Targeted CRISPR-Cas9 screening identifies core transcription factors controlling murine haemato-endothelial fate commitment

Michael Teske; Tobias Wertheimer; Stefan Butz; Pascale Zwicky; Izaskun Mallona; Svenja L Nopper; Christian Münz; Ulrich Elling; Christophe Lancrin; Burkhard Becher; Ana Rita Grosso; Tuncay Baubec; Nina Schmolka

doi:10.1038/s41467-025-66230-9

Targeted CRISPR-Cas9 screening identifies core transcription factors controlling murine haemato-endothelial fate commitment

Michael Teske
, Tobias Wertheimer
, Stefan Butz
, Pascale Zwicky
, Izaskun Mallona
, Svenja L Nopper
, Christian Münz
, Ulrich Elling
, Christophe Lancrin
, Burkhard Becher
, Ana Rita Grosso
, Tuncay Baubec
, Nina Schmolka^*

^*Corresponding author for this work

University of Zurich
Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA)
European Molecular Biology Laboratory
NOVA School of Science and Technology

Research output: Contribution to journal › Article › Academic › peer-review

Abstract

During development, blood generation begins in the yolk sac with the differentiation of haemato-endothelial mesoderm forming haematopoietic progenitors. This study aims to identify the crucial molecular regulators of haemato-endothelial mesoderm formation and to extend our knowledge of the process in an unbiased way. We employ a murine embryonic stem cell model that recapitulates embryonic blood development, and perform targeted CRISPR-Cas9 knock out screens focusing on transcription factors and chromatin regulators. We identify the transcription factors ETV2, LDB1, SMAD1, SIX4 and ZBTB7b as regulators of haemato-endothelial mesoderm commitment. Embryonic stem cells lacking these regulators give rise to mesodermal subsets with a defined lineage differentiation bias, while transcriptome analysis of these cells uncovers the precise impact of each factor on gene expression in the developing mesoderm. Our study reveals molecular pathways governing mesodermal development crucial to allow endothelial and haematopoietic lineage specification and paves the way for future advances in haematopoietic stem cell applications.

Original language	English
Article number	11412
Journal	Nature Communications
Volume	16
Issue number	1
Early online date	13 Dec 2025
DOIs	https://doi.org/10.1038/s41467-025-66230-9
Publication status	Published - 13 Dec 2025

Bibliographical note

Publisher Copyright:
© The Author(s) 2025.

Funding

We thank F. Caiado (University Hospital Zurich) for discussions and advice. We thank members of the Schmolka and Baubec laboratory for their input and criticism. We thank Basak Corak (UZH) for technical advice. Furthermore, we thank members of the Functional Genomics Centre Zurich and members of the Cytometry Facility at the UZH for their support. We thank Single Cell Discoveries for their single-cell sequencing services. Funding: This work was supported by a post-doc fellowship of the University of Zurich, University of Zurich Research Talent Development Fund Award (FAN), Swiss National Science Foundation Ambizione grant (186012) and European Union - ERC-PT-A- Projects of the Portuguese Foundation for Science and Technology all to N.S.

Funders	Funder number
Universitt Zrich (University of Zurich)	FAN
Schweizerischer Nationalfonds zur Frderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)	186012

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Targeted CRISPR-Cas9 screening identifies core transcription factors controlling murine haemato-endothelial fate commitmentFinal published version, 3.58 MBLicence: CC BY

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Teske, M., Wertheimer, T., Butz, S., Zwicky, P., Mallona, I., Nopper, S. L., Münz, C., Elling, U., Lancrin, C., Becher, B., Grosso, A. R., Baubec, T., & Schmolka, N. (2025). Targeted CRISPR-Cas9 screening identifies core transcription factors controlling murine haemato-endothelial fate commitment. Nature Communications, 16(1), Article 11412. https://doi.org/10.1038/s41467-025-66230-9

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abstract = "During development, blood generation begins in the yolk sac with the differentiation of haemato-endothelial mesoderm forming haematopoietic progenitors. This study aims to identify the crucial molecular regulators of haemato-endothelial mesoderm formation and to extend our knowledge of the process in an unbiased way. We employ a murine embryonic stem cell model that recapitulates embryonic blood development, and perform targeted CRISPR-Cas9 knock out screens focusing on transcription factors and chromatin regulators. We identify the transcription factors ETV2, LDB1, SMAD1, SIX4 and ZBTB7b as regulators of haemato-endothelial mesoderm commitment. Embryonic stem cells lacking these regulators give rise to mesodermal subsets with a defined lineage differentiation bias, while transcriptome analysis of these cells uncovers the precise impact of each factor on gene expression in the developing mesoderm. Our study reveals molecular pathways governing mesodermal development crucial to allow endothelial and haematopoietic lineage specification and paves the way for future advances in haematopoietic stem cell applications.",

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Teske, M, Wertheimer, T, Butz, S, Zwicky, P, Mallona, I, Nopper, SL, Münz, C, Elling, U, Lancrin, C, Becher, B, Grosso, AR, Baubec, T & Schmolka, N 2025, 'Targeted CRISPR-Cas9 screening identifies core transcription factors controlling murine haemato-endothelial fate commitment', Nature Communications, vol. 16, no. 1, 11412. https://doi.org/10.1038/s41467-025-66230-9

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AU - Nopper, Svenja L

AU - Münz, Christian

AU - Elling, Ulrich

AU - Lancrin, Christophe

AU - Becher, Burkhard

AU - Grosso, Ana Rita

AU - Baubec, Tuncay

AU - Schmolka, Nina

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Targeted CRISPR-Cas9 screening identifies core transcription factors controlling murine haemato-endothelial fate commitment

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