Systemic interindividual DNA methylation variants in cattle share major hallmarks with those in humans.

Autor: Chang WJ; Department of Pediatrics, USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, United States., Baker MS; Department of Pediatrics, USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, United States., Laritsky E; Department of Pediatrics, USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, United States., Gunasekara CJ; Department of Pediatrics, USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, United States., Maduranga U; Department of Pediatrics, USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, United States., Galliou JC; Department of Animal Science, Cornell University, Ithaca, NY, United States., McFadden JW; Department of Animal Science, Cornell University, Ithaca, NY, United States., Waltemyer JR; Department of Animal Science, Cornell University, Ithaca, NY, United States., Berggren-Thomas B; Department of Animal Science, Cornell University, Ithaca, NY, United States., Tate BN; Department of Animal Science, Cornell University, Ithaca, NY, United States., Zhang H; Department of Animal Science, Cornell University, Ithaca, NY, United States., Rosen BD; Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, United States., Van Tassell CP; Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, United States., Liu GE; Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, United States., Coarfa C; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States.; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, United States., Ren YA; Department of Animal Science, Cornell University, Ithaca, NY, United States. yi.a.ren@cornell.edu., Waterland RA; Department of Pediatrics, USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, United States. waterland@bcm.edu.; Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, United States. waterland@bcm.edu.
Jazyk: angličtina
Zdroj: Genome biology [Genome Biol] 2024 Jul 15; Vol. 25 (1), pp. 185. Date of Electronic Publication: 2024 Jul 15.
DOI: 10.1186/s13059-024-03307-6
Abstrakt: Background: We recently identified ~ 10,000 correlated regions of systemic interindividual epigenetic variation (CoRSIVs) in the human genome. These methylation variants are amenable to population studies, as DNA methylation measurements in blood provide information on epigenetic regulation throughout the body. Moreover, establishment of DNA methylation at human CoRSIVs is labile to periconceptional influences such as nutrition. Here, we analyze publicly available whole-genome bisulfite sequencing data on multiple tissues of each of two Holstein cows to determine whether CoRSIVs exist in cattle.
Results: Focusing on genomic blocks with ≥ 5 CpGs and a systemic interindividual variation index of at least 20, our approach identifies 217 cattle CoRSIVs, a subset of which we independently validate by bisulfite pyrosequencing. Similar to human CoRSIVs, those in cattle are strongly associated with genetic variation. Also as in humans, we show that establishment of DNA methylation at cattle CoRSIVs is particularly sensitive to early embryonic environment, in the context of embryo culture during assisted reproduction.
Conclusions: Our data indicate that CoRSIVs exist in cattle, as in humans, suggesting these systemic epigenetic variants may be common to mammals in general. To the extent that individual epigenetic variation at cattle CoRSIVs affects phenotypic outcomes, assessment of CoRSIV methylation at birth may become an important tool for optimizing agriculturally important traits. Moreover, adjusting embryo culture conditions during assisted reproduction may provide opportunities to tailor agricultural outcomes by engineering CoRSIV methylation profiles.
(© 2024. The Author(s).)
Databáze: MEDLINE
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