, Volume 40, Issue 1, pp 11–29 | Cite as

Analysis of DNA modifications in aging research

  • Dustin R. Masser
  • Niran Hadad
  • Hunter Porter
  • Michael B. Stout
  • Archana Unnikrishnan
  • David R. Stanford
  • Willard M. FreemanEmail author
Review Article


As geroscience research extends into the role of epigenetics in aging and age-related disease, researchers are being confronted with unfamiliar molecular techniques and data analysis methods that can be difficult to integrate into their work. In this review, we focus on the analysis of DNA modifications, namely cytosine methylation and hydroxymethylation, through next-generation sequencing methods. While older techniques for modification analysis performed relative quantitation across regions of the genome or examined average genome levels, these analyses lack the desired specificity, rigor, and genomic coverage to firmly establish the nature of genomic methylation patterns and their response to aging. With recent methodological advances, such as whole genome bisulfite sequencing (WGBS), bisulfite oligonucleotide capture sequencing (BOCS), and bisulfite amplicon sequencing (BSAS), cytosine modifications can now be readily analyzed with base-specific, absolute quantitation at both cytosine-guanine dinucleotide (CG) and non-CG sites throughout the genome or within specific regions of interest by next-generation sequencing. Additional advances, such as oxidative bisulfite conversion to differentiate methylation from hydroxymethylation and analysis of limited input/single-cells, have great promise for continuing to expand epigenomic capabilities. This review provides a background on DNA modifications, the current state-of-the-art for sequencing methods, bioinformatics tools for converting these large data sets into biological insights, and perspectives on future directions for the field.


Epigenetics Methods DNA methylation 



The authors thank Donald Dunn for assistance with figure generation.

Funding information

This work was supported the Donald W. Reynolds Foundation, the Oklahoma Nathan Shock Center of Excellence in the Biology of Aging Targeted DNA Methylation and Mitochondrial Heteroplasmy Core (P30AG050911), the National Institute on Aging (R01AG026607, F31AG038285, T32AG052363, K99AG051661), the National Eye Institute (R01EY021716, R21EY024520, T32EY023202), and the Oklahoma Center for Advancement of Science and Technology (HR14-174).


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Copyright information

© American Aging Association 2018

Authors and Affiliations

  1. 1.Reynolds Oklahoma Center on AgingUniversity of Oklahoma Health Sciences CenterOklahoma CityUSA
  2. 2.Department of PhysiologyUniversity of Oklahoma Health Sciences CenterOklahoma CityUSA
  3. 3.Oklahoma Nathan Shock Center for AgingUniversity of Oklahoma Health Sciences CenterOklahoma CityUSA
  4. 4.Oklahoma Center for NeuroscienceUniversity of Oklahoma Health Sciences CenterOklahoma CityUSA
  5. 5.Department of Nutritional SciencesUniversity of Oklahoma Health Sciences CenterOklahoma CityUSA
  6. 6.Department of Geriatric MedicineUniversity of Oklahoma Health Sciences CenterOklahoma CityUSA

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