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; Steve Horvath

doi:10.1038/s41467-022-28355-z

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, Steve Horvath

Bloomberg School of Public Health

Research output: Contribution to journal › Article › peer-review

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.

Original language	English (US)
Article number	783
Journal	Nature communications
Volume	13
Issue number	1
DOIs	https://doi.org/10.1038/s41467-022-28355-z
State	Published - Dec 2022

ASJC Scopus subject areas

General Physics and Astronomy
General Chemistry
General Biochemistry, Genetics and Molecular Biology

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Arneson, A., Haghani, A., Thompson, M. J., Pellegrini, M., Kwon, S. B., Vu, H., Maciejewski, E., Yao, M., Li, C. Z., Lu, A. T., Morselli, M., Rubbi, L., Barnes, B., Hansen, K. D., Zhou, W., Breeze, C. E., Ernst, J., & Horvath, S. (2022). A mammalian methylation array for profiling methylation levels at conserved sequences. Nature communications, 13(1), Article 783. https://doi.org/10.1038/s41467-022-28355-z

Arneson, A, Haghani, A, Thompson, MJ, Pellegrini, M, Kwon, SB, Vu, H, Maciejewski, E, Yao, M, Li, CZ, Lu, AT, Morselli, M, Rubbi, L, Barnes, B, Hansen, KD, Zhou, W, Breeze, CE, Ernst, J & Horvath, S 2022, 'A mammalian methylation array for profiling methylation levels at conserved sequences', Nature communications, vol. 13, no. 1, 783. https://doi.org/10.1038/s41467-022-28355-z

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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.",

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AU - Maciejewski, Emily

AU - Yao, Mingjia

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AU - Lu, Ake T.

AU - Morselli, Marco

AU - Rubbi, Liudmilla

AU - Barnes, Bret

AU - Hansen, Kasper D.

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AU - Breeze, Charles E.

AU - Ernst, Jason

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A mammalian methylation array for profiling methylation levels at conserved sequences

Abstract

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