Analysis of DNA modifications in aging research

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 nextgeneration 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-theart for sequencing methods, bioinformatics tools for converting these large data sets into biological insights, and perspectives on future directions for the field.

Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia

“…Definitions for the regions around the CpG islands have been established and include shores (2Kb upstream and downstream from CpG island) and shelves (2Kb upstream and downstream from shores). Despite their high CG content, CpG islands are mainly unmethylated while methylation is higher in shores and shelves 27 . Analysis of methylation and hydroxymethylation levels covering CpG islands, shores, and shelves revealed that the shores and shelves of Cx3cr1-NuTRAP INTACT positive fractions cells had significantly higher mCG levels (Supplemental Figure 8 A-B) and significantly lower hmCG levels (Supplemental Figure 8 C-D) compared to the other groups.…”

The role of DNA methylation in epigenetics of aging

“…It is now possibly to differentiate between 5mCs and 5hmCs at the nucleotide level by oxidative bisulfite sequencing where DNA is first oxidized with potassium perruthenate before bisulfite conversion. The oxidation step converts 5hmC to uracil, which results in a final sequence output of only 5mC ( Masser et al, 2018 ). As Fig.…”

“…Over the past three decades several assays for measuring DNA methylation have been developed, and Masser et al (2018) have described the advantages and disadvantages of these assays. For example, anti-bodies have been generated that are specific for mC or hmC, which allow investigators to measure global levels of methylation in a DNA sample or in various tissues by immunochemistry.…”

Evaluation of the pharmacokinetics of metformin and acarbose in the common marmoset

“…Certainly, studies testing the effects of compounds like acarbose and metformin on marmoset lifespan would be informative, but such long-term studies should also include more inclusive assessments of health or healthspan [33]. That is, it will be important to test whether acarbose or metformin (or even combination) will slow the physiological, functional and molecular changes associated with aging in mammalian species [34][35][36][37][38][39][40]…”