• A Corrigendum to this article was published on 21 March 2018

This article has been updated


Vascular and haematopoietic cells organize into specialized tissues during early embryogenesis to supply essential nutrients to all organs and thus play critical roles in development and disease. At the top of the haemato-vascular specification cascade lies cloche, a gene that when mutated in zebrafish leads to the striking phenotype of loss of most endothelial and haematopoietic cells1,2,3,4 and a significant increase in cardiomyocyte numbers5. Although this mutant has been analysed extensively to investigate mesoderm diversification and differentiation1,2,3,4,5,6,7 and continues to be broadly used as a unique avascular model, the isolation of the cloche gene has been challenging due to its telomeric location. Here we used a deletion allele of cloche to identify several new cloche candidate genes within this genomic region, and systematically genome-edited each candidate. Through this comprehensive interrogation, we succeeded in isolating the cloche gene and discovered that it encodes a PAS-domain-containing bHLH transcription factor, and that it is expressed in a highly specific spatiotemporal pattern starting during late gastrulation. Gain-of-function experiments show that it can potently induce endothelial gene expression. Epistasis experiments reveal that it functions upstream of etv2 and tal1, the earliest expressed endothelial and haematopoietic transcription factor genes identified to date. A mammalian cloche orthologue can also rescue blood vessel formation in zebrafish cloche mutants, indicating a highly conserved role in vertebrate vasculogenesis and haematopoiesis. The identification of this master regulator of endothelial and haematopoietic fate enhances our understanding of early mesoderm diversification and may lead to improved protocols for the generation of endothelial and haematopoietic cells in vivo and in vitro.

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Change history

  • 21 March 2018

    Please see accompanying Corrigendum (http://doi.org/10.1038/nature25991). In the Author Information section, the accession for the PacBio whole-genome sequencing data was wrongly stated as LT571435 from the SRA, instead of PRJEB13442 from the European Nucleotide Archive (ENA). The original Letter has been corrected online.


Primary accessions

European Nucleotide Archive


Gene Expression Omnibus


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We thank all laboratory members who have worked on cloche over the years starting with W. Liao and H. Sawyer (UCSF), as well as J. Collins (Sanger Institute) for help in expanding the GRCz10 assembly, W. Coppieters (Liège), Z. Wang (JGI), X. Chen (BGI), H. Yuan (BGI) for their hard work in trying to resolve the cloche locus, C. Helker, M. Higuchi and C. Gerri for reagents, discussions and reading of the manuscript, A. Borchers (Marburg) for help with Xenopus experiments, and funding from the DFG (S.R.), AHA (S.R., S.-W.J., N.C.), NIH (N.C., A.J.G., D.Y.R.S.), the Ragnar Söderberg Foundation and Swedish Research Council (O.A.), and the Packard Foundation and Max Planck Society (D.Y.R.S.).

Author information

Author notes

    • Suk-Won Jin
    • , Miler T. Lee
    • , Ian Fiddes
    • , Taiyi Kuo
    • , Won-Suk Chung
    • , Sherveen Salek
    • , Robert Lerrigo
    • , Jessica Alsiö
    •  & Shujun Luo

    Present addresses: School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea and Yale Cardiovascular Research Center, Yale University School of Medicine, New Haven, Connecticut 06511, USA (S.-W.J.); Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA (M.T.L.); Genomics Institute, University of California Santa Cruz and Howard Hughes Medical Institute, Santa Cruz, California 95064, USA (I.F.); Department of Medicine and Berrie Diabetes Center, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA (T.K.); Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea (W.-S.C.); Johns Hopkins Hospital, Wilmer Eye Institute, Baltimore, Maryland 21224, USA (S.S.); Division of General Internal Medicine, University of Washington, Seattle, Washington 98104, USA (R.L.); Novartis, Basel 4056, Switzerland (J.A.); Personalis, Menlo Park, California 94025, USA (S.L.).

    • Sven Reischauer
    • , Oliver A. Stone
    •  & Alethia Villasenor

    These authors contributed equally to this work.


  1. Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA

    • Sven Reischauer
    • , Oliver A. Stone
    • , Alethia Villasenor
    • , Neil Chi
    • , Suk-Won Jin
    • , Ian Fiddes
    • , Taiyi Kuo
    • , Won-Suk Chung
    • , Sherveen Salek
    • , Robert Lerrigo
    • , Jessica Alsiö
    •  & Didier Y. R. Stainier
  2. Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim 61231, Germany

    • Sven Reischauer
    • , Oliver A. Stone
    • , Alethia Villasenor
    • , Nana Fukuda
    • , Michele Marass
    • , Sruthy M. Augustine
    • , Sophie Mucenieks
    •  & Didier Y. R. Stainier
  3. Department of Medicine, Division of Cardiology, Institute of Genomic Medicine, University of California San Diego, La Jolla, California 92037, USA

    • Neil Chi
    •  & Alec Witty
  4. Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna 17121, Sweden

    • Marcel Martin
  5. Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA

    • Miler T. Lee
    •  & Antonio J. Giraldez
  6. Illumina, San Diego, California 92122, USA

    • Shujun Luo
    •  & Gary P. Schroth
  7. Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm 17177, Sweden

    • Dominika Tworus
    •  & Olov Andersson
  8. Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden

    • Björn Nystedt


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S.R., O.S., A.V. and D.Y.R.S. designed and performed experiments identifying cloche and its function. N.F., Mi.M, S.M.A. and S.M. performed reverse genetics and downstream analysis. N.C., S.-W.J., T.K., W.-S.C., S.S., R.L. and J.A. worked on the meiotic mapping. S.L., Ma.M., M.T.L., I.F. and D.T. contributed to sequencing and bioinformatics. Human embryonic stem cell assays were handled by A.W. Supervision by D.Y.R.S., N.C., O.A., G.P.S., A.J.G. and B.N. All authors contributed to data analysis and manuscript preparation.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Didier Y. R. Stainier.

Zebrafish npas4l sequences have been deposited to GenBank (KX066018, KX066019), RNA-seq data deposited to GEO (GSE76690), and PacBio whole-genome sequencing data to ENA (PRJEB13442).

Reviewer Information

Nature thanks K. Alitalo and K. Poss and the other anonymous reviewer(s) for their contribution to the peer review of this work.

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