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J Am Chem Soc. 2019 Jun 5;141(22):8694-8697. doi: 10.1021/jacs.9b02512. Epub 2019 May 23.

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

Hu L1,2, Liu Y3,4, Han S5,4, Yang L6, Cui X1,2, Gao Y6, Dai Q1,2, Lu X1,2, Kou X6, Zhao Y6, Sheng W7, Gao S6, He X4, He C1,2.

Author information

1
Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics , The University of Chicago , Chicago , Illinois 60637 , United States.
2
Howard Hughes Medical Institute , The University of Chicago , Chicago , Illinois 60637 , United States.
3
Agricultural Genomes Institute at Shenzhen , Chinese Academy of Agricultural Sciences , Shenzhen , Guangdong 518120 , China.
4
Department of Human Genetics , The University of Chicago , Chicago , Illinois 60637 , United States.
5
Joseph J. Zilber School of Public Health , University of Wisconsin , Milwaukee , Wisconsin 53205 , United States.
6
Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology , Tongji University , Shanghai 200092 , China.
7
Department of Mathematics, Statistics and Computer Science , Marquette University , Milwaukee , Wisconsin 53233 , United States.

Abstract

5-Hydroxymethylcytosine (5hmC) arises from the oxidation of 5-methylcytosine (5mC) by Fe2+ 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.

PMID:
31117646
DOI:
10.1021/jacs.9b02512

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