Integrative analysis of an essential epigenetic regulator – INTEGER
INTEGER: integrative analysis of a key epigenetic regulator
DNA methylation is set during development by "de novo" DNA methyltransferases that methylate both strands of previously unmethylated DNA. After this initial establishment the whole genome becomes hemi-methylated during each round of DNA replication, and it must be faithfully converted back to its fully methylated status before the next round of replication, or the mark is lost. Therefore, the mechanisms ensuring the faithful maintenance of DNA methylation following DNA replication are essential.
The broad question that we want to answer in this proposal is: "How is DNA methylation maintenance coupled to DNA replication?"
First, DNA replication is inherently asymmetrical, with different molecular machineries used on the leading and lagging strands. Our Aim 1 will ask: Are the mechanisms of DNA methylation maintenance symmetrical or asymmetrical on the two daughter chromatids? This basic question, which has important conceptual and practical consequences, is currently unresolved. Second, the recruitment and activity of the maintenance methyltransferase depends on the prior ubiquitylation of precise lysine residues in histone tails. Our Aim 2 will address what directs the precise ubiquitylation of histone tails that is critical for DNA methylation maintenance? Third, how are these molecular mechanisms integrated at the cellular level?
We combined stem cell biology, genomics, bioinformatics, and proteomics.
Outcome 1: Review published by all project partners.
Nataliya Petryk was a research scientist supported by the project. Together with the other partners, she wrote a review summarizing the state of the research, and possible research directions. More specifically, We explained that DNA methylation is crucial for development and cellular function. We discussed its role in regulating chromatin modifications, transcription, and splicing. We reviewed how DNA methylation is maintained during replication to prevent its loss. Recent discoveries on the mechanisms and fidelity of this process were highlighted. We also explored its regulation in normal development and misregulation in disease.
Ref : Petryk et al Nucleic Acids Res. 2021 Apr 6;49(6):3020-3032
Outcome 2: Organization of a Franco-German chromatin meeting.
The event we organized aimed to foster scientific interactions between the epigenetics research communities in Paris and Munich. While both communities are strong individually, they can benefit even more from shared knowledge and networks.
The event had two components: A workshop for PhD students and early-career postdocs, and a symposium, a traditional scientific meeting featuring oral presentations of varying lengths (keynote lectures for distinguished guests, standard talks, and short talks) as well as poster presentations. Registration was free and open internationally, with a total of 188 participants.
The website can be seen here:
www.sfb1064.med.uni-muenchen.de/events/paris_munich_epigenetics_2023/index.html
Outcome 3: Published paper associating all partners
Together we showed that UHRF1 plays a broader role in DNA methylation than just stimulating DNMT1. We demonstrated that UHRF1 depletion causes greater methylation loss than DNMT1 depletion, independent of passive demethylation. Our analyses revealed that UHRF1 also interacts with DNMT3A, DNMT3B, and inhibits TET2. These findings highlight UHRF1’s non-canonical functions in DNA methylation regulation. This study has important implications for epigenetics in health and disease.
Ref: Yamaguchi et al Nat Commun. 2024 Apr 5;15(1):2960.
Outcome 4: Paper published by Heinrich Leonhardt
Deis Haxholli was a PhD student supported by this grant. She carried out a successful collaboration with Japanese teams. Together, they showed that UHRF1-dependent DNA methylation is crucial for cell fate maintenance. They demonstrated that DPPA3 inhibits UHRF1 chromatin localization by interacting with its PHD domain. Using NMR, they revealed that DPPA3 forms induced α-helices upon binding, stabilizing the complex through unique interactions. Mutations disrupting this structure impaired UHRF1 binding and chromatin localization. Their findings provided structural insights into how DPPA3 regulates UHRF1 activity.
Ref: Hata et al Nucleic Acids Res. 2022 Nov 28;50(21):12527-12542
We published together 1 review article, 2 papers, and organized a Franco-German chromatin meeting, which will be followed by a return event. The scientific results are still being exploited in papers in preparation or in revision.
DNA methylation is an essential epigenetic mark in mammals. It is necessary for embryonic development, for cell differentiation, and its alteration is at the root of many hereditary or sporadic human diseases, ranging from neuro-degeneration, to immunodeficiency, and many cancers. To better prevent, diagnose, and treat these different diseases, it is necessary to come to a fine understanding of the molecular mechanisms that govern the methylation of mammalian DNA. Our project exists within this perspective.
Our starting point is a protein that is absolutely required for the methylation of DNA, but whose mode of operation is still imperfectly understood: UHRF1. In a collaboration between German, French, English and Japanese teams, we have recently achieved unexpected and important results regarding the function of this crucial molecular actor.
In the proposed project, we will use these recent results to test different hypotheses about the role of this protein in DNA methylation. To achieve this, we have assembled an international consortium of expert teams in complementary fields. One team in France will bring its expertise in molecular biology and genomics. Two teams in Germany will contribute their expertise in chromatin biochemistry, structural biology, genome editing, and stem cell biology. Together, we will perform biochemical investigations and experiments in custom mouse ES cell systems to clarify the function of UHRF1 and, more broadly, to better understand the mechanism of DNA methylation. These results will be communicated through oral presentations, scientific papers and publications, and will contribute to the national and international scientific community.
As an important part of the project, we will participate in university teaching, and we will also recruit junior researchers and provide them with quality scientific training, all of which will contribute positively to the attractiveness and competitiveness of the French and German social and economic systems. Finally, we will interact with the general public through dedicated events presenting our biological research to non-specialists.
Project coordination
Pierre-Antoine Defossez (Epigénétique et destin cellulaire)
The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.
Partnership
CNRS Epigénétique et destin cellulaire
HMGU / IFE Helmholtz Zentrum Munchen / Institute for Functional Epigenetics
LMU Ludwig-Maximilians University Munich
Help of the ANR 297,000 euros
Beginning and duration of the scientific project:
April 2020
- 36 Months
