DNA methylation aging and transcriptomic studies in horses

Steve Horvath; Amin Haghani; Sichong Peng; Erin N Hales; Joseph A Zoller; Ken Raj; Brenda Larison; Todd R Robeck; Jessica L Petersen; Rebecca R Bellone; Carrie J Finno

doi:10.1038/s41467-021-27754-y

DNA methylation aging and transcriptomic studies in horses

Nat Commun. 2022 Jan 10;13(1):40. doi: 10.1038/s41467-021-27754-y.

Authors

Steve Horvath^#^{1

2}, Amin Haghani^#³, Sichong Peng⁴, Erin N Hales⁴, Joseph A Zoller⁵, Ken Raj⁶, Brenda Larison^{7

8}, Todd R Robeck⁹, Jessica L Petersen¹⁰, Rebecca R Bellone^{4

11}, Carrie J Finno¹²

Affiliations

¹ Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA. shorvath@mednet.ucla.edu.
² Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA. shorvath@mednet.ucla.edu.
³ Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
⁴ Department of Population Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA, USA.
⁵ Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA.
⁶ Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, UK.
⁷ Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.
⁸ Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA.
⁹ Zoological Operations, SeaWorld Parks and Entertainment, 7007 SeaWorld Drive, Orlando, FL, USA.
¹⁰ Department of Animal Science, University of Nebraska, Lincoln, NE, USA.
¹¹ Veterinary Genetics Laboratory, University of California, Davis School of Veterinary Medicine, Davis, CA, USA.
¹² Department of Population Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA, USA. cjfinno@ucdavis.edu.

^# Contributed equally.

Abstract

Cytosine methylation patterns have not yet been thoroughly studied in horses. Here, we profile n = 333 samples from 42 horse tissue types at loci that are highly conserved between mammalian species using a custom array (HorvathMammalMethylChip40). Using the blood and liver tissues from horses, we develop five epigenetic aging clocks: a multi-tissue clock, a blood clock, a liver clock and two dual-species clocks that apply to both horses and humans. In addition, using blood methylation data from three additional equid species (plains zebra, Grevy's zebras and Somali asses), we develop another clock that applies across all equid species. Castration does not significantly impact the epigenetic aging rate of blood or liver samples from horses. Methylation and RNA data from the same tissues define the relationship between methylation and RNA expression across horse tissues. We expect that the multi-tissue atlas will become a valuable resource.

Publication types

Meta-Analysis
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Aging / genetics*
Animals
Blood
DNA Methylation*
Epigenesis, Genetic
Epigenomics
Equidae / genetics
Genetic Techniques
Horses / genetics*
Humans
Liver
Transcriptome*

Abstract

Publication types

MeSH terms

Grants and funding