DNA Methylation Sequencing and the Epigenetic Clock

Introduction

The concept of the epigenetic clock represents a groundbreaking means of estimating an individual's biological age by analyzing epigenetic changes within their DNA. Epigenetics delves into the intricate relationship between gene expression patterns and the underlying DNA sequence. Epigenetic clocks rely on the assessment of specific epigenetic marks, such as DNA methylation and histone modifications, to predict an individual's biological age by scrutinizing alterations within their genome.
Please read our article Epigenomics Sequencing: DNA Methylation Analyses Between Eukaryotes and Prokaryotes.

What is the Epigenetic Clock?

As individuals progress through life, their epigenetic marks undergo measurable changes, closely associated with the aging process. These changes offer a unique window into estimating an individual's biological age. It's noteworthy that these epigenetic changes exhibit a consistency across various tissues and cell types. Therefore, by sampling different tissues or cells, researchers can accurately estimate an individual's biological age.

Modeling the Epigenetic Clock

Epigenetic clocks come in various forms, including DNA methylation clocks and histone modification clocks. These clocks are constructed by examining and modeling the correlation between epigenetic marks on DNA and chronological age. The process of epigenetic clock modeling unfolds through a series of well-defined steps:

• Sample Collection and Data Acquisition
  A comprehensive collection of samples, each accompanied by age information, is obtained from diverse sources, including blood, tissues, or other biological specimens. From these samples, DNA is meticulously extracted, and epigenetic markers, such as DNA methylation levels, are precisely quantified.
• Feature Selection
  From the troves of epigenetic marker data, a subset of age-related features is meticulously selected. This selection process often leverages statistical methodologies, machine learning algorithms, and other relevant feature selection techniques.
• Model Building
  The model development journey includes training, evaluation, validation, and optimization. The optimized model is then rigorously tested on independent samples from different datasets to assess its generalization capacity and stability. A validated epigenetic clock model can be wielded to predict the age of unknown samples and to explore age-related phenomena, such as the aging process and disease susceptibility.
• DNA Methylation Analysis and Clock Modeling
  DNA methylation, a fundamental epigenetic modification, significantly influences gene expression by introducing methyl groups to DNA molecules. Recent studies have underlined the pivotal role of DNA methylation in estimating biological age, often referred to as the DNA methylation clock. The process is intrinsically linked to sequencing.

Sequencing Technologies for DNA Methylation Analysis

The advent of next-generation sequencing (NGS) platforms has revolutionized the landscape of methylation analysis within genomics. One of the most common methods for methylation site analysis is based on bisulfite sequencing. Here's how it works: unmethylated cytosine (C) is transformed into uracil (T) through sulfite treatment, while methylated cytosine remains unchanged. The treated DNA samples are subsequently sequenced, and the resultant data is meticulously compared with the reference genome to pinpoint methylation sites.

• Whole Genome Bisulfite Sequencing (WGBS)
  WGBS is a gold-standard bisulfite sequencing method that unveils comprehensive DNA methylation throughout the genome, encompassing both CpG sites and less common non-CpG sites like CNG. This method provides a wealth of data, down to base-level detail at every methylated cytosine site.
  Please read our article Whole Genome Bisulfite Sequencing (WGBS) Data Analysis Pipeline.
• Simplified Representative Bisulfite Sequencing (RRBS)
  RRBS takes bisulfite-based sequencing a step further. It meticulously detects nearly all CpG sites in the entire genome at a base resolution. By strategically cleaving the genome using MspI enzymes (targeting CCGG sites) and employing size selection, RRBS selectively enriches biologically relevant CpG-rich target regions, such as promoters and CpG islands. This method provides a comprehensive view of up to 7-8 million unique CpG sites covering nearly all CpG islands, gene promoters, most genetic regulatory elements, gene bodies, and repetitive DNA sequences.
  Please read our article An Introduction to Reduced Representation Bisulfite Sequencing (RRBS).
• Targeted Bisulfite Sequencing
  Targeted bisulfite sequencing offers the ability to analyze DNA methylation in specific genomic regions at a single nucleotide resolution. It proves invaluable for hypothesis testing within regions of interest, as well as confirming results from genome-wide methylation analyses (e.g., WGBS, RRBS, and MeDIP-seq). Depending on the size of the region of interest, this method may include a PCR-based amplification step for multiple bisulfite-transformed DNA regions in a single reaction or a hybridization capture approach using pre-designed oligonucleotides to isolate DNA regions containing target CpG sites.
  Please read our article Bisulfite Genomic Sequencing (BSP-Seq) - Methylation Identification for ssDNA and dsDNA.

In Conclusion

DNA methylation sequencing serves as a powerful tool for constructing epigenetic clocks, enabling precise estimates of an individual's biological age. Various sequencing methods, such as WGBS, RRBS, and targeted bisulfite sequencing, furnish detailed insights into DNA methylation patterns, facilitating the creation of robust models for age prediction. Moreover, they offer a valuable vantage point for studying the aging process and understanding associated health risks.