Letter | Published:

Long-range enhancers regulating Myc expression are required for normal facial morphogenesis

Nature Genetics volume 46, pages 753758 (2014) | Download Citation

Abstract

Cleft lip with or without cleft palate (CL/P) is one of the most common congenital malformations observed in humans, with 1 occurrence in every 500–1,000 births1,2. A 640-kb noncoding interval at 8q24 has been associated with increased risk of non-syndromic CL/P in humans3,4,5, but the genes and pathways involved in this genetic susceptibility have remained elusive. Using a large series of rearrangements engineered over the syntenic mouse region, we show that this interval contains very remote cis-acting enhancers that control Myc expression in the developing face. Deletion of this interval leads to mild alteration of facial morphology in mice and, sporadically, to CL/P. At the molecular level, we identify misexpression of several downstream genes, highlighting combined impact on the craniofacial developmental network and the general metabolic capacity of cells contributing to the future upper lip. This dual molecular etiology may account for the prominent influence of variants in the 8q24 region on human facial dysmorphologies.

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Acknowledgements

We thank B. Sleckman (Washington University, St. Louis) and A. Trumpp (DKFZ, Heidelberg) for providing the Myctm1Slek strain. We thank members of the EMBL Laboratory Animal Resources Facility for animal welfare and husbandry; the EMBL Genomics Core Facility for advice and support in processing ChIP and RNA sequencing experiments; and Genome Biology Computational Support for help with the analyses. We thank members of the Spitz laboratory and colleagues at EMBL for sharing reagents and helpful comments. V.V.U. and M.P. were supported by PhD fellowships from the Jeff Schell Darwin Trust and the EMBL International PhD program, respectively. This work was supported by EMBL.

Author information

Affiliations

  1. Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.

    • Veli Vural Uslu
    • , Massimo Petretich
    • , Sandra Ruf
    • , Katja Langenfeld
    •  & François Spitz
  2. European Bioinformatics Institute–European Molecular Biology Laboratory (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

    • Nuno A Fonseca
    •  & John C Marioni

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Contributions

F.S. designed the experiments. V.V.U., M.P., S.R. and K.L. performed the experiments. N.A.F. and J.C.M. performed RNA-seq data, bioinformatics and statistical analyses. V.V.U., M.P. and F.S. analyzed the data. F.S. wrote the manuscript with V.V.U., M.P. and J.C.M.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to François Spitz.

Integrated supplementary information

Supplementary information

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    Supplementary Text and Figures

    Supplementary Figures 1–11 and Supplementary Tables 1, 2 and 6–10

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    Supplementary Table 3

    Regions enriched for H3K27ac and H3K4me1.

  2. 2.

    Supplementary Table 4

    Misexpressed genes in del(8–17) versus WT mice (P value < 0.05).

  3. 3.

    Supplementary Table 5

    RNA-seq data for the genes surrounding the MNE.

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DOI

https://doi.org/10.1038/ng.2971

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