Selective Chemical Labeling and Sequencing of 5-Hydroxymethylcytosine in DNA at Single-Base Resolution

Xiaogang Li; Xiaogang Li; Xiaogang Li; Xinxin Shi; Yin Gong; Wenting Guo; Yuanrui Liu; Chunwei Peng; Yingchun Xu; Yingchun Xu

doi:10.3389/fgene.2021.749211

Frontiers in Genetics (Nov 2021)

Selective Chemical Labeling and Sequencing of 5-Hydroxymethylcytosine in DNA at Single-Base Resolution

Xiaogang Li,
Xiaogang Li,
Xiaogang Li,
Xinxin Shi,
Yin Gong,
Wenting Guo,
Yuanrui Liu,
Chunwei Peng,
Yingchun Xu,
Yingchun Xu

Affiliations

Xiaogang Li: Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
Xiaogang Li: Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
Xiaogang Li: Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
Xinxin Shi: Gastrointestinal Surgery Department of the First Affiliated Hospital of Anhui Medical University, Hefei, China
Yin Gong: School of Electronics Engineering and Computer Science, Peking University, Beijing, China
Wenting Guo: Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
Yuanrui Liu: Characteristic Medical Center of the Chinese People’s Armed Police Force, Tianjin, China
Chunwei Peng: Gastrointestinal Surgery Department of the First Affiliated Hospital of Anhui Medical University, Hefei, China
Yingchun Xu: Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
Yingchun Xu: Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China

DOI: https://doi.org/10.3389/fgene.2021.749211
Journal volume & issue: Vol. 12

Abstract

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5-Hydroxymethylcytosine (5hmC), the oxidative product of 5-methylcytosine (5mC) catalyzed by ten-eleven translocation enzymes, plays an important role in many biological processes as an epigenetic mediator. Prior studies have shown that 5hmC can be selectively labeled with chemically modified glucose moieties and enriched using click chemistry with biotin affinity approaches. Besides, DNA deaminases of the AID/APOBEC family can discriminate modified 5hmC bases from cytosine (C) or 5mC. Herein, we developed a method based on embryonic stem cell (ESC) whole-genome analysis, which could enrich 5hmC-containing DNA by selective chemical labeling and locate 5hmC sites at single-base resolution with enzyme-based deamination. The combination experimental design is an extension of previous methods, and we hope that this cost-effective single-base resolution 5hmC sequencing method could be used to promote the mechanism and diagnosis research of 5hmC.

Published in Frontiers in Genetics

ISSN: 1664-8021 (Online)
Publisher: Frontiers Media S.A.
Country of publisher: Switzerland
LCC subjects: Science: Biology (General): Genetics
Website: http://journal.frontiersin.org/journal/genetics

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