UdgX-Mediated Uracil Sequencing at Single-Nucleotide Resolution

Jiang，Liudan1,2,3; Yin，Jiayong4; Qian，Maoxiang4; Rong，Shaoqin5; Zhang，Shengqi1,3; Chen，Kejing1,3; Zhao，Chengchen6; Tan，Yuanqing5; Guo，Jiayin7; Chen，Hao8; Gao，Siyun1,3; Liu，Tingting9; Liu，Yi1,3; Shen，Bin7; Yang，Jian1,3; Zhang，Yong6; Meng，Fei Long9; Hu，Jinchuan2; Ma，Honghui1,3,10; Chen，Yi Han1,3

2022-01-26

10.1021/jacs.1c11269

Journal of the American Chemical Society   影响因子和分区

0002-7863

1520-5126

As an aberrant base in DNA, uracil is generated by either deoxyuridine (dU) misincorporation or cytosine deamination, and involved in multiple physiological and pathological processes. Genome-wide profiles of uracil are important for study of these processes. Current methods for whole-genome mapping of uracil all rely on uracil-DNA N-glycosylase (UNG) and are limited in resolution, specificity, and/or sensitivity. Here, we developed a UdgX cross-linking and polymerase stalling sequencing ("Ucaps-seq") method to detect dU at single-nucleotide resolution. First, the specificity of Ucaps-seq was confirmed on synthetic DNA. Then the effectiveness of the approach was verified on two genomes from different sources. Ucaps-seq not only identified the enrichment of dU at dT sites in pemetrexed-treated cancer cells with globally elevated uracil but also detected dU at dC sites within the "WRC"motif in activated B cells which have increased dU in specific regions. Finally, Ucaps-seq was utilized to detect dU introduced by the cytosine base editor (nCas9-APOBEC) and identified a novel off-target site in cellular context. In conclusion, Ucaps-seq is a powerful tool with many potential applications, especially in evaluation of base editing fidelity.

EI

英语

NI论文

其他

National Natural Science Foundation of China[21807013];National Natural Science Foundation of China[31870804];National Natural Science Foundation of China[31971330];National Natural Science Foundation of China[32170586];National Natural Science Foundation of China[81770397];National Natural Science Foundation of China[81930013];National Natural Science Foundation of China[81973997];National Natural Science Foundation of China[82088101];National Natural Science Foundation of China[82170157];

20220511580712

Amines ; DNA ; Genes ; Nucleotides

Biological Materials and Tissue Engineering:461.2 ; Biology:461.9 ; Organic Compounds:804.1

2-s2.0-85123855505

Scopus

1.Department of Cardiology,Shanghai East Hospital,Tongji University School of Medicine,Shanghai,200120,China
2.Shanghai Fifth People's Hospital,Fudan University,Shanghai Key Laboratory of Medical Epigenetics,International Co-laboratory of Medical Epigenetics and Metabolism,Institutes of Biomedical Sciences,Fudan University,Shanghai,200032,China
3.Key Laboratory of Arrhythmias of the Ministry of Education of China,Tongji University School of Medicine,Shanghai,200092,China
4.Institute of Pediatrics,Department of Hematology and Oncology,Children's Hospital of Fudan University,Shanghai Key Laboratory of Medical Epigenetics,International Co-laboratory of Medical Epigenetics and Metabolism,Institutes of Biomedical Sciences,Fudan University,Shanghai,200032,China
5.Shanghai Key Laboratory of Medical Epigenetics,International Co-laboratory of Medical Epigenetics and Metabolism,Institutes of Biomedical Sciences,Fudan University,Shanghai,200032,China
6.School of Life Science and Technology,Tongji University,Shanghai,200092,China
7.State Key Laboratory of Reproductive Medicine,Nanjing Medical University,Nanjing,211166,China
8.School of Medicine,Southern University of Science and Technology,Shenzhen,518055,China
9.State Key Laboratory of Molecular Biology,Shanghai Institute of Biochemistry and Cell Biology,Center for Excellence in Molecular Cell Science,Chinese Academy of Sciences,Shanghai,200031,China
10.Research Units of Origin and Regulation of Heart Rhythm,Chinese Academy of Medical Sciences,Shanghai,200092,China

Jiang，Liudan,Yin，Jiayong,Qian，Maoxiang,et al. UdgX-Mediated Uracil Sequencing at Single-Nucleotide Resolution[J]. Journal of the American Chemical Society,2022,144(3):1323-1331.

Jiang，Liudan.,Yin，Jiayong.,Qian，Maoxiang.,Rong，Shaoqin.,Zhang，Shengqi.,...&Chen，Yi Han.(2022).UdgX-Mediated Uracil Sequencing at Single-Nucleotide Resolution.Journal of the American Chemical Society,144(3),1323-1331.

Jiang，Liudan,et al."UdgX-Mediated Uracil Sequencing at Single-Nucleotide Resolution".Journal of the American Chemical Society 144.3(2022):1323-1331.