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Platelet function is modified by common sequence variation in megakaryocyte super enhancers

Author

Listed:
  • Romina Petersen

    (University of Cambridge
    National Health Service Blood and Transplant (NHSBT))

  • John J. Lambourne

    (University of Cambridge
    National Health Service Blood and Transplant (NHSBT))

  • Biola M. Javierre

    (Nuclear Dynamics Programme, The Babraham Institute)

  • Luigi Grassi

    (University of Cambridge
    National Health Service Blood and Transplant (NHSBT)
    NIHR BioResource-Rare Diseases, University of Cambridge)

  • Roman Kreuzhuber

    (University of Cambridge
    National Health Service Blood and Transplant (NHSBT)
    European Molecular Biology Laboratory, European Bioinformatics Institute)

  • Dace Ruklisa

    (University of Cambridge
    National Health Service Blood and Transplant (NHSBT)
    Medical Research Council Biostatistics Unit, University of Cambridge)

  • Isabel M. Rosa

    (University of Cambridge
    National Health Service Blood and Transplant (NHSBT))

  • Ana R. Tomé

    (University of Cambridge
    National Health Service Blood and Transplant (NHSBT))

  • Heather Elding

    (The Wellcome Trust Sanger Institute
    Strangeways Research Laboratory, The National Institute for Health Research (NIHR) Blood and Transplant Unit in Donor Health and Genomics at the University of Cambridge, University of Cambridge)

  • Johanna P. van Geffen

    (Cardiovascular Research Institute Maastricht, Maastricht University)

  • Tao Jiang

    (Strangeways Research Laboratory, MRC/British Heart Foundation (BHF) Cardiovascular Epidemiology Unit, University of Cambridge)

  • Samantha Farrow

    (University of Cambridge
    National Health Service Blood and Transplant (NHSBT))

  • Jonathan Cairns

    (Nuclear Dynamics Programme, The Babraham Institute)

  • Abeer M. Al-Subaie

    (University of Cambridge
    National Health Service Blood and Transplant (NHSBT)
    College of Applied Medical Sciences, University of Dammam)

  • Sofie Ashford

    (University of Cambridge
    National Health Service Blood and Transplant (NHSBT)
    NIHR BioResource-Rare Diseases, University of Cambridge)

  • Antony Attwood

    (University of Cambridge
    National Health Service Blood and Transplant (NHSBT)
    NIHR BioResource-Rare Diseases, University of Cambridge)

  • Joana Batista

    (University of Cambridge
    National Health Service Blood and Transplant (NHSBT))

  • Heleen Bouman

    (The Wellcome Trust Sanger Institute)

  • Frances Burden

    (University of Cambridge
    National Health Service Blood and Transplant (NHSBT))

  • Fizzah A. Choudry

    (University of Cambridge
    National Health Service Blood and Transplant (NHSBT))

  • Laura Clarke

    (European Molecular Biology Laboratory, European Bioinformatics Institute)

  • Paul Flicek

    (European Molecular Biology Laboratory, European Bioinformatics Institute)

  • Stephen F. Garner

    (National Health Service Blood and Transplant (NHSBT))

  • Matthias Haimel

    (NIHR BioResource-Rare Diseases, University of Cambridge
    University of Cambridge)

  • Carly Kempster

    (University of Cambridge
    National Health Service Blood and Transplant (NHSBT))

  • Vasileios Ladopoulos

    (University of Cambridge)

  • An-Sofie Lenaerts

    (NIHR Cambridge Biomedical Research Centre hIPSC Core Facility, University of Cambridge
    Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge)

  • Paulina M. Materek

    (NIHR Cambridge Biomedical Research Centre hIPSC Core Facility, University of Cambridge
    Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge)

  • Harriet McKinney

    (University of Cambridge
    National Health Service Blood and Transplant (NHSBT))

  • Stuart Meacham

    (University of Cambridge
    National Health Service Blood and Transplant (NHSBT)
    NIHR BioResource-Rare Diseases, University of Cambridge)

  • Daniel Mead

    (The Wellcome Trust Sanger Institute)

  • Magdolna Nagy

    (Cardiovascular Research Institute Maastricht, Maastricht University)

  • Christopher J. Penkett

    (University of Cambridge
    National Health Service Blood and Transplant (NHSBT)
    NIHR BioResource-Rare Diseases, University of Cambridge)

  • Augusto Rendon

    (University of Cambridge
    National Health Service Blood and Transplant (NHSBT)
    Genomics England Limited, Queen Mary University of London, Dawson Hall)

  • Denis Seyres

    (University of Cambridge
    National Health Service Blood and Transplant (NHSBT)
    NIHR BioResource-Rare Diseases, University of Cambridge)

  • Benjamin Sun

    (Strangeways Research Laboratory, MRC/British Heart Foundation (BHF) Cardiovascular Epidemiology Unit, University of Cambridge)

  • Salih Tuna

    (University of Cambridge
    National Health Service Blood and Transplant (NHSBT)
    NIHR BioResource-Rare Diseases, University of Cambridge)

  • Marie-Elise van der Weide

    (University of Cambridge
    National Health Service Blood and Transplant (NHSBT))

  • Steven W. Wingett

    (Nuclear Dynamics Programme, The Babraham Institute)

  • Joost H. Martens

    (Faculty of Science, Radboud University)

  • Oliver Stegle

    (European Molecular Biology Laboratory, European Bioinformatics Institute)

  • Sylvia Richardson

    (Medical Research Council Biostatistics Unit, University of Cambridge)

  • Ludovic Vallier

    (Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge
    The Wellcome Trust Sanger Institute)

  • David J. Roberts

    (John Radcliffe Hospital, University of Oxford
    Churchill Hospital
    NHSBT, John Radcliffe Hospital)

  • Kathleen Freson

    (Center for Molecular and Vascular Biology, University of Leuven)

  • Lorenz Wernisch

    (Medical Research Council Biostatistics Unit, University of Cambridge)

  • Hendrik G. Stunnenberg

    (Faculty of Science, Radboud University)

  • John Danesh

    (The Wellcome Trust Sanger Institute
    Strangeways Research Laboratory, The National Institute for Health Research (NIHR) Blood and Transplant Unit in Donor Health and Genomics at the University of Cambridge, University of Cambridge
    Strangeways Research Laboratory, MRC/British Heart Foundation (BHF) Cardiovascular Epidemiology Unit, University of Cambridge
    BHF Centre of Excellence, Addenbrooke’s Hospital)

  • Peter Fraser

    (Nuclear Dynamics Programme, The Babraham Institute
    Florida State University)

  • Nicole Soranzo

    (University of Cambridge
    The Wellcome Trust Sanger Institute
    Strangeways Research Laboratory, The National Institute for Health Research (NIHR) Blood and Transplant Unit in Donor Health and Genomics at the University of Cambridge, University of Cambridge
    BHF Centre of Excellence, Addenbrooke’s Hospital)

  • Adam S. Butterworth

    (Strangeways Research Laboratory, The National Institute for Health Research (NIHR) Blood and Transplant Unit in Donor Health and Genomics at the University of Cambridge, University of Cambridge
    Strangeways Research Laboratory, MRC/British Heart Foundation (BHF) Cardiovascular Epidemiology Unit, University of Cambridge
    BHF Centre of Excellence, Addenbrooke’s Hospital)

  • Johan W. Heemskerk

    (Cardiovascular Research Institute Maastricht, Maastricht University)

  • Ernest Turro

    (University of Cambridge
    National Health Service Blood and Transplant (NHSBT)
    NIHR BioResource-Rare Diseases, University of Cambridge
    Medical Research Council Biostatistics Unit, University of Cambridge)

  • Mikhail Spivakov

    (Nuclear Dynamics Programme, The Babraham Institute)

  • Willem H. Ouwehand

    (University of Cambridge
    National Health Service Blood and Transplant (NHSBT)
    The Wellcome Trust Sanger Institute
    Strangeways Research Laboratory, The National Institute for Health Research (NIHR) Blood and Transplant Unit in Donor Health and Genomics at the University of Cambridge, University of Cambridge)

  • William J. Astle

    (University of Cambridge
    National Health Service Blood and Transplant (NHSBT)
    Medical Research Council Biostatistics Unit, University of Cambridge
    Strangeways Research Laboratory, MRC/British Heart Foundation (BHF) Cardiovascular Epidemiology Unit, University of Cambridge)

  • Kate Downes

    (University of Cambridge
    National Health Service Blood and Transplant (NHSBT))

  • Myrto Kostadima

    (University of Cambridge
    National Health Service Blood and Transplant (NHSBT)
    European Molecular Biology Laboratory, European Bioinformatics Institute)

  • Mattia Frontini

    (University of Cambridge
    National Health Service Blood and Transplant (NHSBT)
    BHF Centre of Excellence, Addenbrooke’s Hospital)

Abstract

Linking non-coding genetic variants associated with the risk of diseases or disease-relevant traits to target genes is a crucial step to realize GWAS potential in the introduction of precision medicine. Here we set out to determine the mechanisms underpinning variant association with platelet quantitative traits using cell type-matched epigenomic data and promoter long-range interactions. We identify potential regulatory functions for 423 of 565 (75%) non-coding variants associated with platelet traits and we demonstrate, through ex vivo and proof of principle genome editing validation, that variants in super enhancers play an important role in controlling archetypical platelet functions.

Suggested Citation

  • Romina Petersen & John J. Lambourne & Biola M. Javierre & Luigi Grassi & Roman Kreuzhuber & Dace Ruklisa & Isabel M. Rosa & Ana R. Tomé & Heather Elding & Johanna P. van Geffen & Tao Jiang & Samantha , 2017. "Platelet function is modified by common sequence variation in megakaryocyte super enhancers," Nature Communications, Nature, vol. 8(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_ncomms16058
    DOI: 10.1038/ncomms16058
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    Cited by:

    1. Laureano Tomás-Daza & Llorenç Rovirosa & Paula López-Martí & Andrea Nieto-Aliseda & François Serra & Ainoa Planas-Riverola & Oscar Molina & Rebecca McDonald & Cedric Ghevaert & Esther Cuatrecasas & Do, 2023. "Low input capture Hi-C (liCHi-C) identifies promoter-enhancer interactions at high-resolution," Nature Communications, Nature, vol. 14(1), pages 1-16, December.

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