Oral Presentation 47th Lorne Genome Conference 2026

Polycomb-based epigenetic memory underlies the irreversibility of p16-mediated cell cycle exit (133344)

Hongpei Li 1 2 , Gabriela Santos-Rodriguez 3 4 , Selene Fernandez-Valverde Fernandez-Valverde 3 4 , Scott Berry 1 2 3
  1. EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney, NSW, Australia
  2. School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
  3. UNSW RNA Institute, University of New South Wales, Sydney, NSW, Australia
  4. School of Biotechnology & Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia

Polycomb repressive complexes (PRCs) are multiprotein assemblies that maintain epigenetic memory of gene silencing in mammals. PRC2 establishes and maintains epigenetic memory at target gene loci, which may reinforce cell fate decisions. However, the role of PRC2-mediated memory in establishing irreversible cell fate outcomes remains unclear. Here, we use PRC2 inhibitor-washout experiments and RNA sequencing in human cells to identify genes that exhibit memory: loss of silencing that is stably maintained after transient perturbation. We find that 23 % of PRC2 targets show such memory in keratinocytes, but not in pluripotent cells – in agreement with literature indicating that memory function of PRCs emerges during differentiation.

Among these memory genes in keratinocytes, we focus on p16INK4A, a tumour suppressor that blocks cell cycle progression and acts as a cellular safeguard against uncontrolled proliferation. We find that PRC2-dependent epigenetic memory is critical for irreversibility of cell cycle exit by generating bistable p16 expression states. In contrast, pharmacological CDK4/6 inhibition, which mimics p16 activity and blocks cell cycle progression, leads to only reversible arrest. Probing the dose- and time-dependence of p16 expression on PRC2-inhibition using quantitative immunofluorescence and single-molecule RNA fluorescence in situ hybridisation (smFISH), we further discover that p16 induction can be decoupled from irreversibility: while p16 can respond to low doses of inhibitor, irreversibility only becomes ‘locked-in’ after treatments that cross a certain dose- or time-threshold.

Through cell growth tracking, we find that PRC2 regulation of p16 is coupled to cell division dynamics, creating a self-reinforcing mechanism that stabilises irreversible cell fate decisions. Together, these findings demonstrate that irreversible tumour suppressor-mediated cell cycle exit requires crossing critical epigenetic thresholds, converting graded PRC2 inhibition into binary cell fate decisions maintained by epigenetic memory. This system buffers noise and provides a time window over which growth arrest signals can be integrated.