Abstract

Premature fusion of the cranial sutures (craniosynostosis), affecting 1 in 2,000 newborns, is treated surgically in infancy to prevent adverse neurologic outcomes. To identify mutations contributing to common non-syndromic midline (sagittal and metopic) craniosynostosis, we performed exome sequencing of 132 parent-offspring trios and 59 additional probands. Thirteen probands (7%) had damaging de novo or rare transmitted mutations in SMAD6, an inhibitor of BMP - induced osteoblast differentiation (P < 10-20). SMAD6 mutations nonetheless showed striking incomplete penetrance (<60%). Genotypes of a common variant near BMP2 that is strongly associated with midline craniosynostosis explained nearly all the phenotypic variation in these kindreds, with highly significant evidence of genetic interaction between these loci via both association and analysis of linkage. This epistatic interaction of rare and common variants defines the most frequent cause of midline craniosynostosis and has implications for the genetic basis of other diseases.

Data availability

The following data sets were generated

Article and author information

Author details

  1. Andrew T Timberlake

    Department of Genetics, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8926-9692
  2. Jungmin Choi

    Department of Genetics, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Samir Zaidi

    Department of Genetics, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Qiongshi Lu

    Department of Biostatistics, Yale University School of Medicine, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Carol Nelson-Williams

    Department of Genetics, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Eric D Brooks

    Section of Plastic and Reconstructive Surgery, Department of Surgery, Yale University School of Medicine, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Kaya Bilguvar

    Department of Genetics, Yale University School of Medicine, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Irina Tikhonova

    Yale Center for Genome Analysis, Yale University School of Medicine, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Shrikant Mane

    Department of Genetics, Yale University School of Medicine, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Jenny F Yang

    Section of Plastic and Reconstructive Surgery, Department of Surgery, Yale University School of Medicine, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  11. Rajendra Sawh-Martinez

    Section of Plastic and Reconstructive Surgery, Department of Surgery, Yale University School of Medicine, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  12. Sarah Persing

    Section of Plastic and Reconstructive Surgery, Department of Surgery, Yale University School of Medicine, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  13. Elizabeth G Zellner

    Section of Plastic and Reconstructive Surgery, Department of Surgery, Yale University School of Medicine, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  14. Erin Loring

    Department of Genetics, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  15. Carolyn Chuang

    Section of Plastic and Reconstructive Surgery, Department of Surgery, Yale University School of Medicine, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  16. Amy Galm

    Craniosynostosis and Positional Plagiocephaly Support, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  17. Peter W Hashim

    Section of Plastic and Reconstructive Surgery, Department of Surgery, Yale University School of Medicine, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  18. Derek M Steinbacher

    Section of Plastic and Reconstructive Surgery, Department of Surgery, Yale University School of Medicine, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  19. Michael L DiLuna

    Department of Neurosurgery, Yale University School of Medicine, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  20. Charles C Duncan

    Department of Neurosurgery, Yale University School of Medicine, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  21. Kevin A Pelphrey

    Child Study Center, Yale University School of Medicine, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  22. Hongyu Zhao

    Department of Biostatistics, Yale University School of Medicine, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  23. John A Persing

    Section of Plastic and Reconstructive Surgery, Department of Surgery, Yale University School of Medicine, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  24. Richard P Lifton

    Department of Genetics, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, United States
    For correspondence
    richard.lifton@yale.edu
    Competing interests
    The authors declare that no competing interests exist.

Funding

Yale Center for Mendelian Genomics (NIH M#UM1HG006504-05)

  • Kaya Bilguvar
  • Irina Tikhonova
  • Shrikant Mane

Maxillofacial Surgeons Foundation/ASMS (M#M156301)

  • Eric D Brooks
  • John A Persing

NIH Medical Scientist Training Program (NIH/NIGMS T32GM007205)

  • Andrew T Timberlake
  • Samir Zaidi

Howard Hughes Medical Institute

  • Andrew T Timberlake
  • Jungmin Choi
  • Samir Zaidi
  • Carol Nelson-Williams
  • Erin Loring
  • Richard P Lifton

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Human subjects: All participants or their parents provided written informed consent to participate in a study of genetic causes of craniosynostosis in their family. Written consent was obtained for publication of patient photographs. The study protocol was approved by the Yale Human Investigation Committee Institutional Review Board.

Copyright

© 2016, Timberlake et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 9,853
    views
  • 1,442
    downloads
  • 171
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Andrew T Timberlake
  2. Jungmin Choi
  3. Samir Zaidi
  4. Qiongshi Lu
  5. Carol Nelson-Williams
  6. Eric D Brooks
  7. Kaya Bilguvar
  8. Irina Tikhonova
  9. Shrikant Mane
  10. Jenny F Yang
  11. Rajendra Sawh-Martinez
  12. Sarah Persing
  13. Elizabeth G Zellner
  14. Erin Loring
  15. Carolyn Chuang
  16. Amy Galm
  17. Peter W Hashim
  18. Derek M Steinbacher
  19. Michael L DiLuna
  20. Charles C Duncan
  21. Kevin A Pelphrey
  22. Hongyu Zhao
  23. John A Persing
  24. Richard P Lifton
(2016)
Two locus inheritance of non-syndromic midline craniosynostosis via rare SMAD6 and common BMP2 alleles
eLife 5:e20125.
https://doi.org/10.7554/eLife.20125

Share this article

https://doi.org/10.7554/eLife.20125

Further reading

    1. Chromosomes and Gene Expression
    2. Genetics and Genomics
    Omid Gholamalamdari, Tom van Schaik ... Andrew S Belmont
    Research Article

    Models of nuclear genome organization often propose a binary division into active versus inactive compartments yet typically overlook nuclear bodies. Here, we integrated analysis of sequencing and image-based data to compare genome organization in four human cell types relative to three different nuclear locales: the nuclear lamina, nuclear speckles, and nucleoli. Although gene expression correlates mostly with nuclear speckle proximity, DNA replication timing correlates with proximity to multiple nuclear locales. Speckle attachment regions emerge as DNA replication initiation zones whose replication timing and gene composition vary with their attachment frequency. Most facultative LADs retain a partially repressed state as iLADs, despite their positioning in the nuclear interior. Knock out of two lamina proteins, Lamin A and LBR, causes a shift of H3K9me3-enriched LADs from lamina to nucleolus, and a reciprocal relocation of H3K27me3-enriched partially repressed iLADs from nucleolus to lamina. Thus, these partially repressed iLADs appear to compete with LADs for nuclear lamina attachment with consequences for replication timing. The nuclear organization in adherent cells is polarized with nuclear bodies and genomic regions segregating both radially and relative to the equatorial plane. Together, our results underscore the importance of considering genome organization relative to nuclear locales for a more complete understanding of the spatial and functional organization of the human genome.

    1. Chromosomes and Gene Expression
    2. Genetics and Genomics
    Hans Tobias Gustafsson, Lucas Ferguson ... Oliver J Rando
    Research Article

    Among the major classes of RNAs in the cell, tRNAs remain the most difficult to characterize via deep sequencing approaches, as tRNA structure and nucleotide modifications can each interfere with cDNA synthesis by commonly-used reverse transcriptases (RTs). Here, we benchmark a recently-developed RNA cloning protocol, termed Ordered Two-Template Relay (OTTR), to characterize intact tRNAs and tRNA fragments in budding yeast and in mouse tissues. We show that OTTR successfully captures both full-length tRNAs and tRNA fragments in budding yeast and in mouse reproductive tissues without any prior enzymatic treatment, and that tRNA cloning efficiency can be further enhanced via AlkB-mediated demethylation of modified nucleotides. As with other recent tRNA cloning protocols, we find that a subset of nucleotide modifications leave misincorporation signatures in OTTR datasets, enabling their detection without any additional protocol steps. Focusing on tRNA cleavage products, we compare OTTR with several standard small RNA-Seq protocols, finding that OTTR provides the most accurate picture of tRNA fragment levels by comparison to "ground truth" Northern blots. Applying this protocol to mature mouse spermatozoa, our data dramatically alter our understanding of the small RNA cargo of mature mammalian sperm, revealing a far more complex population of tRNA fragments - including both 5′ and 3′ tRNA halves derived from the majority of tRNAs – than previously appreciated. Taken together, our data confirm the superior performance of OTTR to commercial protocols in analysis of tRNA fragments, and force a reappraisal of potential epigenetic functions of the sperm small RNA payload.