Current Advances in DNA Methylation Analysis Methods.

Ehsaneh Khodadadi,Ehsan Khodadadi,Sounkalo Dao,Mohammad Asgharzadeh,Sepehr Taghizadeh,Bahman Yousefi,Mehdi Yousefi,Leila Fahmideh,Hossein Samadi Kafil,Koichiro Wada

doi:10.1155/2021/8827516

Abstract

DNA methylation is one of the epigenetic changes, which plays a major role in regulating gene expression and, thus, many biological processes and diseases. There are several methods for determining the methylation of DNA samples. However, selecting the most appropriate method for answering biological questions appears to be a challenging task. The primary methods in DNA methylation focused on identifying the state of methylation of the examined genes and determining the total amount of 5-methyl cytosine. The study of DNA methylation at a large scale of genomic levels became possible following the use of microarray hybridization technology. The new generation of sequencing platforms now allows the preparation of genomic maps of DNA methylation at the single-open level. This review includes the majority of methods available to date, introducing the most widely used methods, the bisulfite treatment, biological identification, and chemical cutting along with their advantages and disadvantages. The techniques are then scrutinized according to their robustness, high throughput capabilities, and cost.

Highlights

Epigenetics is a broad concept used to describe various reversible genomic changes [1]
Epigenetics, in the literal sense of “Beyond Genetics,” refers to inherited changes in gene expression, which result from changes in chromosomes without altering the DNA sequence
DNA methylation is associated with a wide range of biological processes, including deactivation of chromosome X, genomic imprinting, stem cell differentiation, gene expression control, and chromosomal stability [7]

Summary

Introduction

Epigenetics is a broad concept used to describe various reversible genomic changes [1]. DNA methylation, the covalent changes in cytosine, is one of the most widely studied changes in the field of epigenetics and provided a molecular mechanism through which the expression of the gene can be regulated [4, 5]. DNA methylation is associated with a wide range of biological processes, including deactivation of chromosome X, genomic imprinting, stem cell differentiation, gene expression control, and chromosomal stability [7]. These findings indicate that DNA methylation is one of the most important modifications which play an essential role in regulating the growth of the cells and their proliferation. This review provides an overview of the major profiling approaches, with a focus on the recent and promising genome-wide methodologies

Techniques Based on Bisulfite Treatment

Methods based on enzymatic digestion

Techniques Based on Biological Identification

Bisulfite-Free and Enzyme-Free Techniques

Conclusion