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Abstract
5-Formyl-2'-deoxycytidine (5fdC) is a naturally occurring nucleobase that is broadly distributed in genomic DNA. 5fdC is produced via the oxidation of 5-methylcytosine (5mdC) by ten-eleven translocation enzyme (TET) and can be further converted to 5-carboxylcytosine (5cadC) by TET. Both 5fdC and 5cadC can be restored to dC by TDG-mediated base excision repair and direct deformylation/decarboxylation. Thus, 5fdC is considered an intermediate in the TET-mediated DNA demethylation pathway. 5fdC also alters the structure and stability of genomic DNA and affects genetic expression. This review summarizes the recent research on 5fdC, detailing its formation, detection and distribution, biological functions and transformation in cells. The challenges and future prospects to further explore the function and metabolism of 5fdC are briefly discussed at the end.
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Affiliation(s)
- Yingqian Zhang
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Chuanzheng Zhou
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin, 300071, China.
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Kizaki S, Zou T, Li Y, Han YW, Suzuki Y, Harada Y, Sugiyama H. Preferential 5-Methylcytosine Oxidation in the Linker Region of Reconstituted Positioned Nucleosomes by Tet1 Protein. Chemistry 2016; 22:16598-16601. [PMID: 27689340 DOI: 10.1002/chem.201602435] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Indexed: 01/31/2023]
Abstract
Tet (ten-eleven translocation) family proteins oxidize 5-methylcytosine (mC) to 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC), and 5-carboxycytosine (caC), and are suggested to be involved in the active DNA demethylation pathway. In this study, we reconstituted positioned mononucleosomes using CpG-methylated 382 bp DNA containing the Widom 601 sequence and recombinant histone octamer, and subjected the nucleosome to treatment with Tet1 protein. The sites of oxidized methylcytosine were identified by bisulfite sequencing. We found that, for the oxidation reaction, Tet1 protein prefers mCs located in the linker region of the nucleosome compared with those located in the core region.
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Affiliation(s)
- Seiichiro Kizaki
- Department of Chemistry, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto-shi, Kyoto, 606-8502, Japan
| | - Tingting Zou
- Department of Chemistry, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto-shi, Kyoto, 606-8502, Japan
| | - Yue Li
- Department of Chemistry, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto-shi, Kyoto, 606-8502, Japan
| | - Yong-Woon Han
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto-shi, Kyoto, 606-8501, Japan
| | - Yuki Suzuki
- Department of Robotics, Graduate School of Engineering, Tohoku University, Aramaki aza Aoba 6-6-01M2-519, Aoba-ku, Sendai, 980-8579, Japan
| | - Yoshie Harada
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto-shi, Kyoto, 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto-shi, Kyoto, 606-8502, Japan.
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto-shi, Kyoto, 606-8501, Japan.
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Booth MJ, Raiber EA, Balasubramanian S. Chemical methods for decoding cytosine modifications in DNA. Chem Rev 2014; 115:2240-54. [PMID: 25094039 PMCID: PMC4378238 DOI: 10.1021/cr5002904] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Michael J Booth
- †Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW United Kingdom
| | - Eun-Ang Raiber
- †Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW United Kingdom
| | - Shankar Balasubramanian
- †Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW United Kingdom.,‡Cambridge Institute, Li Ka Shing Centre, Cancer Research U.K., Robinson Way, Cambridge, CB2 0RE United Kingdom.,§School of Clinical Medicine, The University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0SP United Kingdom
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