DNA methylation dataset of bovine embryonic fibroblast cells treated with epigenetic modifiers and divergent energy supply

Wellison J S Diniz; Matthew S Crouse; Joel S Caton; Kate J Claycombe-Larson; Amanda K Lindholm-Perry; Lawrence P Reynolds; Carl R Dahlen; Pawel P Borowicz; Alison K Ward

doi:10.1016/j.dib.2022.108074

DNA methylation dataset of bovine embryonic fibroblast cells treated with epigenetic modifiers and divergent energy supply

Data Brief. 2022 Mar 22:42:108074. doi: 10.1016/j.dib.2022.108074. eCollection 2022 Jun.

Authors

Wellison J S Diniz¹, Matthew S Crouse², Joel S Caton³, Kate J Claycombe-Larson⁴, Amanda K Lindholm-Perry², Lawrence P Reynolds³, Carl R Dahlen³, Pawel P Borowicz³, Alison K Ward³

Affiliations

¹ Department of Animal Sciences, Auburn University, Auburn, AL, 36849. United States.
² U.S. Meat Animal Research Center, Clay Center, USDA, ARS, NE 68933. United States.
³ Department of Animal Sciences, North Dakota State University, Fargo, 58108. United States.
⁴ Grand Forks Human Nutrition Research Center, USDA, ARS, ND, 58203. United States.

Abstract

Fetal programming is established early in life, likely through epigenetic mechanisms that control gene expression. Micronutrients can act as epigenetic modifiers (EM) by modulating the genome through mechanisms that include DNA methylation and post-translational modification of chromatin. Among the EM, methionine, choline, folate, and vitamin B₁₂ have been suggested as key players of DNA methylation. However, the effects of supplementing these four EM, involved in the methionine folate cycle on DNA methylation, are still under investigation. This manuscript provides the genome-wide DNA methylation dataset (GSE180362) of bovine embryonic fibroblast cells exposed to different supplementation levels of glucose and methionine, choline, folate, and vitamin B₁₂ (collectively named as Epigenetic Modifiers - EM). The DNA methylation was measured using MSP-I digestion and Reduced Representation Bisulfite Sequencing. Bioinformatics analyses included data quality control, read mapping, methylation calling, and differential methylation analyses. Supplementary file S1 and data analysis codes are within this article. To our knowledge, this is the first dataset investigating the effects of four EM in bovine embryonic fibroblast DNA methylation profiles. Furthermore, this data and its findings provide information on putative candidate genes responsive to DNA methylation due to EM supplementation.

Keywords: Embryonic fibroblasts; Epigenetics; Fetal programming; Methylation; One-carbon metabolites.