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Jump-seq: Genome-Wide Capture and Amplification of 5-Hydroxymethylcytosine Sites

Year: 2019
Type: article
Abstract: and 2-oxoglutarate-dependent 10-11 translocation (TET) family proteins. Substantial levels of 5hmC accumulate in many mammalian tissues, especially in neurons and embryonic stem cells, suggesting a potential active role for 5hmC in epigenetic regulation beyond being simply an intermediate of active DNA demethylation. 5mC and 5hmC undergo dynamic changes during embryogenesis, neurogenesis, hematopoietic development, and oncogenesis. While methods have been developed to map 5hmC, more efficient approaches to detect 5hmC at base resolution are still highly desirable. Herein, we present a new method, Jump-seq, to capture and amplify 5hmC in genomic DNA. The principle of this method is to label 5hmC by the 6- N3-glucose moiety and connect a hairpin DNA oligonucleotide carrying an alkyne group to the azide-modified 5hmC via Huisgen cycloaddition (click) chemistry. Primer extension starts from the hairpin motif to the modified 5hmC site and then continues to "land" on genomic DNA. 5hmC sites are inferred from genomic DNA sequences immediately spanning the 5-prime junction. This technology was validated, and its utility in 5hmC identification was confirmed.
DOI: 10.1021/jacs.9b02512
Authors: Lulu Hu, Yuwen Liu, Shengtong Han, Lei Yang, Xiaolong Cui, Yawei Gao, Qing Dai, Xingyu Lu, Xiaochen Kou, Yanhong Zhao, Wenhui Sheng, Shaorong Gao, Xin He, Chuan He
Institutions: Howard Hughes Medical Institute, University of Chicago, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, University of Wisconsin–Milwaukee, Tongji University, Shanghai First Maternity and Infant Hospital, Marquette University
Language: English
Open Access status: green
Funders: Chicago Community Trust, National Natural Science Foundation of China, Ministry of Science and Technology of the People's Republic of China, Science and Technology Commission of Shanghai Municipality, National Institute of Mental Health, National Human Genome Research Institute, National Institute of Neurological Disorders and Stroke
Awards: G4190123819, Epigenetic regulation of neurogenesis, G5413263592, G6984904867, G8014499405, G8651217627, Labeling and sequencing of 5hmC and 5mC in DNA-Renewal
OpenAlex ID: W2944860976
FWCI: 1.36
Cites: 22
Cited by: 37
Related to: 10