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Shen C, Wang K, Deng X, Chen J. DNA N 6-methyldeoxyadenosine in mammals and human disease. Trends Genet 2022; 38:454-467. [PMID: 34991904 PMCID: PMC9007851 DOI: 10.1016/j.tig.2021.12.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/02/2021] [Accepted: 12/07/2021] [Indexed: 01/07/2023]
Abstract
N6-methyladenine (6mA) is the most prevalent DNA modification in prokaryotes. However, its presence and significance in eukaryotes remain elusive. Recently, with methodology advances in detection and sequencing of 6mA in eukaryotes, 6mA is back in the spotlight. Although multiple studies have reported that 6mA is an important epigenetic mark in eukaryotes and plays a regulatory role in DNA transcription, transposon activation, stress response, and other bioprocesses, there are some discrepancies in the current literature. We review the recent advances in 6mA research in eukaryotes, especially in mammals. In particular, we describe the abundance/distribution of 6mA, its potential role in regulating gene expression, identified regulators, and pathological roles in human diseases, especially in cancer. The limitations faced by the field and future perspectives in 6mA research are also discussed.
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Affiliation(s)
- Chao Shen
- Department of Systems Biology, City of Hope, Monrovia 91007, USA
| | - Kitty Wang
- Department of Systems Biology, City of Hope, Monrovia 91007, USA
| | - Xiaolan Deng
- Department of Systems Biology, City of Hope, Monrovia 91007, USA
| | - Jianjun Chen
- Department of Systems Biology, City of Hope, Monrovia 91007, USA
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Luo GZ, Hao Z, Luo L, Shen M, Sparvoli D, Zheng Y, Zhang Z, Weng X, Chen K, Cui Q, Turkewitz AP, He C. N 6-methyldeoxyadenosine directs nucleosome positioning in Tetrahymena DNA. Genome Biol 2018; 19:200. [PMID: 30454035 PMCID: PMC6245762 DOI: 10.1186/s13059-018-1573-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 10/22/2018] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND N6-methyldeoxyadenosine (6mA or m6dA) was shown more than 40 years ago in simple eukaryotes. Recent studies revealed the presence of 6mA in more prevalent eukaryotes, even in vertebrates. However, functional characterizations have been limited. RESULTS We use Tetrahymena thermophila as a model organism to examine the effects of 6mA on nucleosome positioning. Independent methods reveal the enrichment of 6mA near and after transcription start sites with a periodic pattern and anti-correlation relationship with the positions of nucleosomes. The distribution pattern can be recapitulated by in vitro nucleosome assembly on native Tetrahymena genomic DNA but not on DNA without 6mA. Model DNA containing artificially installed 6mA resists nucleosome assembling compared to unmodified DNA in vitro. Computational simulation indicates that 6mA increases dsDNA rigidity, which disfavors nucleosome wrapping. Knockout of a potential 6mA methyltransferase leads to a transcriptome-wide change of gene expression. CONCLUSIONS These findings uncover a mechanism by which DNA 6mA assists to shape the nucleosome positioning and potentially affects gene expression.
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Affiliation(s)
- Guan-Zheng Luo
- The State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510060, China.
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA.
- Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA.
| | - Ziyang Hao
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
| | - Liangzhi Luo
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, 550025, China
| | - Mingren Shen
- Graduate Program in Biophysics, Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 Univ. Ave., Madison, WI, 53706, USA
| | - Daniela Sparvoli
- Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 East 58th Street, Chicago, IL, 60637, USA
| | - Yuqing Zheng
- Graduate Program in Biophysics, Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 Univ. Ave., Madison, WI, 53706, USA
| | - Zijie Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
| | - Xiaocheng Weng
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
| | - Kai Chen
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
| | - Qiang Cui
- Graduate Program in Biophysics, Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 Univ. Ave., Madison, WI, 53706, USA
| | - Aaron P Turkewitz
- Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 East 58th Street, Chicago, IL, 60637, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA.
- Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA.
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