A mammalian methylation array for profiling methylation levels at conserved sequences

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 Barnes, Kasper D. Hansen, Wanding Zhou, Charles E. Breeze, Jason Ernst () and Steve Horvath ()
Additional contact information
Adriana Arneson: University of California
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
Ha Vu: University of California
Emily Maciejewski: 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
Wanding Zhou: Children’s Hospital of Philadelphia
Charles E. Breeze: Altius Institute for Biomedical Sciences
Jason Ernst: University of California
Steve Horvath: University of California Los Angeles

Nature Communications, 2022, vol. 13, issue 1, 1-13

Abstract: 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.

Date: 2022
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DOI: 10.1038/s41467-022-28355-z

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