The Developmental Epigenetics group of Hendrik Marks studies how the zygote can generate many different cell types present in an organism, focussing on early cellular specialisation. The group is part of RIMLS-Science.
Developmental Epigenetics
Research group
Research focus
Our team pioneered and explored a 2D cell model to study genome regulation during early mouse embryogenesis, uncovering epigenetic mechanisms that drive Inner Cell Mass (ICM) cells to further develop. This system has since become a mainstream tool in developmental biology. To refine our model and gain insight into implantation, we characterised new mouse pluripotent stem cells representing peri-implantation stages.
We are currently building on these findings, including studying X inactivation in female PSCs. In addition, we established a network of material scientists and synthetic- and computational biologists to initiate single-cell -omics studies on cellular interplay within complex post-implantation 3D models (gastruloids). By means of a public-private partnership with Fluidigm, we have developed miniaturised platforms for -omics profiling, essential for the embryo models that we use.
The Marks team recently initiated a new third research line on pre-implantation human embryogenesis. Within this research line, we focus on the effect of the embryo sex on embryogenesis, as well an on how human embryos cope with aneuploidies that regularly occur. Among others, such insights underlie further improvement of in vitro fertilization, in which the pre-implantation human embryos obtained often contain aneuploidies.
Epigenetic regulation of human blastocyst formation
- Use of human blastoids and directed differentiation assays from hESCs
- Histone marks and chromatin associated protein(complexe)s
- Molecular mechanisms regulating chromatin dynamics
- Transcriptional and epigenetic regulators of cell fate decision
Gene regulation during mouse pluripotency progression and gastrulation
- Use of mouse gastruloids and directed differentiation from mESCs
- Cellular interactions
- Sex specific gene regulation
- Mechanisms of patterning and symmetry breaking
- Novel methods to investigate chromatin biology
News
About the Developmental Epigenetics group
Click on one of the links below for more information about this research group or contact one of the members of this group.
Principal investigator
Hendrik Marks
PhD candidates
Nick Bovee
Jeske Strik
Zicong Liu
Danique Bax
Lab manager
Anouk Klein Kranenbarg
- 2025 - 2028 ZonMW PSIDER TOP (500k euro; enige aanvrager): seXY blastoids: Developing female and male human blastoids to study sex specific early embryogenesis More information
- 2025 - 2028 Comenius Senior fellowship (education; 100k euro; enige aanvrager): Stronger together: Preparation for the labour market through multi-level collaboration within company projects More information
- 2024 - 2029 ZonMW Open (750k euro; coordinator), together with Maastricht University, MERLN and Maastricht University Medical Center+ (MUMC+): Genetic plasticity - How do human embryos cope with aneuploid cells? More information
- 2023 - 2028 NWO ENW-XL (2 million euro; coordinator), together with Hubrecht Institute, Dutch Cancer Institute (NKI) en University of Amsterdam (UvA): From random state to robust fate: Defining cellular states that are responsive to inductive signaling in early mammalian development More information
- 2021 - 2026 CSC Chinese Fellowship (Zicong Liu): Identification of epigenetic factors that drive the transition from totipotency to pluripotency More information
- PRC1 and PRC2 proximal interactome in mouse embryonic stem cells.Zijlmans DW, Stelloo S, Bax D, Yordanov Y, Toebosch P, Raas MWD, Verhelst S, Lamers LA, Baltissen MPA, Jansen PWTC, van Mierlo G, Dhaenens M, Marks H, Vermeulen M (*shared last and corresponding authors). Cell Rep. 2025 Mar 25;44(3):115362. doi:10.1016/j.celrep.2025.115362. PMID: 40053453 Full text
- Integrated multi-omics reveal polycomb repressive complex 2 restricts human trophoblast induction. Zijlmans DW, Talon I, Verhelst S, Bendall A, Van Nerum K, Javali A, Malcolm AA, van Knippenberg SSFA, Biggins L, To SK, Janiszewski A, Admiraal D, Knops R, Corthout N, Balaton BP, Georgolopoulos G, Panda A, Bhanu NV, Collier AJ, Fabian C, Allsop RN, Chappell J, Pham TXA, Oberhuemer M, Ertekin C, Vanheer L, Athanasouli P, Lluis F, Deforce D, Jansen JH, Garcia BA, Vermeulen M, Rivron N, Dhaenens M*, Marks H*, Rugg-Gunn PJ*, Pasque V* (*shared last and corresponding authors). Nat Cell Biol. 2022 Jun;24(6):858-871. doi:10.1038/s41556-022-00932-w. PMID: 35697783 Full Text
- A plug and play microfluidic platform for standardized sensitive low-input chromatin immunoprecipitation. Dirks RAM, Thomas PC, Wu H, Jones RC, Stunnenberg HG, Marks H. Genome Res. 2021 May;31(5):919-933. doi:10.1101/gr.260745.120. PMID: 33707229 Full Text
- Integrative Proteomic Profiling Reveals PRC2-Dependent Epigenetic Crosstalk Maintains Ground-State Pluripotency. van Mierlo G, Dirks RAM, De Clerck L, Brinkman AB, Huth M, Kloet SL, Saksouk N, Kroeze LI, Willems S, Farlik M, Bock C, Jansen JH, Deforce D, Vermeulen M, Déjardin J, Dhaenens M, Marks H. Cell Stem Cell. 2019 Jan 3;24(1):123-137.e8. doi:10.1016/j.stem.2018.10.017. PMID: 30472157 Full Text
- The transcriptional and epigenomic foundations of ground state pluripotency. Marks H, Kalkan T, Menafra R, Denissov S, Jones K, Hofemeister H, Nichols J, Kranz A, Stewart AF, Smith A, Stunnenberg HG. Cell. 2012 Apr 27;149(3):590-604. doi:10.1016/j.cell.2012.03.026. PMID: 22541430 Full text
About Hendrik Marks
Hendrik Marks is a curious and creative molecular biologist fascinated by how a single fertilised cell develops into the many specialised cells that make up an organism. With a deep interest in epigenetics, Hendrik explores how pluripotent cells decide their fate and how gene regulation shapes early development. Using integrative omics and stem cell models, Hendrik uncovers the molecular principles that guide this remarkable transformation.
Behind the scenes
Contact information
Interested in our research or would you like to join our group? Please get in touch with Vesna Andonov.