Tunable DNMT1 degradation reveals DNMT1/DNMT3B synergy in DNA methylation and genome organization

  • J Cell Biol. 2024 Apr 1;223(4):e202307026. doi: 10.1083/jcb.202307026.
Andrea Scelfo  1 ,  Viviana Barra  #  1  2 ,  Nezar Abdennur  #  3  4  5 ,  George Spracklin  #  4  5 ,  Florence Busato  6 ,  Catalina Salinas-Luypaert  1 ,  Elena Bonaiti  1 ,  Guillaume Velasco  7 ,  Frédéric Bonhomme  8 ,  Anna Chipont  9 ,  Andréa E Tijhuis  10 ,  Diana C J Spierings  10 ,  Coralie Guérin  9  11 ,  Paola Arimondo  8 ,  Claire Francastel  7 ,  Floris Foijer  10 ,  Jӧrg Tost  6 ,  Leonid Mirny  5  12 ,  Daniele Fachinetti  1
Affiliations
  • 1. Institut Curie, PSL Research University, Sorbonne Université, CNRS, UMR 144 , Paris, France.
  • 2. Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy.
  • 3. Program in Bioinformatics and Integrative Biology, UMass Chan Medical School , Worcester, MA, USA.
  • 4. Department of Systems Biology, UMass Chan Medical School, Worcester, MA, USA.
  • 5. Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology , Cambridge, MA, USA.
  • 6. Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Université Paris-Saclay , Evry, France.
  • 7. Université de Paris Cité, CNRS UMR 7216 , Paris, France.
  • 8. Epigenetic Chemical Biology, Institut Pasteur, CNRS UMR n°3523 Chem4Life, Université Paris Cité , Paris, France.
  • 9. Cytometry Platform, Institut Curie , Paris, France.
  • 10. European Research Institute for the Biology of Ageing, University Groningen, University Medical Center Groningen , Groningen, Netherlands.
  • 11. Université Paris Cité, INSERM , Paris, France.
  • 12. Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.
  • # Contributed equally.
PMID: 38376465 DOI: 10.1083/jcb.202307026
Abstract

DNA methylation (DNAme) is a key epigenetic MARK that regulates critical biological processes maintaining overall genome stability. Given its pleiotropic function, studies of DNAme dynamics are crucial, but currently available tools to interfere with DNAme have limitations and major cytotoxic side effects. Here, we present cell models that allow inducible and reversible DNAme modulation through DNMT1 depletion. By dynamically assessing whole genome and locus-specific effects of induced passive demethylation through cell divisions, we reveal a cooperative activity between DNMT1 and DNMT3B, but not of DNMT3A, to maintain and control DNAme. We show that gradual loss of DNAme is accompanied by progressive and reversible changes in heterochromatin, compartmentalization, and peripheral localization. DNA methylation loss coincides with a gradual reduction of cell fitness due to G1 arrest, with minor levels of mitotic failure. Altogether, this system allows DNMTs and DNA methylation studies with fine temporal resolution, which may help to reveal the etiologic link between DNAme dysfunction and human disease.

Products