T., Montpetit, B., Zenklusen, D.# & Oeffinger, M.# (2022) Nuclear mRNA metabolism drives selective basket assembly on a subset of nuclear pore complexes in budding yeast. Molecular Cell 82: 3856-3871. https://doi.org/10.1016/j.molcel.2022.09.019
2. Adivarahan, S., Livingston, N., Nicholson, B., Rahman, S., Wu, B., Rissland, O.S. & Zenklusen, D. (2018) Spatial organization of single mRNPs at different stages of the gene expression pathway. Molecular Cell 72: 727-738. https://doi.org/10.1016/j.molcel.2018.10.010
3. Rahman, S., Zorca, C.E., Traboulsi, T., Noutahi, E., Krause, M.R., Mader, S. & Zenklusen, D. (2017) Single-cell profiling reveals that eRNA accumulation at enhancer-promoter loops is not required to sustain transcription. Nucleic Acids Research 45: 3017-3030. https://doi.org/10.1093/nar/gkw1220
4. Zenklusen, D., Larson, D.R. & Singer, R.H. (2008) Single-RNA counting reveals alternative modes of gene expression in yeast. Nature Structural & Molecular Biology 15: 1263-1271. https://doi.org/10.1038/nsmb.1514

To apply: Please send your CV and cover letter to nicole.francis@ircm.qc.ca. 3 letters of recommendation will be requested if your application is pursued.