A genome-wide catalog of sites where peripheral DNA methylation reflects the brain

Nishitani, S.; Han, S.; Ishii, T.; Shimura, A.; Phuong, N. J.; Kato, A.; Chambers, M.; Wang, T.; Isozaki, M.; Higashino, Y.; Yamauchi, T.; Kawajiri, S.; Arishima, H.; Kodera, T.; Imoto, H.; Nomura, S.; Yamanishi, K.; Aoyama, B.; Genc, I.; Sakuma, R.; Nguyen, H. D.; Gorantla, N.; Ghasemi, E.; Yao, A.; Kurata, S.; Fujisawa, T. X.; Braun, P. R.; Nagao, T.; Yamanashi, T.; Tomoda, A.; Kikuta, K.; Ooka, T.; Grant, G. A.; Hooper, J. E.; Howard, M. A.; Kawasaki, H.; Potash, J. B.; Snyder, M. P.; Shinozaki, G.

doi:10.64898/2026.10.23.761276

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bioRxiv · 10.64898/2026.10.23.761276

A genome-wide catalog of sites where peripheral DNA methylation reflects the brain

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Abstract

Epigenetic studies of psychiatric and neurological disorders rely largely on peripheral tissues, yet where peripheral DNA methylation (DNAm) reflects the brain remains unclear. We generated a paired brain and peripheral DNAm dataset from 148 donors in three cohorts and combined it with five published cohorts for consensus brain-peripheral correlations. By cross-validation across cohorts, we defined brain epigenome shared sites (BrESS), more than 100,000 CpGs per tissue at which peripheral DNAm reproducibly predicts brain DNAm. BrESS lay at promoters active in both brain and periphery and in housekeeping genes, and most were not explained by genetic effects. BrESS did not contribute to the heritability of seven disorders, and CpGs from epigenome-wide association studies of these disorders were not enriched at BrESS. Peripheral DNAm reflects the brain mainly in a regulatory compartment shared across tissues, outside which disease signals largely lie, and BrESS separate peripheral signals attributable to the brain from others.

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Nishitani, S., Han, S., Ishii, T., Shimura, A., Phuong, N. J., Kato, A., Chambers, M., Wang, T., Isozaki, M., Higashino, Y., Yamauchi, T., Kawajiri, S., Arishima, H., Kodera, T., Imoto, H., Nomura, S., Yamanishi, K., Aoyama, B., Genc, I., Sakuma, R., Nguyen, H. D., Gorantla, N., Ghasemi, E., Yao, A., Kurata, S., Fujisawa, T. X., Braun, P. R., Nagao, T., Yamanashi, T., Tomoda, A., Kikuta, K., Ooka, T., Grant, G. A., Hooper, J. E., Howard, M. A., Kawasaki, H., Potash, J. B., Snyder, M. P., Shinozaki, G.. 2026-10-24. A genome-wide catalog of sites where peripheral DNA methylation reflects the brain. https://doi.org/10.64898/2026.10.23.761276

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