» Articles » PMID: 34458826

Quantification and Mapping of DNA Modifications

Overview
Journal RSC Chem Biol
Specialty Biology
Date 2021 Aug 30
PMID 34458826
Citations 17
Authors
Affiliations
Soon will be listed here.
Abstract

Apart from the four canonical nucleobases, DNA molecules carry a number of natural modifications. Substantial evidence shows that DNA modifications can regulate diverse biological processes. Dynamic and reversible modifications of DNA are critical for cell differentiation and development. Dysregulation of DNA modifications is closely related to many human diseases. The research of DNA modifications is a rapidly expanding area and has been significantly stimulated by the innovations of analytical methods. With the recent advances in methods and techniques, a series of new DNA modifications have been discovered in the genomes of prokaryotes and eukaryotes. Deciphering the biological roles of DNA modifications depends on the sensitive detection, accurate quantification, and genome-wide mapping of modifications in genomic DNA. This review provides an overview of the recent advances in analytical methods and techniques for both the quantification and genome-wide mapping of natural DNA modifications. We discuss the principles, advantages, and limitations of these developed methods. It is anticipated that new methods and techniques will resolve the current challenges in this burgeoning research field and expedite the elucidation of the functions of DNA modifications.

Citing Articles

Orthologous mammalian A3A-mediated single-nucleotide resolution sequencing of DNA epigenetic modification 5-hydroxymethylcytosine.

Guo X, Wu J, Ji T, Wang M, Zhang S, Xiong J Chem Sci. 2025; 16(9):3953-3963.

PMID: 39906385 PMC: 11788818. DOI: 10.1039/d4sc08660k.


Epigenetic regulation of cardiovascular diseases induced by behavioral and environmental risk factors: Mechanistic, diagnostic, and therapeutic insights.

Bi F, Gao C, Guo H FASEB Bioadv. 2024; 6(11):477-502.

PMID: 39512842 PMC: 11539034. DOI: 10.1096/fba.2024-00080.


DNA Adductomics: A Narrative Review of Its Development, Applications, and Future.

Cao M, Zhang X Biomolecules. 2024; 14(9).

PMID: 39334939 PMC: 11430648. DOI: 10.3390/biom14091173.


Adenosine Deaminase-Like Gene-Carried Lentivirus Toolkit for Identification of DNA N-Methyladenine Origins.

Liang Z, Chen S, Li Y, Lai W, Wang H Adv Sci (Weinh). 2024; 11(35):e2403376.

PMID: 39023073 PMC: 11425204. DOI: 10.1002/advs.202403376.


Simultaneous detection of 5-methylcytosine and 5-hydroxymethylcytosine at specific genomic loci by engineered deaminase-assisted sequencing.

Xie N, Wang M, Ji T, Guo X, Gang F, Hao Y Chem Sci. 2024; 15(26):10073-10083.

PMID: 38966352 PMC: 11220598. DOI: 10.1039/d4sc00930d.


References
1.
Luo G, Wang F, Weng X, Chen K, Hao Z, Yu M . Characterization of eukaryotic DNA N(6)-methyladenine by a highly sensitive restriction enzyme-assisted sequencing. Nat Commun. 2016; 7:11301. PMC: 4835550. DOI: 10.1038/ncomms11301. View

2.
Chen K, Zhang J, Guo Z, Ma Q, Xu Z, Zhou Y . Loss of 5-hydroxymethylcytosine is linked to gene body hypermethylation in kidney cancer. Cell Res. 2015; 26(1):103-18. PMC: 4816137. DOI: 10.1038/cr.2015.150. View

3.
Boulias K, Greer E . Detection of DNA Methylation in Genomic DNA by UHPLC-MS/MS. Methods Mol Biol. 2020; 2198:79-90. PMC: 8281577. DOI: 10.1007/978-1-0716-0876-0_7. View

4.
Wang Y, Liu C, Yang W, Zou G, Zhang X, Wu F . Naphthalimide derivatives as multifunctional molecules for detecting 5-formylpyrimidine by both PAGE analysis and dot-blot assays. Chem Commun (Camb). 2018; 54(12):1497-1500. DOI: 10.1039/c7cc08715b. View

5.
Hayashi G, Koyama K, Shiota H, Kamio A, Umeda T, Nagae G . Base-Resolution Analysis of 5-Hydroxymethylcytosine by One-Pot Bisulfite-Free Chemical Conversion with Peroxotungstate. J Am Chem Soc. 2016; 138(43):14178-14181. DOI: 10.1021/jacs.6b06428. View