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Chen H, Xue J, Zhang Z, Zhang G, Xu X, Li H, Zhang R, Ullah N, Chen L, Amanullah, Zang Z, Lai S, He X, Li W, Guan M, Li J, Chen L, Deng C. High-speed rail model reveals the gene tandem amplification mediated by short repeated sequence in eukaryote. Sci Rep 2022; 12:2289. [PMID: 35145182 PMCID: PMC8831618 DOI: 10.1038/s41598-022-06250-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 01/24/2022] [Indexed: 02/08/2023] Open
Abstract
The occurrence of gene duplication/amplification (GDA) provide potential material for adaptive evolution with environmental stress. Several molecular models have been proposed to explain GDA, recombination via short stretches of sequence similarity plays a crucial role. By screening genomes for such events, we propose a “SRS (short repeated sequence) *N + unit + SRS*N” amplified unit under USCE (unequal sister-chromatid exchange) for tandem amplification mediated by SRS with different repeat numbers in eukaryotes. The amplified units identified from 2131 well-organized amplification events that generate multi gene/element copy amplified with subsequent adaptive evolution in the respective species. Genomic data we analyzed showed dynamic changes among related species or subspecies or plants from different ecotypes/strains. This study clarifies the characteristics of variable copy number SRS on both sides of amplified unit under USCE mechanism, to explain well-organized gene tandem amplification under environmental stress mediated by SRS in all eukaryotes.
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Affiliation(s)
- Haidi Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, China
| | - Jingwen Xue
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, China
| | - Zhenghou Zhang
- The Fourth Affiliated Hospital of China Medical University, Shenyang, 110032, China
| | - Geyu Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, China
| | - Xinyuan Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, China
| | - He Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, China
| | - Ruxue Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, China
| | - Najeeb Ullah
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, China
| | - Lvxing Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, China
| | - Amanullah
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, China
| | - Zhuqing Zang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, China
| | - Shanshan Lai
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, China
| | - Ximiao He
- Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.,Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.,Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Wei Li
- Department of Dermatovenereology, Institutes for Systems Genetics, Rare Disease Center, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang Street, Chengdu, 610041, Sichuan, China
| | - Miao Guan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, China.
| | - Jingyi Li
- M.D. Department of Dermatology and Venereology, West China Hospital of Sichuan University, No. 37 Guo Xue Lane, Chengdu, 610041, China.
| | - Liangbiao Chen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education), Institute of Experimental Pathology, Shanghai Ocean University, Shanghai, 201306, China.
| | - Cheng Deng
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, China.
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Zan H, Tat C, Qiu Z, Taylor JR, Guerrero JA, Shen T, Casali P. Rad52 competes with Ku70/Ku86 for binding to S-region DSB ends to modulate antibody class-switch DNA recombination. Nat Commun 2017; 8:14244. [PMID: 28176781 PMCID: PMC5309807 DOI: 10.1038/ncomms14244] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 12/12/2016] [Indexed: 12/13/2022] Open
Abstract
Antibody class-switch DNA recombination (CSR) is initiated by AID-introduced DSBs in the switch (S) regions targeted for recombination, as effected by Ku70/Ku86-mediated NHEJ. Ku-deficient B cells, however, undergo (reduced) CSR through an alternative(A)-NHEJ pathway, which introduces microhomologies in S-S junctions. As microhomology-mediated end-joining requires annealing of single-strand DNA ends, we addressed the contribution of single-strand annealing factors HR Rad52 and translesion DNA polymerase θ to CSR. Compared with their Rad52+/+ counterparts, which display normal CSR, Rad52-/- B cells show increased CSR, fewer intra-Sμ region recombinations, no/minimal microhomologies in S-S junctions, decreased c-Myc/IgH translocations and increased Ku70/Ku86 recruitment to S-region DSB ends. Rad52 competes with Ku70/Ku86 for binding to S-region DSB ends. It also facilitates a Ku-independent DSB repair, which favours intra-S region recombination and mediates, particularly in Ku absence, inter-S-S recombination, as emphasized by the significantly greater CSR reduction in Rad52-/- versus Rad52+/+ B cells on Ku86 knockdown.
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Affiliation(s)
- Hong Zan
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas School of Medicine, UT Health Science Center, San Antonio, Texas 78229, USA
| | - Connie Tat
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas School of Medicine, UT Health Science Center, San Antonio, Texas 78229, USA
| | - Zhifang Qiu
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas School of Medicine, UT Health Science Center, San Antonio, Texas 78229, USA
| | - Julia R. Taylor
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas School of Medicine, UT Health Science Center, San Antonio, Texas 78229, USA
| | - Justin A. Guerrero
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas School of Medicine, UT Health Science Center, San Antonio, Texas 78229, USA
| | - Tian Shen
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas School of Medicine, UT Health Science Center, San Antonio, Texas 78229, USA
| | - Paolo Casali
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas School of Medicine, UT Health Science Center, San Antonio, Texas 78229, USA
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Knisbacher BA, Gerber D, Levanon EY. DNA Editing by APOBECs: A Genomic Preserver and Transformer. Trends Genet 2016; 32:16-28. [PMID: 26608778 DOI: 10.1016/j.tig.2015.10.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 10/18/2015] [Accepted: 10/22/2015] [Indexed: 10/22/2022]
Abstract
Information warfare is not limited to the cyber world because it is waged within our cells as well. The unique AID (activation-induced cytidine deaminase)/APOBEC (apolipoprotein B mRNA editing enzyme, catalytic polypeptide) family comprises proteins that alter DNA sequences by converting deoxycytidines to deoxyuridines through deamination. This C-to-U DNA editing enables them to inhibit parasitic viruses and retrotransposons by disrupting their genomic content. In addition to attacking genomic invaders, APOBECs can target their host genome, which can be beneficial by initiating processes that create antibody diversity needed for the immune system or by accelerating the rate of evolution. AID can also alter gene regulation by removing epigenetic modifications from genomic DNA. However, when uncontrolled, these powerful agents of change can threaten genome stability and eventually lead to cancer.
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Affiliation(s)
- Binyamin A Knisbacher
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900 Israel
| | - Doron Gerber
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900 Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900 Israel.
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