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Review
. 2021 May 21;2(4):1096-1114.
doi: 10.1039/d1cb00022e. eCollection 2021 Aug 5.

Quantification and mapping of DNA modifications

Yi Dai  1 , Bi-Feng Yuan  1   2 , Yu-Qi Feng  1   2
Affiliations
Review

Quantification and mapping of DNA modifications

Yi Dai et al. RSC Chem Biol. .

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.

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Conflict of interest statement

The authors declare no competing financial interest.

Figures

Fig. 1
Fig. 1. Schematic illustration for the overall detection and mapping of DNA modifications. The chemical structures shown in DNA strand represent 5mC, 5hmC, 5fC, 5caC, 6mA, 5hmU, 5fU, base J, 5-glyceryl-mC, 4mC, 6hmA, OG, dADG, dPreQ0 and dPreQ1.
Fig. 2
Fig. 2. Schematic illustration of the chemical conversion-sequencing methods for mapping DNA modifications. (A) Bisulfite sequencing. (B) Bisulfite-free sequencing.
Fig. 3
Fig. 3. Reaction of the chemical labeling-assisted enrichment sequencing of fU-seq (A), fC-seq (B) and OG-seq (C) for mapping DNA modifications.
Fig. 4
Fig. 4. Reaction of the chemical labeling-mediated base transition sequencing of fC-CET (A), CLEVER-seq (B), fC-seq (C-D) and 6mA-seq (E) for mapping DNA modifications.
Fig. 5
Fig. 5. Reaction of the enzyme-mediated labeling-sequencing of hmC-seq (A), hmC-seal (B), GLIB (C) and hmU-seq (D) for mapping DNA modifications.
None
Yi Dai
None
Bi-Feng Yuan
None
Yu-Qi Feng
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