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Analysis of DNA modifications in aging research

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Abstract

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.

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Acknowledgements

The authors thank Donald Dunn for assistance with figure generation.

Funding

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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Authors and Affiliations

  1. Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA

    Dustin R. Masser, Niran Hadad, Hunter Porter, Michael B. Stout, Archana Unnikrishnan, David R. Stanford & Willard M. Freeman

  2. Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA

    Dustin R. Masser, David R. Stanford & Willard M. Freeman

  3. Oklahoma Nathan Shock Center for Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA

    Dustin R. Masser, Niran Hadad, Hunter Porter & Willard M. Freeman

  4. Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA

    Niran Hadad, Hunter Porter, David R. Stanford & Willard M. Freeman

  5. Department of Nutritional Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA

    Michael B. Stout & Willard M. Freeman

  6. Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA

    Archana Unnikrishnan

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  1. Dustin R. Masser
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Correspondence to Willard M. Freeman.

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Masser, D.R., Hadad, N., Porter, H. et al. Analysis of DNA modifications in aging research. GeroScience 40, 11–29 (2018). https://doi.org/10.1007/s11357-018-0005-3

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