title: Absence of genomic hypomethylation or regulation of cytosine-modifying enzymes with aging in male and female mice.
abstract: BACKGROUND
  Changes to the epigenome with aging, and DNA modifications in particular, have been proposed as a central regulator of the aging process, a predictor of mortality, and a contributor to the pathogenesis of age-related diseases. In the central nervous system, control of learning and memory, neurogenesis, and plasticity require changes in cytosine methylation and hydroxymethylation. Although genome-wide decreases in methylation with aging are often reported as scientific dogma, primary research reports describe decreases, increases, or lack of change in methylation and hydroxymethylation and their principle regulators, DNA methyltransferases and ten-eleven translocation dioxygenases in the hippocampus. Furthermore, existing data are limited to only male animals.
  
  
  RESULTS
  Through examination of the hippocampus in young, adult, and old male and female mice by antibody-based, pyrosequencing, and whole-genome oxidative bisulfite sequencing methods, we provide compelling evidence that contradicts the genomic hypomethylation theory of aging. We also demonstrate that expression of DNA methyltransferases and ten-eleven translocation dioxygenases is not differentially regulated with aging or between the sexes, including the proposed cognitive aging regulator DNMT3a2. Using oxidative bisulfite sequencing that discriminates methylation from hydroxymethylation and by cytosine (CG and non-CG) context, we observe sex differences in average CG methylation and hydroxymethylation of the X chromosome, and small age-related differences in hydroxymethylation of CG island shores and shelves, and methylation of promoter regions.
  
  
  CONCLUSIONS
  These findings clarify a long-standing misconception of the epigenomic response to aging and demonstrate the need for studies of base-specific methylation and hydroxymethylation with aging in both sexes.
authors.affiliation: Oklahoma Center for Neuroscience, Oklahoma City, OK USA ; Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK 73104 USA.
authors.forename: Niran
authors.initials: N
authors.lastname: Hadad
authors.affiliation: Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK 73104 USA ; Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA.
authors.forename: Dustin R
authors.initials: DR
authors.lastname: Masser
authors.affiliation: Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK 73104 USA.
authors.forename: Sreemathi
authors.initials: S
authors.lastname: Logan
authors.affiliation: Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK 73104 USA ; Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Wronowski
authors.affiliation: Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA USA.
authors.forename: Colleen A
authors.initials: CA
authors.lastname: Mangold
authors.affiliation: Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK 73104 USA ; Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Clark
authors.affiliation: Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK 73104 USA ; Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA.
authors.forename: Laura
authors.initials: L
authors.lastname: Otalora
authors.affiliation: Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK 73104 USA.
authors.forename: Archana
authors.initials: A
authors.lastname: Unnikrishnan
authors.affiliation: Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR USA.
authors.forename: Matthew M
authors.initials: MM
authors.lastname: Ford
authors.affiliation: Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA.
authors.forename: Cory B
authors.initials: CB
authors.lastname: Giles
authors.affiliation: Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA ; Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA.
authors.forename: Jonathan D
authors.initials: JD
authors.lastname: Wren
authors.affiliation: Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK 73104 USA ; Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA ; Oklahoma City VA Medical Center, Oklahoma City, OK USA ; Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA.
authors.forename: Arlan
authors.initials: A
authors.lastname: Richardson
authors.affiliation: Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK 73104 USA ; Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA.
authors.forename: William E
authors.initials: WE
authors.lastname: Sonntag
authors.affiliation: Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK 73104 USA ; Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA.
authors.forename: David R
authors.initials: DR
authors.lastname: Stanford
authors.affiliation: Oklahoma Center for Neuroscience, Oklahoma City, OK USA ; Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK 73104 USA ; Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA ; Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA.
authors.forename: Willard
authors.identifier: 0000-0001-7027-999X
authors.initials: W
authors.lastname: Freeman
keywords: 5hmC; 5mC; Aging; DNA hydroxymethylation; DNA methylation; DNMT; Hippocampus; TET