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Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence

Nature Genetics volume 41, pages 359–364 (2009)Cite this article

Abstract

Pierre Robin sequence (PRS) is an important subgroup of cleft palate. We report several lines of evidence for the existence of a 17q24 locus underlying PRS, including linkage analysis results, a clustering of translocation breakpoints 1.06–1.23 Mb upstream of SOX9, and microdeletions both ∼1.5 Mb centromeric and ∼1.5 Mb telomeric of SOX9. We have also identified a heterozygous point mutation in an evolutionarily conserved region of DNA with in vitro and in vivo features of a developmental enhancer. This enhancer is centromeric to the breakpoint cluster and maps within one of the microdeletion regions. The mutation abrogates the in vitro enhancer function and alters binding of the transcription factor MSX1 as compared to the wild-type sequence. In the developing mouse mandible, the 3-Mb region bounded by the microdeletions shows a regionally specific chromatin decompaction in cells expressing Sox9. Some cases of PRS may thus result from developmental misexpression of SOX9 due to disruption of very-long-range cis-regulatory elements.

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Figure 1: Family trees and highly conserved noncoding element (HCNE) rearrangements.
Figure 2: HCNEs at the PRS1 locus have tissue-specific enhancer activity.
Figure 3: HCNE-F2 has enhancer activity.
Figure 4: Chromatin characteristics of the region around SOX9.

Accession codes

Accessions

GenBank/EMBL/DDBJ

NCBI Reference Sequence

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Acknowledgements

We are grateful to the affected individuals and their families who participated in this study, to the Associations Françaises du Syndrome de Robin, to the Centres de Références Anomalies Cranio-Faciales Rares (AP-HP, Necker and Trousseau hospitals), and to C. Ozilou, G. Staub and G. Guédu-Molina for assistance. We thank T. Attié-Bitach, G. Couly and L. Legeai-Mallet (Necker) and V. van Heyningen and R. Hill (MRC HGU) for useful discussion. This study was underwritten by grants from the Agence Nationale de la Recherche (ERARE grant CraniRare), EUROCRAN FP5, the Fondation pour la Recherche Médicale (FRM), the MRC (UK) and the National Health and Medical Research Council (Australia). S.T. was supported in part by grant NS039818 from the US National Institutes of Health and S.B. by the FRM.

Author information

Author notes

  1. Sabina Benko, Judy A Fantes, David R FitzPatrick and Stanislas Lyonnet: These authors contributed equally to this work.

Authors and Affiliations

  1. INSERM U-781, Hôpital Necker–Enfants Malades, Paris, France

    Sabina Benko, Jeanne Amiel, Sophie Thomas, Christelle Golzio, Michel Vekemans, Arnold Munnich, Heather C Etchevers, Anna Pelet & Stanislas Lyonnet

  2. Medical Research Council Human Genetics Unit (MRC HGU), Institute of Genetic and Molecular Medicine, Edinburgh, EH4 2XU, UK

    Judy A Fantes, Dirk-Jan Kleinjan, Jacqueline Ramsay, Abdelkader Essafi, Simon Heaney, David McBride, Malcolm Fisher, Paul Perry, Nicholas D Hastie & David R FitzPatrick

  3. Département de Génétique, Assistance Publique–Hôpitaux de Paris (AP-HP), Hôpital Necker–Enfants Malades, Paris, France.,

    Jeanne Amiel, Michel Vekemans, Arnold Munnich & Stanislas Lyonnet

  4. Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Australia

    Negar Jamshidi, Christopher T Gordon, Nicky Kilpatrick, Paul Thomas & Peter G Farlie

  5. Université Paris Descartes, Faculté de Médecine, Paris, France

    Véronique Abadie, Michel Vekemans, Arnold Munnich & Stanislas Lyonnet

  6. AP-HP, Service de Pédiatrie, Hôpital Necker–Enfants Malades, Paris, France

    Véronique Abadie

  7. Fundación Jiménez Díaz, Genética, Ciberer Madrid, Spain

    Carmen Ayuso

  8. CHRU de Lille, Hôpital Jeanne de Flandre, Lille, France

    Muriel Holder-Espinasse

  9. North Thames Regional Genetics Service, Great Ormond Street Hospital, London, UK

    Melissa M Lees

  10. AP-HP, Service de Chirurgie Maxillo-Faciale et Chirurgie Plastique, Hôpital d'Enfants Armand Trousseau, Paris, France

    Arnaud Picard & Marie-Paule Vazquez

  11. Université Pierre et Marie Curie–Paris 6, UFR de Médecine Pierre et Marie Curie, Paris

    Arnaud Picard & Marie-Paule Vazquez

  12. Division of Human Genetics, Wessex Clinical Genetics Academic Group, University of Southampton, Southampton, UK

    I Karen Temple

  13. Department of Biology, École Normale Supérieure, CNRS, Paris, UMR-8541, France

    Hugues Roest Crollius

Authors
  1. Sabina Benko
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  2. Judy A Fantes
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Contributions

S.B., J.A.F. and A.P. performed molecular genetics studies. J.A.F., C.T.G. and N.J. performed chromosomal studies. S.B. and J.R. performed the in vitro enhancer activity experiments. S.B., S.T., C.G., M.V. and H.C.E. performed human expression studies. J.R., S.B. and A.E. performed immunoprecipitation experiments. D.-J.K. performed transgenic assays. J.A.F., S.H., P.P. and D.B. performed the in vivo chromatin compaction studies. M.F. did the OPT image analysis. S.B. and H.R.C. performed the comparative genomic analysis. J.A., V.A., C.A., M.H.-E., N.K., M.M.L., A.P., I.K.T., M.V., P.T., M.-P.V., D.R.F. and S.L. recruited individuals and families affected with PRS. S.L., D.R.F., P.G.F. and J.A. contributed to the concept, strategy, study design and project management. S.B., H.C.E., S.T., P.G.F., D.R.F. and S.L. contributed to the writing of the manuscript. All authors discussed the results.

Corresponding authors

Correspondence to David R FitzPatrick or Stanislas Lyonnet.

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Supplementary Figures 1–5, Supplementary Note, Supplementary Methods and Supplementary Table 1 (PDF 2655 kb)

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Benko, S., Fantes, J., Amiel, J. et al. Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence. Nat Genet 41, 359–364 (2009). https://doi.org/10.1038/ng.329

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