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Chromatin Dynamics in Mammalian Development

MAXIM GREENBERG

DNA methylation is a stable epigenetic mark that is absolutely essential for proper mammalian development. In the Greenberg lab, the primary focus is understanding the various mechanisms and functions of DNA methylation in the context of development. We take a multidisciplinary approach, utilizing genetics, genomics, and biochemistry. We also strive to comprehend how DNA methylation interacts with other chromatin pathways to gain a holistic picture of chromatin-based gene regulation

Keywords: DNA methylation, epigenetics, chromatin, murine embryonic stem cells, development

Office: +33 (0) 1 57 27 81 20  Lab: +33 (0) 1 57 27 80 32     maxim.greenberg(at)ijm.fr     @maxvcg   

https://www.maximgreenberglab.com/

RESEARCH AIM

We strive to gain a clear understanding of the profound epigenetic consequences of DNA methylation in a window of development, which occurs in the first week of mouse embryogenesis, and the second of human, but the repercussions of which can ripple throughout life.

 

BACKGROUND

Immediately after fertilization, mammalian genomes undergo a dramatic reshaping of the epigenome as the embryo transitions from the zygote into the pluripotent cells primed for lineage commitment. This is best exemplified by DNA methylation reprogramming, as the gametic patterns are largely erased, and the embryonic genome undergoes a wave of de novo DNA methylation. Moreover, once DNA methylation patterns are established, mechanisms faithfully maintain the mark across cell division. Thus, there is latent potential for DNA methylation deposited in the early embryo to exhibit a lifelong effect.

DNA methylation is a modification that is typically associated with gene repression at repetitive elements and at a minority of protein coding genes. We previously described the regulation of the Zdbf2 gene in mice, which is programmed during the de novo DNA methylation program. Challenging the paradigm, in this case DNA methylation is required for activation of a gene via antagonism of the polycomb-group of silencing proteins. If the DNA methylation fails to occur, the gene stays silent throughout life, resulting in a reduced growth phenotype.

 

GOALS

We will try to answer a broad question: what is DNA methylation doing when it’s not at promoters? And its corollary: how do promoters stay DNA methylation free?

It has long been known that DNA methylation at CpG-dense promoters, also known as CpG island (CGI) promoters, is associated with gene silencing. However, the mammalian genome is highly methylated with the exception of CGI promoters. This means that DNA methylation is important for silencing only a small subset of protein coding genes. It is less clear what the function DNA methylation serves in intergenic regions and the bodies of transcribed genes, for example.

 

One key relationship we are interested in based on our studies of Zdbf2 is the antagonism observed between DNA methylation and the polycomb silencing machinery. We are highly motivated to gain insights into the mechanistic underpinnings of DNA methylation-based gene regulation. Crucially, we want to understand the relevance of non-canonical forms of DNA methylation for development.

 

METHODS

In the Greenberg lab our playground is mouse embryonic stem cells (ESCs). ESCs offer a number of advantages for DNA methylation studies: they are resilient to mutations in DNA methyltransferase genes, they are highly amenable to CRISPR/Cas9 genome editing and genetic screens, and they can be readily harvested in high numbers for robust experiments. Importantly, we utilize a differentiation system that recapitulates the DNA methylation reprogramming that occurs in vivo. Much as we did with Zdbf2, findings we make in our cell system will be complemented in mouse models to validate the developmental importance.

We will rely on next generation sequencing (NGS) approaches to gain an in-depth view of DNA methylation regulation. This includes CUT&RUN and CUT&Tag for profiling of chromatin bound factors and targeted deep bisulfite sequencing for DNA methylation analysis. It is an exciting time in the epigenetics field with the emergence of the epigenome editing tool kit. Using CRISPR/Cas9-based targeting, we can explore with precision the function of DNA methylation at a locus-by-locus basis.

In the future, we are excited to employ genome-wide CRISPR/Cas9-based genetic screens for discovery of novel factors, as well as working with the top line proteomics platform at IJM for mass spectrometry-based approaches. We are always open to new technologies and ideas, so our methods will constantly be evolving! If you are interested in our research and want to learn more, don’t hesitate to contact us!

Team leader

  • Maxim GREENBERG, Chercheur, GREENBERG LAB
    01 57 27 81 20, room 542B

Members

  • Hortense BOUVIER, Stagiaire d études, GREENBERG LAB
    01 57 27 81 20, room 542B
  • Angélique DAVID, Doctorant, GREENBERG LAB
    01 57 27 81 20, room 542B
  • Priscillia LHOUMAUD, Chercheur, GREENBERG LAB
    01 57 27 81 20, room 542B
  • Nathalie MARCOTTE, Stagiaire d études, GREENBERG LAB
  • Lea PROVENT, Stagiaire d études, GREENBERG LAB
  • Julien RICHARD ALBERT, Chercheur, GREENBERG LAB
    01 57 27 81 20, room 542B
  • Margherita SCARPA, Ingénieur technicien, GREENBERG LAB
    01 57 27 81 20, room 542B
  • Teresa URLI, Doctorant, GREENBERG LAB
    01 57 27 81 20, room 542B

To contact a member of the team by e-mail: name.surname@ijm.fr

Publications since 2015

(*) Denotes first co-authorship

(†) Denotes corresponding authorship

Gupta N., Yakhou L., Albert, J. R., Miura F., Ferry L., Kirsh O., Laisné M., Yamaguchi K., Domrane C., Bonhomme F., Sarkar A., Delagrange M., Ducos M., Greenberg M.V.C., Cristofari G., Bultmann S., Ito T., Defossez P.A. (2021) A genome-wide knock-out screen for actors of epigenetic silencing reveals new regulators of germline genes and 2-cell like cell state. bioRxiv doi: https://doi.org/10.1101/2021.05.03.442415

Greenberg M.V.C. (2021) Get Out and Stay Out: New Insights into DNA Methylation Reprogramming in Mammals. Front. Cell Dev. Biol. 8:629068

Greenberg M.V.C, Bourc’his D. (2019) The diverse roles of DNA methylation in mammalian development and disease. Nature Reviews Molecular Cell Biology 20:590-607

Greenberg M.V.C.†, Teissandier A., Walter, M., Noordermeer D., Bourc’his D†. (2019) Dynamic enhancer partitioning instructs activation of a growth-related gene during exit from naïve pluripotency. eLife 8:e44057

Greenberg M.V.C.*, Glaser J.*, Borsos M., El Marjou F., Walter M., Teissandier A., Bourc’his D. (2017) Transient transcription in the early embryo sets an epigenetic state that programs postnatal growth. Nature Genet. 49:110-118

F1000Prime recommendation – F1000Prime.com/726971069#eval793526035

Greenberg M.V.C., Bourc’his D. (2015) Cultural relativism: maintenance of genomic imprints in pluripotent stem cell culture systems. Curr. Op. Genet. & Dev. 31:42–49

Publication 

Mancheno-Ferris, A., Immarigeon, C., Rivero, A., Depierre, D., Schickele, N., Fosseprez, O., Chanard, N., Aughey, G., Lhoumaud, P., Anglade, J., Southall, T., Plaza, S., Payre, F., Cuvier, O., & Polesello, C. (2024). Crosstalk between chromatin and Shavenbaby defines transcriptional output along the Drosophila intestinal stem cell lineage. IScience, 27(1), 108624. https://doi.org/10.1016/j.isci.2023.108624
Schulz, M., Teissandier, A., De La Mata Santaella, E., Armand, M., Iranzo, J., El Marjou, F., Gestraud, P., Walter, M., Kinston, S., Göttgens, B., Greenberg, M. V. C., & Bourc’his, D. (2024). DNA methylation restricts coordinated germline and neural fates in embryonic stem cell differentiation. Nature Structural & Molecular Biology, 1–13. https://doi.org/10.1038/s41594-023-01162-w
Canat, A., Veillet, A., Batrin, R., Dubourg, C., Lhoumaud, P., Arnau-Romero, P., Greenberg, M. V. C., Bonhomme, F., Arimondo, P. B., Illingworth, R., Fabre, E., & Therizols, P. (2023). DAXX safeguards heterochromatin formation in embryonic stem cells. Journal of Cell Science, jcs.261092. https://doi.org/10.1242/jcs.261092
Yakhou, L., Azogui, A., Gupta, N., Richard Albert, J., Miura, F., Ferry, L., Yamaguchi, K., Battault, S., Therizols, P., Bonhomme, F., Bethuel, E., Sarkar, A., Greenberg, M. V. C., Arimondo, P. B., Cristofari, G., Kirsh, O., Ito, T., & Defossez, P.-A. (2023). A genetic screen identifies BEND3 as a regulator of bivalent gene expression and global DNA methylation. Nucleic Acids Research, gkad719. https://doi.org/10.1093/nar/gkad719
Gupta, N., Yakhou, L., Albert, J. R., Azogui, A., Ferry, L., Kirsh, O., Miura, F., Battault, S., Yamaguchi, K., Laisné, M., Domrane, C., Bonhomme, F., Sarkar, A., Delagrange, M., Ducos, B., Cristofari, G., Ito, T., Greenberg, M. V. C., & Defossez, P.-A. (2023). A genome-wide screen reveals new regulators of the 2-cell-like cell state. Nature Structural & Molecular Biology, 1–14. https://doi.org/10.1038/s41594-023-01038-z
Dubois, A., Vincenti, L., Chervova, A., Greenberg, M. V. C., Vandormael-Pournin, S., Bourc’his, D., Cohen-Tannoudji, M., & Navarro, P. (2022). H3K9 tri-methylation at Nanog times differentiation commitment and enables the acquisition of primitive endoderm fate. Development (Cambridge, England), dev.201074. https://doi.org/10.1242/dev.201074
Manceau, L., Richard Albert, J., Lollini, P.-L., Greenberg, M. V. C., Gilardi-Hebenstreit, P., & Ribes, V. (2022). Divergent transcriptional and transforming properties of PAX3-FOXO1 and PAX7-FOXO1 paralogs. PLoS Genetics, 18(5), e1009782. https://doi.org/10.1371/journal.pgen.1009782

 

Preprint 

Monteagudo-Sánchez, A., Albert, J. R., Scarpa, M., Noordermeer, D., & Greenberg, M. V. C. (2023). The embryonic DNA methylation program modulates the cis-regulatory landscape via CTCF antagonism. bioRxiv. https://doi.org/10.1101/2023.11.16.567349
Albert, J. R., Urli, T., Monteagudo-Sánchez, A., Breton, A. L., Sultanova, A., David, A., Schulz, M., & Greenberg, M. V. C. (2023). DNA methylation shapes the Polycomb landscape during the exit from naïve pluripotency. bioRxiv. https://doi.org/10.1101/2023.09.14.557729
Richard Albert, J., Kobayashi, T., Inoue, A., Monteagudo-Sánchez, A., Kumamoto, S., Takashima, T., Miura, A., Oikawa, M., Miura, F., Takada, S., Hirabayashi, M., Korthauer, K., Kurimoto, K., Greenberg, M. V. C., Lorincz, M., & Kobayashi, H. (2023). Conservation and divergence of canonical and non-canonical imprinting in murids. Genome Biology, 24(1), 48. https://doi.org/10.1186/s13059-023-02869-1
Gupta, N., Yakhou, L., Albert, J. R., Miura, F., Ferry, L., Kirsh, O., Laisné, M., Yamaguchi, K., Domrane, C., Bonhomme, F., Sarkar, A., Delagrange, M., Ducos, B., Greenberg, M. V. C., Cristofari, G., Bultmann, S., Ito, T., & Defossez, P.-A. (2021). A genome-wide knock-out screen for actors of epigenetic silencing reveals new regulators of germline genes and 2-cell like cell state. bioRxiv. https://doi.org/10.1101/2021.05.03.442415

 

Review

Monteagudo-Sánchez, A., Noordermeer, D., & Greenberg, M. V. C. (2024). The impact of DNA methylation on CTCF-mediated 3D genome organization. Nature Structural & Molecular Biology, 31(3), 404–412. https://doi.org/10.1038/s41594-024-01241-6
Albert, J. R., & Greenberg, M. V. C. (2023). Non-canonical imprinting in the spotlight. Development, 150(12), dev201087. https://doi.org/10.1242/dev.201087
Richard Albert, J., & Greenberg, M. V. C. (2021). The Polycomb landscape in mouse development. Nature Genetics, 53(4), 427–429. https://doi.org/10.1038/s41588-021-00833-y
Greenberg, M. V. C. (2020). Get Out and Stay Out: New Insights Into DNA Methylation Reprogramming in Mammals. Frontiers in Cell and Developmental Biology, 8, 629068. https://doi.org/10.3389/fcell.2020.629068

ANR “REMEDY”:

Pierre-Antoine Defossez (Coordinator), Epigenetics and Cell Fate, CNRS, Université Paris Cité, Paris

Salvatore Spicuglia (Partner), TAGC, INSERM, Aix-Marseille University, Marseille

 

LabEx Who Am I? “DECODERS”:

Benoit Palancade (Coordinator), Université Paris Cité, Institut Jacques Monod, CNRS, Paris

ERC Starting Grant, ATIP-Avenir, ANR, Labex Who Am I?