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Genome-scale Capture C promoter interactions implicate effector genes at GWAS loci for bone mineral density

Author

Listed:
  • Alessandra Chesi

    (Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia)

  • Yadav Wagley

    (University of Michigan Medical School)

  • Matthew E. Johnson

    (Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia)

  • Elisabetta Manduchi

    (Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia
    University of Pennsylvania Perelman School of Medicine)

  • Chun Su

    (Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia)

  • Sumei Lu

    (Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia)

  • Michelle E. Leonard

    (Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia)

  • Kenyaita M. Hodge

    (Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia)

  • James A. Pippin

    (Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia)

  • Kurt D. Hankenson

    (University of Michigan Medical School)

  • Andrew D. Wells

    (Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia
    University of Pennsylvania Perelman School of Medicine)

  • Struan F. A. Grant

    (Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia
    University of Pennsylvania Perelman School of Medicine
    Children’s Hospital of Philadelphia)

Abstract

Osteoporosis is a devastating disease with an essential genetic component. GWAS have discovered genetic signals robustly associated with bone mineral density (BMD), but not the precise localization of effector genes. Here, we carry out physical and direct variant to gene mapping in human mesenchymal progenitor cell-derived osteoblasts employing a massively parallel, high resolution Capture C based method in order to simultaneously characterize the genome-wide interactions of all human promoters. By intersecting our Capture C and ATAC-seq data, we observe consistent contacts between candidate causal variants and putative target gene promoters in open chromatin for ~ 17% of the 273 BMD loci investigated. Knockdown of two novel implicated genes, ING3 at ‘CPED1-WNT16’ and EPDR1 at ‘STARD3NL’, inhibits osteoblastogenesis, while promoting adipogenesis. This approach therefore aids target discovery in osteoporosis, here on the example of two relevant genes involved in the fate determination of mesenchymal progenitors, and can be applied to other common genetic diseases.

Suggested Citation

  • Alessandra Chesi & Yadav Wagley & Matthew E. Johnson & Elisabetta Manduchi & Chun Su & Sumei Lu & Michelle E. Leonard & Kenyaita M. Hodge & James A. Pippin & Kurt D. Hankenson & Andrew D. Wells & Stru, 2019. "Genome-scale Capture C promoter interactions implicate effector genes at GWAS loci for bone mineral density," Nature Communications, Nature, vol. 10(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-09302-x
    DOI: 10.1038/s41467-019-09302-x
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    Cited by:

    1. Matthew C. Pahl & Claudia A. Doege & Kenyaita M. Hodge & Sheridan H. Littleton & Michelle E. Leonard & Sumei Lu & Rick Rausch & James A. Pippin & Maria Caterina Rosa & Alisha Basak & Jonathan P. Bradf, 2021. "Cis-regulatory architecture of human ESC-derived hypothalamic neuron differentiation aids in variant-to-gene mapping of relevant complex traits," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    2. Tiantian Jing & Dianhui Wei & Xiaoli Xu & Chengsi Wu & Lili Yuan & Yiwen Huang & Yizhen Liu & Yanyi Jiang & Boshi Wang, 2024. "Transposable elements-mediated recruitment of KDM1A epigenetically silences HNF4A expression to promote hepatocellular carcinoma," Nature Communications, Nature, vol. 15(1), pages 1-21, December.

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