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A mammalian methylation array for profiling methylation levels at conserved sequences

Author

Listed:
  • Adriana Arneson

    (University of California
    University of California, Los Angeles)

  • Amin Haghani

    (University of California Los Angeles)

  • Michael J. Thompson

    (University of California Los Angeles)

  • Matteo Pellegrini

    (University of California Los Angeles)

  • Soo Bin Kwon

    (University of California
    University of California, Los Angeles)

  • Ha Vu

    (University of California
    University of California, Los Angeles)

  • Emily Maciejewski

    (University of California, Los Angeles
    University of California, Los Angeles)

  • Mingjia Yao

    (University of California Los Angeles)

  • Caesar Z. Li

    (University of California Los Angeles)

  • Ake T. Lu

    (University of California Los Angeles)

  • Marco Morselli

    (University of California Los Angeles)

  • Liudmilla Rubbi

    (University of California Los Angeles)

  • Bret Barnes

    (Illumina, Inc)

  • Kasper D. Hansen

    (Johns Hopkins Bloomberg School of Public Health
    Johns Hopkins School of Medicine)

  • Wanding Zhou

    (Children’s Hospital of Philadelphia)

  • Charles E. Breeze

    (Altius Institute for Biomedical Sciences)

  • Jason Ernst

    (University of California
    University of California, Los Angeles
    University of California, Los Angeles
    Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at University of California, Los Angeles)

  • Steve Horvath

    (University of California Los Angeles
    University of California Los Angeles
    Altos Labs)

Abstract

Infinium methylation arrays are not available for the vast majority of non-human mammals. Moreover, even if species-specific arrays were available, probe differences between them would confound cross-species comparisons. To address these challenges, we developed the mammalian methylation array, a single custom array that measures up to 36k CpGs per species that are well conserved across many mammalian species. We designed a set of probes that can tolerate specific cross-species mutations. We annotate the array in over 200 species and report CpG island status and chromatin states in select species. Calibration experiments demonstrate the high fidelity in humans, rats, and mice. The mammalian methylation array has several strengths: it applies to all mammalian species even those that have not yet been sequenced, it provides deep coverage of conserved cytosines facilitating the development of epigenetic biomarkers, and it increases the probability that biological insights gained in one species will translate to others.

Suggested Citation

  • Adriana Arneson & Amin Haghani & Michael J. Thompson & Matteo Pellegrini & Soo Bin Kwon & Ha Vu & Emily Maciejewski & Mingjia Yao & Caesar Z. Li & Ake T. Lu & Marco Morselli & Liudmilla Rubbi & Bret B, 2022. "A mammalian methylation array for profiling methylation levels at conserved sequences," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-28355-z
    DOI: 10.1038/s41467-022-28355-z
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    References listed on IDEAS

    as
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    Cited by:

    1. Steve Horvath & Joshua Zhang & Amin Haghani & Ake T. Lu & Zhe Fei, 2024. "Fundamental equations linking methylation dynamics to maximum lifespan in mammals," Nature Communications, Nature, vol. 15(1), pages 1-17, December.

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