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Ni H, Yong-Villalobos L, Gu M, López-Arredondo DL, Chen M, Geng L, Xu G, Herrera-Estrella LR. Adaptive dynamics of extrachromosomal circular DNA in rice under nutrient stress. Nat Commun 2025; 16:4150. [PMID: 40320403 PMCID: PMC12050283 DOI: 10.1038/s41467-025-59572-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Accepted: 04/23/2025] [Indexed: 05/08/2025] Open
Abstract
Extrachromosomal circular DNAs (eccDNAs) have been identified in various eukaryotic organisms and are known to play crucial roles in genomic plasticity. However, in crop plants, the role of eccDNAs in responses to environmental cues, particularly nutritional stresses, remains unexplored. Rice (Oryza sativa ssp. japonica), a vital crop for over half the world's population and an excellent model plant for genomic studies, faces numerous environmental challenges during growth. Therefore, we conduct comprehensive studies investigating the distribution, sequence, and potential responses of rice eccDNAs to nutritional stresses. We describe the changes in the eccDNA landscape at various developmental stages of rice in optimal growth. We also identify eccDNAs overlapping with genes (ecGenes), transposable elements (ecTEs), and full-length repeat units (full-length ecRepeatUnits), whose prevalence responds to nitrogen (N) and phosphorus (P) deficiency. We analyze multiple-fragment eccDNAs and propose a potential TE-mediated homologous recombination mechanism as the origin of rice's multiple-fragment eccDNAs. We provide evidence for the role of eccDNAs in the rice genome plasticity under nutritional stresses and underscore the significance of their abundance and specificity.
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Affiliation(s)
- Hanfang Ni
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing, China
| | - Lenin Yong-Villalobos
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech University, Lubbock, TX, USA
| | - Mian Gu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing, China
| | - Damar Lizbeth López-Arredondo
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech University, Lubbock, TX, USA
| | - Min Chen
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing, China
| | - Liyan Geng
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing, China
| | - Guohua Xu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China.
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing, China.
| | - Luis Rafael Herrera-Estrella
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech University, Lubbock, TX, USA.
- Unidad de Genómica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Gto, Mexico.
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Simonassi-Paiva B, Luz JA, Ribeiro JH, da Silveira JC, de Souza CA, Pappas Jr GJ, de Carvalho JL, Lynch M, Pogue R, Rowan NJ. Identification of eccDNA in Extracellular Vesicles Derived from Human Dermal Fibroblasts Through Nanopore Sequencing. Int J Mol Sci 2025; 26:4144. [PMID: 40362382 PMCID: PMC12071958 DOI: 10.3390/ijms26094144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2025] [Revised: 04/23/2025] [Accepted: 04/23/2025] [Indexed: 05/15/2025] Open
Abstract
Extrachromosomal circular DNAs (eccDNAs) are heterogeneous circular DNA molecules derived from genomic DNA, and believed to be involved in intercellular communication and in natural biological processes. Extracellular vesicles (EVs) are membrane-bound particles released from all cells, and have been shown to contain various classes of nucleic acids. EVs can play a role in intercellular communication and may be used as biomarkers. This constitutes the first study to demonstrate that EVs derived from healthy human dermal fibroblasts carry eccDNA. eccDNA from EVs and their corresponding donor cells were isolated and sequenced on the Oxford Nanopore MinIon platform, followed by the identification of potential eccDNAs through four different bioinformatic pipelines, namely ecc_Finder, cyrcular-calling, CReSIL, and Flec. Our main findings demonstrate that EVs derived from human dermal fibroblasts carry eccDNA; there is variability in the number of eccDNAs identified in the same sample through different pipelines; and there is variability in the identified eccDNAs across biological replicates. Additionally, eccDNAs characterized in this research had (a) sequences as small as 306 base pairs and as large as 28,958 base pairs across all samples, (b) uneven chromosomal distribution, and (c) an average of 49.7% of the identified eccDNAs harboring gene fragments. Future implications for this novel research include using this framework method to elucidate factors and conditions that may influence the skin aging process and related biogenesis in human dermal cells.
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Affiliation(s)
- Bianca Simonassi-Paiva
- Faculty of Science & Health, Technological University of the Shannon, Athlone Campus, N37HD68 Athlone, Ireland; (B.S.-P.); (M.L.)
| | - Julia Alves Luz
- Department of Cell Biology, University of Brasilia, Brasilia 70910-900, DF, Brazil; (J.A.L.); (G.J.P.J.)
| | - Julia Hellena Ribeiro
- Genomic Sciences and Biotechnology Program, Catholic University of Brasília, Brasilia 71966-700, DF, Brazil;
| | - Juliano Coelho da Silveira
- Department of Veterinary Medicine, School of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga 13635-900, SP, Brazil; (J.C.d.S.); (C.A.d.S.)
| | - Camila Azzolin de Souza
- Department of Veterinary Medicine, School of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga 13635-900, SP, Brazil; (J.C.d.S.); (C.A.d.S.)
| | - Georgios Joannis Pappas Jr
- Department of Cell Biology, University of Brasilia, Brasilia 70910-900, DF, Brazil; (J.A.L.); (G.J.P.J.)
| | | | - Mark Lynch
- Faculty of Science & Health, Technological University of the Shannon, Athlone Campus, N37HD68 Athlone, Ireland; (B.S.-P.); (M.L.)
| | - Robert Pogue
- Genomic Sciences and Biotechnology Program, Catholic University of Brasília, Brasilia 71966-700, DF, Brazil;
| | - Neil J. Rowan
- Faculty of Science & Health, Technological University of the Shannon, Athlone Campus, N37HD68 Athlone, Ireland; (B.S.-P.); (M.L.)
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3
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Mao X, Rao G, Li G, Chen S. Insights into Extrachromosomal DNA in Cancer: Biogenesis, Methodologies, Functions, and Therapeutic Potential. Adv Biol (Weinh) 2025; 9:e2400433. [PMID: 39945006 DOI: 10.1002/adbi.202400433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Revised: 02/01/2025] [Indexed: 03/17/2025]
Abstract
Originating from, but independent of, linear chromosomes, extrachromosomal DNA (ecDNA) exists in a more active state of transcription and autonomous replication. It plays a crucial role in the development of malignancies and therapy resistance. Since its discovery in eukaryotic cells more than half a century ago, the biological characteristics and functions of ecDNA have remained unclear due to limitations in detection methods. However, recent advancements in research tools have transformed ecDNA research. It is believed that ecDNA exhibits greater activity in the abnormal amplification of oncogenes, thereby driving cancer progression through their overexpression. Notably, compared to linear DNA, ecDNA can also function as a genomic element with regulatory roles, including both trans- and cis-acting functions. Its critical roles in tumorigenesis, evolution, progression, and drug resistance in malignant tumors are increasingly recognized. This review provides a comprehensive summary of the evolutionary context of ecDNA and highlights significant progress in understanding its biological functions and potential applications as a therapeutic target in malignant tumors.
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Affiliation(s)
- Xudong Mao
- Department of Urology, The Affiliated Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, 310000, P. R. China
| | - Guocheng Rao
- Department of Endocrinology & Metabolism, Daepartment of Biotherapy, Center for Diabetes and Metabolism Research, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610000, P. R. China
| | - Gonghui Li
- Department of Urology, The Affiliated Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, 310000, P. R. China
| | - Shihan Chen
- Department of Endocrinology, The Affiliated Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, 310000, P. R. China
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4
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Dong Y, Yang G, Yang Y, Zhang S, Wang Y, Xu H. Dynamic characterization of circulating tumor DNA in HER2-altered advanced non-small cell lung cancer treated with pyrotinib and apatinib: Exploratory biomarker analysis from PATHER2 study. Lung Cancer 2025; 200:108062. [PMID: 39827483 DOI: 10.1016/j.lungcan.2024.108062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 12/01/2024] [Accepted: 12/14/2024] [Indexed: 01/22/2025]
Abstract
BACKGROUND HER2 mutations are critical drivers of non-small cell lung cancer (NSCLC), affecting 2 %-3 % of patients and often leads to poor prognosis and limited response to conventional therapies. This study investigates the genomic characteristics and prognostic relevance of dynamic circulating tumor DNA (ctDNA) monitoring in advanced NSCLC patients with HER2 mutations treated with pyrotinib and apatinib. METHODS The PATHER2 study included 33 advanced NSCLC patients harboring HER2 mutations or amplification, who received combination therapy of pyrotinib and apatinib. Among them, 27 patients had baseline blood samples available for analysis. Baseline blood samples (n = 27), follow-up samples after one treatment cycle (n = 13), and samples upon disease progression (n = 18) were collected. ctDNA was extracted and sequenced using a 556-gene panel. RESULTS At baseline, HER2 mutations were detected in 21 of 27 patients through ctDNA, and 19 showed consistent results between tissue and blood sample testing. Patients with TP53 and DNMT3A alterations at baseline had significantly shorter progression-free survival (PFS). Dynamic ctDNA monitoring revealed that patients without detectable HER2 mutations after one treatment cycle had longer PFS and a trend toward longer overall survival (OS) compared to those with persistent HER2 mutations. The newly emerged mutations after resistance were infrequently found in HER2, instead primarily enriched in the chromatin remodeling pathway. CONCLUSION ctDNA holds significant value in guiding the treatment of patients with HER2 mutations. Baseline TP53 and DNMT3A alterations, along with persistent HER2 mutations after initial treatment, are associated with poorer prognosis. The primary mechanism of resistance to pyrotinib and apatinib in these patients may be attributed to chromatin remodeling rather than on-target alterations.
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Affiliation(s)
- Yucheng Dong
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Guangjian Yang
- Department of Respiratory Medical Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China
| | - Yaning Yang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Shuyang Zhang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yan Wang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
| | - Haiyan Xu
- Department of Comprehensive Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
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5
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Zhu H, Huangfu L, Chen J, Ji J, Xing X. Exploring the potential of extrachromosomal DNA as a novel oncogenic driver. SCIENCE CHINA. LIFE SCIENCES 2025; 68:144-157. [PMID: 39349791 DOI: 10.1007/s11427-024-2710-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 08/13/2024] [Indexed: 01/03/2025]
Abstract
Extrachromosomal DNA (ecDNA) is a form of circular DNA mostly found in tumor cells. Unlike the typical chromosomal DNA, ecDNA is circular, self-replicating, and carries complete or partial gene fragments. Although ecDNA occurrence remains a rare event in cancer, recent studies have shown that oncogene amplification on ecDNA is widespread throughout many types of cancer, implying that ecDNA plays a central role in accelerating tumor evolution. ecDNA has also been associated with increased tumor mutation burden, chromosomal instability, and even tumor microenvironment remodeling. ecDNA may be crucial in influencing tumor heterogeneity, drug sensitivity, oncogenic senescence, and tumor immunogenicity, leading to a worsening prognosis for tumor patients. In this way, several clinical trials have been conducted to investigate the importance of ecDNA in clinical treatment. In this review, we summarize the biogenesis, characteristics, and current research methods of ecDNA, discuss the vital role of ecDNA-caused tumor heterogeneity in cancers, and highlight the potential role of ecDNA in cancer therapy.
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Affiliation(s)
- Huanbo Zhu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Gastrointestinal Cancer Translational Research Laboratory, Peking University Cancer Hospital & Institute, Beijing, 100142, China
- Department of Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Longtao Huangfu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Gastrointestinal Cancer Translational Research Laboratory, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Junbing Chen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Gastrointestinal Cancer Translational Research Laboratory, Peking University Cancer Hospital & Institute, Beijing, 100142, China
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Jiafu Ji
- Department of Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing, 100142, China.
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Division of Gastrointestinal Cancer Translational Research Laboratory, Peking University Cancer Hospital & Institute, Beijing, 100142, China.
| | - Xiaofang Xing
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Division of Gastrointestinal Cancer Translational Research Laboratory, Peking University Cancer Hospital & Institute, Beijing, 100142, China.
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6
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Wang Z, Yu J, Zhu W, Hong X, Xu Z, Mao S, Huang L, Han P, He C, Song C, Xiang X. Unveiling the mysteries of extrachromosomal circular DNA: from generation to clinical relevance in human cancers and health. Mol Cancer 2024; 23:276. [PMID: 39707444 DOI: 10.1186/s12943-024-02187-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2024] [Accepted: 11/26/2024] [Indexed: 12/23/2024] Open
Abstract
Extrachromosomal circular DNAs (eccDNAs) are a type of circular DNAs originating from but independent of chromosomal DNAs. Nowadays, with the rapid development of sequencing and bioinformatics, the accuracy of eccDNAs detection has significantly improved. This advancement has consequently enhanced the feasibility of exploring the biological characteristics and functions of eccDNAs. This review elucidates the potential mechanisms of eccDNA generation, the existing methods for their detection and analysis, and their basic features. Furthermore, it focuses on the biological functions of eccDNAs in regulating gene expression under both physiological and pathological conditions. Additionally, the review summarizes the clinical implications of eccDNAs in human cancers and health.
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Affiliation(s)
- Zilong Wang
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China
- Department of Andrology, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Jiaying Yu
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Wenli Zhu
- School of Medicine, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Xiaoning Hong
- Clinical Big Data Research Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Zhen Xu
- Department of Andrology, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Shuang Mao
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Lei Huang
- School of Medicine, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Peng Han
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China
- Department of Biology, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Chunxiao He
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China.
| | - Changze Song
- Department of Andrology, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China.
| | - Xi Xiang
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China.
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7
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Kazancev M, Merkulov P, Tiurin K, Demurin Y, Soloviev A, Kirov I. Comparative Analysis of Active LTR Retrotransposons in Sunflower ( Helianthus annuus L.): From Extrachromosomal Circular DNA Detection to Protein Structure Prediction. Int J Mol Sci 2024; 25:13615. [PMID: 39769378 PMCID: PMC11728184 DOI: 10.3390/ijms252413615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2024] [Revised: 11/30/2024] [Accepted: 12/17/2024] [Indexed: 01/16/2025] Open
Abstract
Plant genomes possess numerous transposable element (TE) insertions that have occurred during evolution. Most TEs are silenced or diverged; therefore, they lose their ability to encode proteins and are transposed in the genome. Knowledge of active plant TEs and TE-encoded proteins essential for transposition and evasion of plant cell transposon silencing mechanisms remains limited. This study investigated active long terminal repeat (LTR) retrotransposons (RTEs) in sunflowers (Helianthus annuus), revealing heterogeneous and phylogenetically distinct RTEs triggered by epigenetic changes and heat stress. Many of these RTEs belong to three distinct groups within the Tekay clade, showing significant variations in chromosomal insertion distribution. Through protein analysis of these active RTEs, it was found that Athila RTEs and Tekay group 2 elements possess additional open reading frames (aORFs). The aORF-encoded proteins feature a transposase domain, a transmembrane domain, and nuclear localization signals. The aORF proteins of the Tekay subgroup exhibited remarkable conservation among over 500 Tekay members, suggesting their functional importance in RTE mobility. The predicted 3D structure of the sunflower Tekay aORF protein showed significant homology with Tekay proteins in rice, maize, and sorghum. Additionally, the structural features of aORF proteins resemble those of plant DRBM-containing proteins, suggesting their potential role in RNA-silencing modulation. These findings offer insights into the diversity and activity of sunflower RTEs, emphasizing the conservation and structural characteristics of aORF-encoded proteins.
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Affiliation(s)
- Mikhail Kazancev
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (M.K.); (P.M.); (K.T.); (A.S.)
| | - Pavel Merkulov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (M.K.); (P.M.); (K.T.); (A.S.)
| | - Kirill Tiurin
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (M.K.); (P.M.); (K.T.); (A.S.)
| | - Yakov Demurin
- Pustovoit All-Russia Research Institute of Oilseed Crops, Filatova St. 17, 350038 Krasnodar, Russia;
| | - Alexander Soloviev
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (M.K.); (P.M.); (K.T.); (A.S.)
- All-Russia Center for Plant Quarantine, 140150 Ramenski, Russia
| | - Ilya Kirov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (M.K.); (P.M.); (K.T.); (A.S.)
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Gao X, Liu K, Luo S, Tang M, Liu N, Jiang C, Fang J, Li S, Hou Y, Guo C, Qu K. Comparative analysis of methodologies for detecting extrachromosomal circular DNA. Nat Commun 2024; 15:9208. [PMID: 39448595 PMCID: PMC11502736 DOI: 10.1038/s41467-024-53496-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 10/14/2024] [Indexed: 10/26/2024] Open
Abstract
Extrachromosomal circular DNA (eccDNA) is crucial in oncogene amplification, gene transcription regulation, and intratumor heterogeneity. While various analysis pipelines and experimental methods have been developed for eccDNA identification, their detection efficiencies have not been systematically assessed. To address this, we evaluate the performance of 7 analysis pipelines using seven simulated datasets, in terms of accuracy, identity, duplication rate, and computational resource consumption. We also compare the eccDNA detection efficiency of 7 experimental methods through twenty-one real sequencing datasets. Here, we show that Circle-Map and Circle_finder (bwa-mem-samblaster) outperform the other short-read pipelines. However, Circle_finder (bwa-mem-samblaster) exhibits notable redundancy in its outcomes. CReSIL is the most effective pipeline for eccDNA detection in long-read sequencing data at depths higher than 10X. Moreover, long-read sequencing-based Circle-Seq shows superior efficiency in detecting copy number-amplified eccDNA over 10 kb in length. These results offer valuable insights for researchers in choosing the suitable methods for eccDNA research.
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Affiliation(s)
- Xuyuan Gao
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Ke Liu
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Songwen Luo
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Meifang Tang
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China
| | - Nianping Liu
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Chen Jiang
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China
| | - Jingwen Fang
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- HanGene Biotech, Xiaoshan Innovation Polis, Hangzhou, Zhejiang, China
| | - Shouzhen Li
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yanbing Hou
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Chuang Guo
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
- School of Pharmacy, Bengbu Medical University, Bengbu, China.
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
| | - Kun Qu
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China.
- School of Biomedical Engineering, Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, China.
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9
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Giurgiu M, Wittstruck N, Rodriguez-Fos E, Chamorro González R, Brückner L, Krienelke-Szymansky A, Helmsauer K, Hartebrodt A, Euskirchen P, Koche RP, Haase K, Reinert K, Henssen AG. Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil. Genome Res 2024; 34:1355-1364. [PMID: 39111816 PMCID: PMC11529853 DOI: 10.1101/gr.279123.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 07/29/2024] [Indexed: 08/23/2024]
Abstract
Circular extrachromosomal DNA (ecDNA) is a form of oncogene amplification found across cancer types and associated with poor outcome in patients. ecDNA can be structurally complex and can contain rearranged DNA sequences derived from multiple chromosome locations. As the structure of ecDNA can impact oncogene regulation and may indicate mechanisms of its formation, disentangling it at high resolution from sequencing data is essential. Even though methods have been developed to identify and reconstruct ecDNA in cancer genome sequencing, it remains challenging to resolve complex ecDNA structures, in particular amplicons with shared genomic footprints. We here introduce Decoil, a computational method that combines a breakpoint-graph approach with LASSO regression to reconstruct complex ecDNA and deconvolve co-occurring ecDNA elements with overlapping genomic footprints from long-read nanopore sequencing. Decoil outperforms de novo assembly and alignment-based methods in simulated long-read sequencing data for both simple and complex ecDNAs. Applying Decoil on whole-genome sequencing data uncovered different ecDNA topologies and explored ecDNA structure heterogeneity in neuroblastoma tumors and cell lines, indicating that this method may improve ecDNA structural analyses in cancer.
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Affiliation(s)
- Mădălina Giurgiu
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany;
- Experimental and Clinical Research Center of the Max Delbrück Center and Charité Berlin, 13125 Berlin, Germany
- Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
- Freie Universität Berlin, 14195 Berlin, Germany
| | - Nadine Wittstruck
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
- Experimental and Clinical Research Center of the Max Delbrück Center and Charité Berlin, 13125 Berlin, Germany
- Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Elias Rodriguez-Fos
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
- Experimental and Clinical Research Center of the Max Delbrück Center and Charité Berlin, 13125 Berlin, Germany
- Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Rocío Chamorro González
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
- Experimental and Clinical Research Center of the Max Delbrück Center and Charité Berlin, 13125 Berlin, Germany
- Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
- Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Lotte Brückner
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
- Experimental and Clinical Research Center of the Max Delbrück Center and Charité Berlin, 13125 Berlin, Germany
- Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
- Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Annabell Krienelke-Szymansky
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
- Experimental and Clinical Research Center of the Max Delbrück Center and Charité Berlin, 13125 Berlin, Germany
- Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Konstantin Helmsauer
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
- Experimental and Clinical Research Center of the Max Delbrück Center and Charité Berlin, 13125 Berlin, Germany
- Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Anne Hartebrodt
- Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Philipp Euskirchen
- German Cancer Consortium (DKTK), partner site Berlin, a partnership between DKFZ and Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Kerstin Haase
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
- Experimental and Clinical Research Center of the Max Delbrück Center and Charité Berlin, 13125 Berlin, Germany
- Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | | | - Anton G Henssen
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany;
- Experimental and Clinical Research Center of the Max Delbrück Center and Charité Berlin, 13125 Berlin, Germany
- Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
- Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
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10
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Li F, Ming W, Lu W, Wang Y, Dong X, Bai Y. Bioinformatics advances in eccDNA identification and analysis. Oncogene 2024; 43:3021-3036. [PMID: 39209966 DOI: 10.1038/s41388-024-03138-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 08/09/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024]
Abstract
Extrachromosomal circular DNAs (eccDNAs) are a unique class of chromosome-originating circular DNA molecules, which are closely linked to oncogene amplification. Due to recent technological advances, particularly in high-throughput sequencing technology, bioinformatics methods based on sequencing data have become primary approaches for eccDNA identification and functional analysis. Currently, eccDNA-relevant databases incorporate previously identified eccDNA and provide thorough functional annotations and predictions, thereby serving as a valuable resource for eccDNA research. In this review, we collected around 20 available eccDNA-associated bioinformatics tools, including identification tools and annotation databases, and summarized their properties and capabilities. We evaluated some of the eccDNA detection methods in simulated data to offer recommendations for future eccDNA detection. We also discussed the current limitations and prospects of bioinformatics methodologies in eccDNA research.
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Affiliation(s)
- Fuyu Li
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, PR China
| | - Wenlong Ming
- Institute for AI in Medicine, School of Artificial Intelligence, Nanjing University of Information Science and Technology, Nanjing, 210044, PR China.
| | - Wenxiang Lu
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, PR China
| | - Ying Wang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, PR China
| | - Xianjun Dong
- Adams Center of Parkinson's Disease Research, Yale School of Medicine, Yale University, 100 College St, New Haven, CT, 06511, USA.
- Department of Neurology, Yale School of Medicine, Yale University, 100 College St, New Haven, CT, 06511, USA.
| | - Yunfei Bai
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, PR China.
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11
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Yuan XQ, Zhou N, Song SJ, Xie YX, Chen SQ, Yang TF, Peng X, Zhang CY, Zhu YH, Peng L. Decoding the genomic enigma: Approaches to studying extrachromosomal circular DNA. Heliyon 2024; 10:e36659. [PMID: 39263178 PMCID: PMC11388731 DOI: 10.1016/j.heliyon.2024.e36659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 08/19/2024] [Accepted: 08/20/2024] [Indexed: 09/13/2024] Open
Abstract
Extrachromosomal circular DNA (eccDNA), a pervasive yet enigmatic component of the eukaryotic genome, exists autonomously from its chromosomal counterparts. Ubiquitous in eukaryotes, eccDNA plays a critical role in the orchestration of cellular processes and the etiology of diseases, particularly cancers. However, the full scope of its influence on health and disease remains elusive, presenting a rich vein of research yet to be mined. Unraveling the complexities of eccDNA necessitates a distillation of methodologies - from biogenesis to functional analysis - a landscape we overview in this study with precision and clarity. Here, we systematically outline cutting-edge methodologies from high-throughput sequencing and bioinformatics to experimental validations, showcasing the intricate world of eccDNAs. We combed through a treasure trove of auxiliary research resources and analytical tools. Moreover, we chart a course for future inquiry, illuminating the horizon with potential groundbreaking strategies for designing eccDNA research projects and pioneering new methodological frontiers.
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Affiliation(s)
- Xiao-Qing Yuan
- Guangdong Provincial Key Laboratory of Cancer Pathogenesis and Precision Diagnosis and Treatment, Shenshan Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Shanwei, 516621, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Nan Zhou
- The Affiliated Brain Hospital, Guangzhou Medical University, Guangzhou, 510370, China
| | - Shi-Jian Song
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Yi-Xia Xie
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Shui-Qin Chen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Teng-Fei Yang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Xian Peng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
- Puai Medical College, Shaoyang University, Shaoyang, 422100, China
| | - Chao-Yang Zhang
- Research Unit Analytical Pathology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, 85764, Germany
| | - Ying-Hua Zhu
- Department of Genetic Medicine, Dongguan Children's Hospital Affiliated to Guangdong Medical University, Dongguan, 523325, China
| | - Li Peng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
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12
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Gumińska N, Hałakuc P, Zakryś B, Milanowski R. Circular extrachromosomal DNA in Euglena gracilis under normal and stress conditions. Protist 2024; 175:126033. [PMID: 38574508 DOI: 10.1016/j.protis.2024.126033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/10/2024] [Accepted: 03/27/2024] [Indexed: 04/06/2024]
Abstract
Extrachromosomal circular DNA (eccDNA) enhances genomic plasticity, augmenting its coding and regulatory potential. Advances in high-throughput sequencing have enabled the investigation of these structural variants. Although eccDNAs have been investigated in numerous taxa, they remained understudied in euglenids. Therefore, we examined eccDNAs predicted from Illumina sequencing data of Euglena gracilis Z SAG 1224-5/25, grown under optimal photoperiod and exposed to UV irradiation. We identified approximately 1000 unique eccDNA candidates, about 20% of which were shared across conditions. We also observed a significant enrichment of mitochondrially encoded eccDNA in the UV-irradiated sample. Furthermore, we found that the heterogeneity of eccDNA was reduced in UV-exposed samples compared to cells that were grown in optimal conditions. Hence, eccDNA appears to play a role in the response to oxidative stress in Euglena, as it does in other studied organisms. In addition to contributing to the understanding of Euglena genomes, our results contribute to the validation of bioinformatics pipelines on a large, non-model genome.
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Affiliation(s)
- Natalia Gumińska
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, 101 Żwirki i Wigury Street, 02-089 Warsaw, Poland; Laboratory of RNA Biology, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Street, 02-109 Warsaw, Poland.
| | - Paweł Hałakuc
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, 101 Żwirki i Wigury Street, 02-089 Warsaw, Poland
| | - Bożena Zakryś
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, 101 Żwirki i Wigury Street, 02-089 Warsaw, Poland
| | - Rafał Milanowski
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, 101 Żwirki i Wigury Street, 02-089 Warsaw, Poland.
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13
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Zhou L, Tang W, Ye B, Zou L. Characterization, biogenesis model, and current bioinformatics of human extrachromosomal circular DNA. Front Genet 2024; 15:1385150. [PMID: 38746056 PMCID: PMC11092383 DOI: 10.3389/fgene.2024.1385150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 04/12/2024] [Indexed: 05/16/2024] Open
Abstract
Human extrachromosomal circular DNA, or eccDNA, has been the topic of extensive investigation in the last decade due to its prominent regulatory role in the development of disorders including cancer. With the rapid advancement of experimental, sequencing and computational technology, millions of eccDNA records are now accessible. Unfortunately, the literature and databases only provide snippets of this information, preventing us from fully understanding eccDNAs. Researchers frequently struggle with the process of selecting algorithms and tools to examine eccDNAs of interest. To explain the underlying formation mechanisms of the five basic classes of eccDNAs, we categorized their characteristics and functions and summarized eight biogenesis theories. Most significantly, we created a clear procedure to help in the selection of suitable techniques and tools and thoroughly examined the most recent experimental and bioinformatics methodologies and data resources for identifying, measuring and analyzing eccDNA sequences. In conclusion, we highlighted the current obstacles and prospective paths for eccDNA research, specifically discussing their probable uses in molecular diagnostics and clinical prediction, with an emphasis on the potential contribution of novel computational strategies.
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Affiliation(s)
- Lina Zhou
- School of Medicine, Chongqing University, Department of Clinical Data Research, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing University, Chongqing, China
| | - Wenyi Tang
- School of Medicine, Chongqing University, Department of Clinical Data Research, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing University, Chongqing, China
| | - Bo Ye
- School of Medicine, Chongqing University, Department of Clinical Data Research, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing University, Chongqing, China
| | - Lingyun Zou
- School of Medicine, Chongqing University, Department of Clinical Data Research, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing University, Chongqing, China
- School of Medicine, Jinan University, Guangzhou, Guangdong, China
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14
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Deng E, Fan X. Categorizing Extrachromosomal Circular DNA as Biomarkers in Serum of Cancer. Biomolecules 2024; 14:488. [PMID: 38672504 PMCID: PMC11048305 DOI: 10.3390/biom14040488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/07/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Extrachromosomal circular DNA (eccDNA), a double-stranded circular DNA molecule found in multiple organisms, has garnered an increasing amount of attention in recent years due to its close association with the initiation, malignant progression, and heterogeneous evolution of cancer. The presence of eccDNA in serum assists in non-invasive tumor diagnosis as a biomarker that can be assessed via liquid biopsies. Furthermore, the specific expression patterns of eccDNA provide new insights into personalized cancer therapy. EccDNA plays a pivotal role in tumorigenesis, development, diagnosis, and treatment. In this review, we comprehensively outline the research trajectory of eccDNA, discuss its role as a diagnostic and prognostic biomarker, and elucidate its regulatory mechanisms in cancer. In particular, we emphasize the potential application value of eccDNA in cancer diagnosis and treatment and anticipate the development of novel tumor diagnosis strategies based on serum eccDNA in the future.
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Affiliation(s)
- Enze Deng
- Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, China
| | - Xiaoying Fan
- Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, China
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510005, China
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15
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Zhuang J, Zhang Y, Zhou C, Fan D, Huang T, Feng Q, Lu Y, Zhao Y, Zhao Q, Han B, Lu T. Dynamics of extrachromosomal circular DNA in rice. Nat Commun 2024; 15:2413. [PMID: 38499575 PMCID: PMC10948907 DOI: 10.1038/s41467-024-46691-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 03/06/2024] [Indexed: 03/20/2024] Open
Abstract
The genome's dynamic nature, exemplified by elements like extrachromosomal circular DNA (eccDNA), is crucial for biodiversity and adaptation. Yet, the role of eccDNA in plants, particularly rice, remains underexplored. Here, we identify 25,598 eccDNAs, unveiling the widespread presence of eccDNA across six rice tissues and revealing its formation as a universal and random process. Interestingly, we discover that direct repeats play a pivotal role in eccDNA formation, pointing to a unique origin mechanism. Despite eccDNA's prevalence in coding sequences, its impact on gene expression is minimal, implying its roles beyond gene regulation. We also observe the association between eccDNA's formation and minor chromosomal deletions, providing insights of its possible function in regulating genome stability. Further, we discover eccDNA specifically accumulated in rice leaves, which may be associated with DNA damage caused by environmental stressors like intense light. In summary, our research advances understanding of eccDNA's role in the genomic architecture and offers valuable insights for rice cultivation and breeding.
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Affiliation(s)
- Jundong Zhuang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Yaoxin Zhang
- National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Congcong Zhou
- National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Danlin Fan
- National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Tao Huang
- National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Qi Feng
- National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yiqi Lu
- National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yan Zhao
- National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Qiang Zhao
- National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Bin Han
- National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Tingting Lu
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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16
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Ko I, Kranse OP, Senatori B, Eves-van den Akker S. A Critical Appraisal of DNA Transfer from Plants to Parasitic Cyst Nematodes. Mol Biol Evol 2024; 41:msae030. [PMID: 38366574 PMCID: PMC10899095 DOI: 10.1093/molbev/msae030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 11/15/2023] [Accepted: 12/18/2023] [Indexed: 02/18/2024] Open
Abstract
Plant-parasitic nematodes are one of the most economically important pests of crops. It is widely accepted that horizontal gene transfer-the natural acquisition of foreign genes in parasitic nematodes-contributes to parasitism. However, an apparent paradox has emerged from horizontal gene transfer analyses: On the one hand, distantly related organisms with very dissimilar genetic structures (i.e. bacteria), and only transient interactions with nematodes as far as we know, dominate the list of putative donors, while on the other hand, considerably more closely related organisms (i.e. the host plant), with similar genetic structure (i.e. introns) and documented long-term associations with nematodes, are rare among the list of putative donors. Given that these nematodes ingest cytoplasm from a living plant cell for several weeks, there seems to be a conspicuous absence of plant-derived cases. Here, we used comparative genomic approaches to evaluate possible plant-derived horizontal gene transfer events in plant parasitic nematodes. Our evidence supports a cautionary message for plant-derived horizontal gene transfer cases in the sugar beet cyst nematode, Heterodera schachtii. We propose a 4-step model for horizontal gene transfer from plant to parasite in order to evaluate why the absence of plant-derived horizontal gene transfer cases is observed. We find that the plant genome is mobilized by the nematode during infection, but that uptake of the said "mobilome" is the first major barrier to horizontal gene transfer from host to nematode. These results provide new insight into our understanding of the prevalence/role of nucleic acid exchange in the arms race between plants and plant parasites.
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Affiliation(s)
- Itsuhiro Ko
- Department of Plant Sciences, The Crop Science Centre, University of Cambridge, Cambridge CB2 3EA, UK
- Present address: Department of Plant Pathology, Washington State University, Pullman 99163, USA
| | - Olaf Prosper Kranse
- Department of Plant Sciences, The Crop Science Centre, University of Cambridge, Cambridge CB2 3EA, UK
| | - Beatrice Senatori
- Department of Plant Sciences, The Crop Science Centre, University of Cambridge, Cambridge CB2 3EA, UK
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17
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Fang M, Fang J, Luo S, Liu K, Yu Q, Yang J, Zhou Y, Li Z, Sun R, Guo C, Qu K. eccDNA-pipe: an integrated pipeline for identification, analysis and visualization of extrachromosomal circular DNA from high-throughput sequencing data. Brief Bioinform 2024; 25:bbae034. [PMID: 38349061 PMCID: PMC10862650 DOI: 10.1093/bib/bbae034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/22/2023] [Accepted: 01/11/2024] [Indexed: 02/15/2024] Open
Abstract
Extrachromosomal circular DNA (eccDNA) is currently attracting considerable attention from researchers due to its significant impact on tumor biogenesis. High-throughput sequencing (HTS) methods for eccDNA identification are continually evolving. However, an efficient pipeline for the integrative and comprehensive analysis of eccDNA obtained from HTS data is still lacking. Here, we introduce eccDNA-pipe, an accessible software package that offers a user-friendly pipeline for conducting eccDNA analysis starting from raw sequencing data. This dataset includes data from various sequencing techniques such as whole-genome sequencing (WGS), Circle-seq and Circulome-seq, obtained through short-read sequencing or long-read sequencing. eccDNA-pipe presents a comprehensive solution for both upstream and downstream analysis, encompassing quality control and eccDNA identification in upstream analysis and downstream tasks such as eccDNA length distribution analysis, differential analysis of genes enriched with eccDNA and visualization of eccDNA structures. Notably, eccDNA-pipe automatically generates high-quality publication-ready plots. In summary, eccDNA-pipe provides a comprehensive and user-friendly pipeline for customized analysis of eccDNA research.
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Affiliation(s)
- Minghao Fang
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
- Institute of Advanced Technology, University of Science and Technology of China, Hefei, 230027, China
- Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, 230088, China
| | - Jingwen Fang
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
- HanGene Biotech, Xiaoshan Innovation Polis, Hangzhou, Zhejiang 311200, China
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, 215123, China
| | - Songwen Luo
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Ke Liu
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Qiaoni Yu
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Jiaxuan Yang
- HanGene Biotech, Xiaoshan Innovation Polis, Hangzhou, Zhejiang 311200, China
| | - Youyang Zhou
- HanGene Biotech, Xiaoshan Innovation Polis, Hangzhou, Zhejiang 311200, China
| | - Zongkai Li
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Ruoming Sun
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Chuang Guo
- Department of Rheumatology and Immunology, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230021, China
- School of Pharmacy, Bengbu Medical University, Bengbu, 233030, China
| | - Kun Qu
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
- Institute of Advanced Technology, University of Science and Technology of China, Hefei, 230027, China
- Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, 230088, China
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, 215123, China
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18
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Wu N, Wei L, Zhu Z, Liu Q, Li K, Mao F, Qiao J, Zhao X. Innovative insights into extrachromosomal circular DNAs in gynecologic tumors and reproduction. Protein Cell 2024; 15:6-20. [PMID: 37233789 PMCID: PMC10762679 DOI: 10.1093/procel/pwad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/03/2023] [Indexed: 05/27/2023] Open
Abstract
Originating but free from chromosomal DNA, extrachromosomal circular DNAs (eccDNAs) are organized in circular form and have long been found in unicellular and multicellular eukaryotes. Their biogenesis and function are poorly understood as they are characterized by sequence homology with linear DNA, for which few detection methods are available. Recent advances in high-throughput sequencing technologies have revealed that eccDNAs play crucial roles in tumor formation, evolution, and drug resistance as well as aging, genomic diversity, and other biological processes, bringing it back to the research hotspot. Several mechanisms of eccDNA formation have been proposed, including the breakage-fusion-bridge (BFB) and translocation-deletion-amplification models. Gynecologic tumors and disorders of embryonic and fetal development are major threats to human reproductive health. The roles of eccDNAs in these pathological processes have been partially elucidated since the first discovery of eccDNA in pig sperm and the double minutes in ovarian cancer ascites. The present review summarized the research history, biogenesis, and currently available detection and analytical methods for eccDNAs and clarified their functions in gynecologic tumors and reproduction. We also proposed the application of eccDNAs as drug targets and liquid biopsy markers for prenatal diagnosis and the early detection, prognosis, and treatment of gynecologic tumors. This review lays theoretical foundations for future investigations into the complex regulatory networks of eccDNAs in vital physiological and pathological processes.
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Affiliation(s)
- Ning Wu
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Ling Wei
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, China
- Cancer Center, Peking University Third Hospital, Beijing 100191, China
| | - Zhipeng Zhu
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, China
- Cancer Center, Peking University Third Hospital, Beijing 100191, China
| | - Qiang Liu
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Kailong Li
- Department of Biochemistry and Biophysics, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Fengbiao Mao
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, China
- Cancer Center, Peking University Third Hospital, Beijing 100191, China
| | - Jie Qiao
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
- Beijing Advanced Innovation Center for Genomics, Beijing 100191, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100191, China
| | - Xiaolu Zhao
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
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19
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Lu W, Li F, Ouyang Y, Jiang Y, Zhang W, Bai Y. A comprehensive analysis of library preparation methods shows high heterogeneity of extrachromosomal circular DNA but distinct chromosomal amount levels reflecting different cell states. Analyst 2023; 149:148-160. [PMID: 37987554 DOI: 10.1039/d3an01300f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Extrachromosomal circular DNA (eccDNA) was discovered several decades ago, but little is known about its function. With the development of sequencing technology, several library preparation methods have been developed to elucidate the biogenesis and function of eccDNA. However, different treatment methods have certain biases that can lead to their erroneous interpretation. To address these issues, we compared the performance of different library preparation methods. Our investigation revealed that the utilization of rolling-circle amplification (RCA) and restriction enzyme linearization of mitochondrial DNA (mtDNA) significantly enhanced the efficiency of enriching extrachromosomal circular DNA (eccDNA). However, it also introduced certain biases, such as an unclear peak in ∼160-200 bp periodicity and the absence of a typical motif pattern. Furthermore, given that RCA can lead to a disproportionate change in copy numbers, eccDNA quantification using split and discordant reads should be avoided. Analysis of the genomic and elements distribution of the overall population of eccDNA molecules revealed a high correlation between the replicates, and provided a possible stability signature for eccDNA, which could potentially reflect different cell lines or cell states. However, we found only a few eccDNA with identical junction sites in each replicate, showing a high degree of heterogeneity of eccDNA. The emergence of different motif patterns flanking junctional sites in eccDNAs of varying sizes suggests the involvement of multiple potential mechanisms in eccDNA generation. This study comprehensively compares and discusses various essential approaches for eccDNA library preparation, offering valuable insights and practical advice to researchers involved in characterizing eccDNA.
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Affiliation(s)
- Wenxiang Lu
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096, China.
| | - Fuyu Li
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096, China.
| | - Yunfei Ouyang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096, China.
| | - Yali Jiang
- The Friendship Hospital of Ili Kazakh Autonomous Prefecture, Ili & Jiangsu Joint Institute of Health, Yining, Xinjiang Uygur Autonomous Region, 835000, China
| | - Weizhong Zhang
- Department of Ophthalmology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210029, China
| | - Yunfei Bai
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096, China.
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20
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Smalheiser NR. Mobile circular DNAs regulating memory and communication in CNS neurons. Front Mol Neurosci 2023; 16:1304667. [PMID: 38125007 PMCID: PMC10730651 DOI: 10.3389/fnmol.2023.1304667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023] Open
Abstract
Stimuli that stimulate neurons elicit transcription of immediate-early genes, a process which requires local sites of chromosomal DNA to form double-strand breaks (DSBs) generated by topoisomerase IIb within a few minutes, followed by repair within a few hours. Wakefulness, exploring a novel environment, and contextual fear conditioning also elicit turn-on of synaptic genes requiring DSBs and repair. It has been reported (in non-neuronal cells) that extrachromosomal circular DNA can form at DSBs as the sites are repaired. I propose that activated neurons may generate extrachromosomal circular DNAs during repair at DSB sites, thus creating long-lasting "markers" of that activity pattern which contain sequences from their sites of origin and which regulate long-term gene expression. Although the population of extrachromosomal DNAs is diverse and overall associated with pathology, a subclass of small circular DNAs ("microDNAs," ∼100-400 bases long), largely derives from unique genomic sequences and has attractive features to act as stable, mobile circular DNAs to regulate gene expression in a sequence-specific manner. Circular DNAs can be templates for the transcription of RNAs, particularly small inhibitory siRNAs, circular RNAs and other non-coding RNAs that interact with microRNAs. These may regulate translation and transcription of other genes involved in synaptic plasticity, learning and memory. Another possible fate for mobile DNAs is to be inserted stably into chromosomes after new DSB sites are generated in response to subsequent activation events. Thus, the insertions of mobile DNAs into activity-induced genes may tend to inactivate them and aid in homeostatic regulation to avoid over-excitation, as well as providing a "counter" for a neuron's activation history. Moreover, activated neurons release secretory exosomes that can be transferred to recipient cells to regulate their gene expression. Mobile DNAs may be packaged into exosomes, released in an activity-dependent manner, and transferred to recipient cells, where they may be templates for regulatory RNAs and possibly incorporated into chromosomes. Finally, aging and neurodegenerative diseases (including Alzheimer's disease) are also associated with an increase in DSBs in neurons. It will become important in the future to assess how pathology-associated DSBs may relate to activity-induced mobile DNAs, and whether the latter may potentially contribute to pathogenesis.
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Affiliation(s)
- Neil R. Smalheiser
- Department of Psychiatry, University of Illinois College of Medicine, Chicago, IL, United States
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21
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Zhao X, Zhao H, Liu Y, Guo Z. Methods, bioinformatics tools and databases in ecDNA research: An overview. Comput Biol Med 2023; 167:107680. [PMID: 37976817 DOI: 10.1016/j.compbiomed.2023.107680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/25/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023]
Abstract
Extrachromosomal DNA (ecDNA), derived from chromosomes, is a cancer-specific circular DNA molecule. EcDNA drives tumor initiation and progression, which is associated with poor clinical outcomes and drug resistance in a wide range of cancers. Although ecDNA was first discovered in 1965, tremendous technological revolutions in recent years have provided crucial new insights into its key biological functions and regulatory mechanisms. Here, we provide a thorough overview of the methods, bioinformatics tools, and database resources used in ecDNA research, mainly focusing on their performance, strengths, and limitations. This study can provide important reference for selecting the most appropriate method in ecDNA research. Furthermore, we offer suggestions for the current bioinformatics analysis of ecDNA and provide an outlook to the future research.
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Affiliation(s)
- Xinyu Zhao
- School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Huan Zhao
- Key Laboratory of Marine Bio-resource Restoration and Habitat Reparation, Dalian Ocean University, Dalian, 116023, China
| | - Yupeng Liu
- School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Zhiyun Guo
- School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu, 610031, China.
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22
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Hu J, Zhang Z, Xiao S, Cao Y, Chen Y, Weng J, Jiang H, Li W, Chen JY, Liu C. Microhomology-mediated circular DNA formation from oligonucleosomal fragments during spermatogenesis. eLife 2023; 12:RP87115. [PMID: 37847146 PMCID: PMC10581685 DOI: 10.7554/elife.87115] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023] Open
Abstract
The landscape of extrachromosomal circular DNA (eccDNA) during mammalian spermatogenesis, as well as the biogenesis mechanism, remains to be explored. Here, we revealed widespread eccDNA formation in human sperms and mouse spermatogenesis. We noted that germline eccDNAs are derived from oligonucleosomal DNA fragmentation in cells likely undergoing cell death, providing a potential new way for quality assessment of human sperms. Interestingly, small-sized eccDNAs are associated with euchromatin, while large-sized ones are preferentially generated from heterochromatin. By comparing sperm eccDNAs with meiotic recombination hotspots and structural variations, we found that they are barely associated with de novo germline deletions. We further developed a bioinformatics pipeline to achieve nucleotide-resolution eccDNA detection even with the presence of microhomologous sequences that interfere with precise breakpoint identification. Empowered by our method, we provided strong evidence to show that microhomology-mediated end joining is the major eccDNA biogenesis mechanism. Together, our results shed light on eccDNA biogenesis mechanism in mammalian germline cells.
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Affiliation(s)
- Jun Hu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Department of Andrology, Nanjing Drum Tower Hospital, Nanjing UniversityNanjingChina
| | - Zhe Zhang
- Department of Urology, Department of Reproductive Medicine Center, Peking University Third HospitalBeijingChina
| | - Sai Xiao
- Guangzhou Women and Children's Medical Center, Guangzhou Medical UniversityGuangzhouChina
| | - Yalei Cao
- Department of Urology, Department of Reproductive Medicine Center, Peking University Third HospitalBeijingChina
| | - Yinghong Chen
- Guangzhou Women and Children's Medical Center, Guangzhou Medical UniversityGuangzhouChina
| | - Jiaming Weng
- Department of Urology, Department of Reproductive Medicine Center, Peking University Third HospitalBeijingChina
| | - Hui Jiang
- Department of Urology, Department of Reproductive Medicine Center, Peking University Third HospitalBeijingChina
- Department of Urology, Peking University First Hospital Institute of UrologyBeijingChina
| | - Wei Li
- Guangzhou Women and Children's Medical Center, Guangzhou Medical UniversityGuangzhouChina
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of ScienceBeijingChina
| | - Jia-Yu Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Department of Andrology, Nanjing Drum Tower Hospital, Nanjing UniversityNanjingChina
- Nanchuang (Jiangsu) Institute of Chemistry and HealthNanjingChina
| | - Chao Liu
- Guangzhou Women and Children's Medical Center, Guangzhou Medical UniversityGuangzhouChina
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of ScienceBeijingChina
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23
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Li F, Ming W, Lu W, Wang Y, Li X, Dong X, Bai Y. FLED: a full-length eccDNA detector for long-reads sequencing data. Brief Bioinform 2023; 24:bbad388. [PMID: 37930031 PMCID: PMC10632013 DOI: 10.1093/bib/bbad388] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/24/2023] [Accepted: 09/30/2023] [Indexed: 11/07/2023] Open
Abstract
Reconstructing the full-length sequence of extrachromosomal circular DNA (eccDNA) from short sequencing reads has proved challenging given the similarity of eccDNAs and their corresponding linear DNAs. Previous sequencing methods were unable to achieve high-throughput detection of full-length eccDNAs. Herein, a novel algorithm was developed, called Full-Length eccDNA Detection (FLED), to reconstruct the sequence of eccDNAs based on the strategy that combined rolling circle amplification and nanopore long-reads sequencing technology. Seven human epithelial and cancer cell line samples were analyzed by FLED and over 5000 full-length eccDNAs were identified per sample. The structures of identified eccDNAs were validated by both Polymerase Chain Reaction (PCR) and Sanger sequencing. Compared to other published nanopore-based eccDNA detectors, FLED exhibited higher sensitivity. In cancer cell lines, the genes overlapped with eccDNA regions were enriched in cancer-related pathways and cis-regulatory elements can be predicted in the upstream or downstream of intact genes on eccDNA molecules, and the expressions of these cancer-related genes were dysregulated in tumor cell lines, indicating the regulatory potency of eccDNAs in biological processes. The proposed method takes advantage of nanopore long reads and enables unbiased reconstruction of full-length eccDNA sequences. FLED is implemented using Python3 which is freely available on GitHub (https://github.com/FuyuLi/FLED).
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Affiliation(s)
- Fuyu Li
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, P. R. China
| | - Wenlong Ming
- Institute for AI in Medicine, School of Artificial Intelligence, Nanjing University of Information Science and Technology, Nanjing, 210044, P. R. China
| | - Wenxiang Lu
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, P. R. China
| | - Ying Wang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, P. R. China
| | - Xiaohan Li
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, P. R. China
| | - Xianjun Dong
- Genomics and Bioinformatics Hub, Brigham and Women's Hospital, Boston, MA 02115, USA
- Precision Neurology Program, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Yunfei Bai
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, P. R. China
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24
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Zhang P, Mbodj A, Soundiramourtty A, Llauro C, Ghesquière A, Ingouff M, Keith Slotkin R, Pontvianne F, Catoni M, Mirouze M. Extrachromosomal circular DNA and structural variants highlight genome instability in Arabidopsis epigenetic mutants. Nat Commun 2023; 14:5236. [PMID: 37640706 PMCID: PMC10462705 DOI: 10.1038/s41467-023-41023-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/21/2023] [Indexed: 08/31/2023] Open
Abstract
Abundant extrachromosomal circular DNA (eccDNA) is associated with transposable element (TE) activity. However, how the eccDNA compartment is controlled by epigenetic regulations and what is its impact on the genome is understudied. Here, using long reads, we sequence both the eccDNA compartment and the genome of Arabidopsis thaliana mutant plants affected in DNA methylation and post-transcriptional gene silencing. We detect a high load of TE-derived eccDNA with truncated and chimeric forms. On the genomic side, on top of truncated and full length TE neo-insertions, we detect complex structural variations (SVs) notably at a disease resistance cluster being a natural hotspot of SV. Finally, we serendipitously identify large tandem duplications in hypomethylated plants, suggesting that SVs could have been overlooked in epigenetic mutants. We propose that a high eccDNA load may alter DNA repair pathways leading to genome instability and the accumulation of SVs, at least in plants.
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Affiliation(s)
- Panpan Zhang
- Institut de Recherche pour le Développement (IRD), Laboratory of Plant Genome and Development, Perpignan, France
- EMR269 MANGO (CNRS/IRD/UPVD), Laboratory of Plant Genome and Development, Perpignan, France
- University of Montpellier, Montpellier, France
| | - Assane Mbodj
- Institut de Recherche pour le Développement (IRD), Laboratory of Plant Genome and Development, Perpignan, France
- EMR269 MANGO (CNRS/IRD/UPVD), Laboratory of Plant Genome and Development, Perpignan, France
| | - Abirami Soundiramourtty
- EMR269 MANGO (CNRS/IRD/UPVD), Laboratory of Plant Genome and Development, Perpignan, France
- University of Perpignan, Perpignan, France
| | - Christel Llauro
- EMR269 MANGO (CNRS/IRD/UPVD), Laboratory of Plant Genome and Development, Perpignan, France
- Centre National de la Recherche Scientifique (CNRS), Laboratory of Plant Genome and Development, Perpignan, France
| | - Alain Ghesquière
- DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France
| | - Mathieu Ingouff
- DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Frédéric Pontvianne
- Centre National de la Recherche Scientifique (CNRS), Laboratory of Plant Genome and Development, Perpignan, France
| | - Marco Catoni
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Marie Mirouze
- Institut de Recherche pour le Développement (IRD), Laboratory of Plant Genome and Development, Perpignan, France.
- EMR269 MANGO (CNRS/IRD/UPVD), Laboratory of Plant Genome and Development, Perpignan, France.
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25
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Lin M, Chen Y, Xia S, He Z, Yu X, Huang L, Lin S, Liang B, Huang Z, Mei S, Liu D, Zheng L, Luo Y. Integrative profiling of extrachromosomal circular DNA in placenta and maternal plasma provides insights into the biology of fetal growth restriction and reveals potential biomarkers. Front Genet 2023; 14:1128082. [PMID: 37476414 PMCID: PMC10354665 DOI: 10.3389/fgene.2023.1128082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 02/24/2023] [Indexed: 07/22/2023] Open
Abstract
Introduction: Fetal growth restriction (FGR) is a placenta-mediated pregnancy complication that predisposes fetuses to perinatal complications. Maternal plasma cell-free DNA harbors DNA originating from placental trophoblasts, which is promising for the prenatal diagnosis and prediction of pregnancy complications. Extrachromosomal circular DNA (eccDNA) is emerging as an ideal biomarker and target for several diseases. Methods: We utilized eccDNA sequencing and bioinformatic pipeline to investigate the characteristics and associations of eccDNA in placenta and maternal plasma, the role of placental eccDNA in the pathogenesis of FGR, and potential plasma eccDNA biomarkers of FGR. Results: Using our bioinformatics pipelines, we identified multi-chromosomal-fragment and single-fragment eccDNA in placenta, but almost exclusively single-fragment eccDNA in maternal plasma. Relative to that in plasma, eccDNA in placenta was larger and substantially more abundant in exons, untranslated regions, promoters, repetitive elements [short interspersed nuclear elements (SINEs)/Alu, SINEs/mammalian-wide interspersed repeats, long terminal repeats/endogenous retrovirus-like elements, and single recognition particle RNA], and transcription factor binding motifs. Placental multi-chromosomal-fragment eccDNA was enriched in confident enhancer regions predicted to pertain to genes in apoptosis, energy, cell growth, and autophagy pathways. Placental eccDNA-associated genes whose abundance differed between the FGR and control groups were associated with immunity-related gene ontology (GO) terms. The combined analysis of plasma and placental eccDNA-associated genes in the FGR and control groups led to the identification of potential biomarkers that were assigned to the GO terms of the epigenetic regulation of gene expression and nutrient-related processes, respectively. Conclusion: Together, our results highlight links between placenta functions and multi-chromosomal-fragment and single-fragment eccDNA. The integrative analysis of placental and plasma eccDNA confirmed the potential of these molecules as disease-specific biomarkers of FGR.
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Affiliation(s)
- Minhuan Lin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yiqing Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shuting Xia
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zhiming He
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xuegao Yu
- Clinical Laboratory, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Linhuan Huang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shaobin Lin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Binrun Liang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ziliang Huang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shiqiang Mei
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Dong Liu
- Clinical Laboratory, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Lingling Zheng
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yanmin Luo
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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26
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Dong Y, He Q, Chen X, Yang F, He L, Zheng Y. Extrachromosomal DNA (ecDNA) in cancer: mechanisms, functions, and clinical implications. Front Oncol 2023; 13:1194405. [PMID: 37448518 PMCID: PMC10338009 DOI: 10.3389/fonc.2023.1194405] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/05/2023] [Indexed: 07/15/2023] Open
Abstract
Extrachromosomal DNA (ecDNA) is circular DNA that plays an important role in the development and heterogeneity of cancer. The rapid evolution of methods to detect ecDNA, including microscopic and sequencing approaches, has greatly enhanced our knowledge of the role of ecDNA in cancer development and evolution. Here, we review the molecular characteristics, functions, mechanisms of formation, and detection methods of ecDNA, with a focus on the potential clinical implications of ecDNA in cancer. Specifically, we consider the role of ecDNA in acquired drug resistance, as a diagnostic and prognostic biomarker, and as a therapeutic target in the context of cancer. As the pathological and clinical significance of ecDNA continues to be explored, it is anticipated that ecDNA will have broad applications in the diagnosis, prognosis, and treatment of patients with cancer.
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Affiliation(s)
- Yucheng Dong
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qi He
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xinyu Chen
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Fan Yang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li He
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma, OK, United States
| | - Yongchang Zheng
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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27
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Merkulov P, Egorova E, Kirov I. Composition and Structure of Arabidopsis thaliana Extrachromosomal Circular DNAs Revealed by Nanopore Sequencing. PLANTS (BASEL, SWITZERLAND) 2023; 12:2178. [PMID: 37299157 PMCID: PMC10255303 DOI: 10.3390/plants12112178] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 05/19/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023]
Abstract
Extrachromosomal circular DNAs (eccDNAs) are enigmatic DNA molecules that have been detected in a range of organisms. In plants, eccDNAs have various genomic origins and may be derived from transposable elements. The structures of individual eccDNA molecules and their dynamics in response to stress are poorly understood. In this study, we showed that nanopore sequencing is a useful tool for the detection and structural analysis of eccDNA molecules. Applying nanopore sequencing to the eccDNA molecules of epigenetically stressed Arabidopsis plants grown under various stress treatments (heat, abscisic acid, and flagellin), we showed that TE-derived eccDNA quantity and structure vary dramatically between individual TEs. Epigenetic stress alone did not cause eccDNA up-regulation, whereas its combination with heat stress triggered the generation of full-length and various truncated eccDNAs of the ONSEN element. We showed that the ratio between full-length and truncated eccDNAs is TE- and condition-dependent. Our work paves the way for further elucidation of the structural features of eccDNAs and their connections with various biological processes, such as eccDNA transcription and eccDNA-mediated TE silencing.
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Affiliation(s)
- Pavel Merkulov
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia;
- All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia;
| | - Ekaterina Egorova
- All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia;
| | - Ilya Kirov
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia;
- All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia;
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28
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Jiang R, Yang M, Zhang S, Huang M. Advances in sequencing-based studies of microDNA and ecDNA: Databases, identification methods, and integration with single-cell analysis. Comput Struct Biotechnol J 2023; 21:3073-3080. [PMID: 37273851 PMCID: PMC10238454 DOI: 10.1016/j.csbj.2023.05.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 05/17/2023] [Accepted: 05/17/2023] [Indexed: 06/06/2023] Open
Abstract
Extrachromosomal circular DNA (eccDNA) is a class of circular DNA molecules that originate from genomic DNA but are separate from chromosomes. They are common in various organisms, with sizes ranging from a few hundred to millions of base pairs. A special type of large extrachromosomal DNA (ecDNA) is prevalent in cancer cells. Research on ecDNA has significantly contributed to our comprehension of cancer development, progression, evolution, and drug resistance. The use of next-generation (NGS) and third-generation sequencing (TGS) techniques to identify eccDNAs throughout the genome has become a trend in current research. Here, we briefly review current advances in the biological mechanisms and applications of two distinct types of eccDNAs: microDNA and ecDNA. In addition to presenting available identification tools based on sequencing data, we summarize the most recent efforts to integrate ecDNA with single-cell analysis and put forth suggestions to promote the process.
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Affiliation(s)
| | | | - Shufan Zhang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China
| | - Moli Huang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China
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Gerovska D, Araúzo-Bravo MJ. Skeletal Muscles of Sedentary and Physically Active Aged People Have Distinctive Genic Extrachromosomal Circular DNA Profiles. Int J Mol Sci 2023; 24:ijms24032736. [PMID: 36769072 PMCID: PMC9917053 DOI: 10.3390/ijms24032736] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/19/2023] [Accepted: 01/26/2023] [Indexed: 02/04/2023] Open
Abstract
To bring new extrachromosomal circular DNA (eccDNA) enrichment technologies closer to the clinic, specifically for screening, early diagnosis, and monitoring of diseases or lifestyle conditions, it is paramount to identify the differential pattern of the genic eccDNA signal between two states. Current studies using short-read sequenced purified eccDNA data are based on absolute numbers of unique eccDNAs per sample or per gene, length distributions, or standard methods for RNA-seq differential analysis. Previous analyses of RNA-seq data found significant transcriptomics difference between sedentary and active life style skeletal muscle (SkM) in young people but very few in old. The first attempt using circulomics data from SkM and blood of aged lifelong sedentary and physically active males found no difference at eccDNA level. To improve the capability of finding differences between circulomics data groups, we designed a computational method to identify Differentially Produced per Gene Circles (DPpGCs) from short-read sequenced purified eccDNA data based on the circular junction, split-read signal, of the eccDNA, and implemented it into a software tool DifCir in Matlab. We employed DifCir to find to the distinctive features of the influence of the physical activity or inactivity in the aged SkM that would have remained undetected by transcriptomics methods. We mapped the data from tissue from SkM and blood from two groups of aged lifelong sedentary and physically active males using Circle_finder and subsequent merging and filtering, to find the number and length distribution of the unique eccDNA. Next, we used DifCir to find up-DPpGCs in the SkM of the sedentary and active groups. We assessed the functional enrichment of the DPpGCs using Disease Gene Network and Gene Set Enrichment Analysis. To find genes that produce eccDNA in a group without comparison with another group, we introduced a method to find Common PpGCs (CPpGCs) and used it to find CPpGCs in the SkM of the sedentary and active group. Finally, we found the eccDNA that carries whole genes. We discovered that the eccDNA in the SkM of the sedentary group is not statistically different from that of physically active aged men in terms of number and length distribution of eccDNA. In contrast, with DifCir we found distinctive gene-associated eccDNA fingerprints. We identified statistically significant up-DPpGCs in the two groups, with the top up-DPpGCs shed by the genes AGBL4, RNF213, DNAH7, MED13, and WWTR1 in the sedentary group, and ZBTB7C, TBCD, ITPR2, and DDX11-AS1 in the active group. The up-DPpGCs in both groups carry mostly gene fragments rather than whole genes. Though the subtle transcriptomics difference, we found RYR1 to be both transcriptionally up-regulated and up-DPpGCs gene in sedentary SkM. DifCir emphasizes the high sensitivity of the circulome compared to the transcriptome to detect the molecular fingerprints of exercise in aged SkM. It allows efficient identification of gene hotspots that excise more eccDNA in a health state or disease compared to a control condition.
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Affiliation(s)
- Daniela Gerovska
- Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, Calle Doctor Begiristain s/n, 20014 San Sebastian, Spain
- Correspondence: (D.G.); (M.J.A.-B.)
| | - Marcos J. Araúzo-Bravo
- Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, Calle Doctor Begiristain s/n, 20014 San Sebastian, Spain
- Basque Foundation for Science, IKERBASQUE, Calle María Díaz Harokoa 3, 48013 Bilbao, Spain
- CIBER of Frailty and Healthy Aging (CIBERfes), 28029 Madrid, Spain
- Max Planck Institute for Molecular Biomedicine, Computational Biology and Bioinformatics, Röntgenstr. 20, 48149 Münster, Germany
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of Basque Country (UPV/EHU), 48940 Leioa, Spain
- Correspondence: (D.G.); (M.J.A.-B.)
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Kang J, Dai Y, Li J, Fan H, Zhao Z. Investigating cellular heterogeneity at the single-cell level by the flexible and mobile extrachromosomal circular DNA. Comput Struct Biotechnol J 2023; 21:1115-1121. [PMID: 36789262 PMCID: PMC9900259 DOI: 10.1016/j.csbj.2023.01.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
Extrachromosomal circular DNA (eccDNA) is a special class of DNA derived from linear chromosomes. It coexists independently with linear chromosomes in the nucleus. eccDNA has been identified in multiple organisms, including Homo sapiens, and has been shown to play important roles relevant to tumor progression and drug resistance. To date, computational tools developed for eccDNA detection are only applicable to bulk tissue. Investigating eccDNA at the single-cell level using a computational approach will elucidate the heterogeneous and cell-type-specific landscape of eccDNA within cellular context. Here, we performed the first eccDNA analysis at the single-cell level using data generated by single-cell Assay for Transposase-Accessible Chromatin with sequencing (scATAC-seq) in adult and pediatric glioblastoma (GBM) samples. Glioblastoma multiforme (GBM) is an aggressive tumor of the central nervous system with a poor prognosis. Our analysis provides an overview of cellular origins, genomic distribution, as well as the differential regulations between linear and circular genome under disease- and cell-type-specific conditions across the open chromatin regions in GBM. We focused on some eccDNA elements that are potential mobile enhancers acting in a trans-regulation manner. In summary, this pilot study revealed novel eccDNA features in the cellular context of brain tumor, supporting the strong need for eccDNA investigation at the single-cell level.
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Affiliation(s)
- Jiajinlong Kang
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Yulin Dai
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jinze Li
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA,Department of Epidemiology, Human Genetics, and Environment Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Huihui Fan
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA,Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA,Correspondence to: Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 600, Houston, TX 77030, USA.
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA,Department of Epidemiology, Human Genetics, and Environment Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA,Correspondence to: Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 600, Houston, TX 77030, USA.
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Bajus M, Macko-Podgórni A, Grzebelus D, Baránek M. A review of strategies used to identify transposition events in plant genomes. FRONTIERS IN PLANT SCIENCE 2022; 13:1080993. [PMID: 36531345 PMCID: PMC9751208 DOI: 10.3389/fpls.2022.1080993] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
Transposable elements (TEs) were initially considered redundant and dubbed 'junk DNA'. However, more recently they were recognized as an essential element of genome plasticity. In nature, they frequently become active upon exposition of the host to stress conditions. Even though most transposition events are neutral or even deleterious, occasionally they may happen to be beneficial, resulting in genetic novelty providing better fitness to the host. Hence, TE mobilization may promote adaptability and, in the long run, act as a significant evolutionary force. There are many examples of TE insertions resulting in increased tolerance to stresses or in novel features of crops which are appealing to the consumer. Possibly, TE-driven de novo variability could be utilized for crop improvement. However, in order to systematically study the mechanisms of TE/host interactions, it is necessary to have suitable tools to globally monitor any ongoing TE mobilization. With the development of novel potent technologies, new high-throughput strategies for studying TE dynamics are emerging. Here, we present currently available methods applied to monitor the activity of TEs in plants. We divide them on the basis of their operational principles, the position of target molecules in the process of transposition and their ability to capture real cases of actively transposing elements. Their possible theoretical and practical drawbacks are also discussed. Finally, conceivable strategies and combinations of methods resulting in an improved performance are proposed.
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Affiliation(s)
- Marko Bajus
- Mendeleum—Institute of Genetics, Faculty of Horticulture, Mendel University in Brno, Lednice, Czechia
| | - Alicja Macko-Podgórni
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Kraków, Poland
| | - Dariusz Grzebelus
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Kraków, Poland
| | - Miroslav Baránek
- Mendeleum—Institute of Genetics, Faculty of Horticulture, Mendel University in Brno, Lednice, Czechia
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Joubert PM, Krasileva KV. The extrachromosomal circular DNAs of the rice blast pathogen Magnaporthe oryzae contain a wide variety of LTR retrotransposons, genes, and effectors. BMC Biol 2022; 20:260. [PMID: 36424609 PMCID: PMC9694575 DOI: 10.1186/s12915-022-01457-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/03/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND One of the ways genomes respond to stress is by producing extrachromosomal circular DNAs (eccDNAs). EccDNAs can contain genes and dramatically increase their copy number. They can also reinsert into the genome, generating structural variation. They have been shown to provide a source of phenotypic and genotypic plasticity in several species. However, whole circularome studies have so far been limited to a few model organisms. Fungal plant pathogens are a serious threat to global food security in part because of their rapid adaptation to disease prevention strategies. Understanding the mechanisms fungal pathogens use to escape disease control is paramount to curbing their threat. RESULTS We present a whole circularome sequencing study of the rice blast pathogen, Magnaporthe oryzae. We find that M. oryzae has a highly diverse circularome that contains many genes and shows evidence of large LTR retrotransposon activity. We find that genes enriched on eccDNAs in M. oryzae occur in genomic regions prone to presence-absence variation and that disease-associated genes are frequently on eccDNAs. Finally, we find that a subset of genes is never present on eccDNAs in our data, which indicates that the presence of these genes on eccDNAs is selected against. CONCLUSIONS Our study paves the way to understanding how eccDNAs contribute to adaptation in M. oryzae. Our analysis also reveals how M. oryzae eccDNAs differ from those of other species and highlights the need for further comparative characterization of eccDNAs across species to gain a better understanding of these molecules.
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Affiliation(s)
- Pierre M Joubert
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.
| | - Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.
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Wanchai V, Jenjaroenpun P, Leangapichart T, Arrey G, Burnham CM, Tümmler MC, Delgado-Calle J, Regenberg B, Nookaew I. CReSIL: accurate identification of extrachromosomal circular DNA from long-read sequences. Brief Bioinform 2022; 23:bbac422. [PMID: 36198068 PMCID: PMC10144670 DOI: 10.1093/bib/bbac422] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/17/2022] [Accepted: 08/30/2022] [Indexed: 12/14/2022] Open
Abstract
Extrachromosomal circular DNA (eccDNA) of chromosomal origin is found in many eukaryotic species and cell types, including cancer, where eccDNAs with oncogenes drive tumorigenesis. Most studies of eccDNA employ short-read sequencing for their identification. However, short-read sequencing cannot resolve the complexity of genomic repeats, which can lead to missing eccDNA products. Long-read sequencing technologies provide an alternative to constructing complete eccDNA maps. We present a software suite, Construction-based Rolling-circle-amplification for eccDNA Sequence Identification and Location (CReSIL), to identify and characterize eccDNA from long-read sequences. CReSIL's performance in identifying eccDNA, with a minimum F1 score of 0.98, is superior to the other bioinformatic tools based on simulated data. CReSIL provides many useful features for genomic annotation, which can be used to infer eccDNA function and Circos visualization for eccDNA architecture investigation. We demonstrated CReSIL's capability in several long-read sequencing datasets, including datasets enriched for eccDNA and whole genome datasets from cells containing large eccDNA products. In conclusion, the CReSIL suite software is a versatile tool for investigating complex and simple eccDNA in eukaryotic cells.
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Affiliation(s)
- Visanu Wanchai
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Piroon Jenjaroenpun
- Division of Bioinformatics and Data Management for Research, Research Group and Research Network Division, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Thongpan Leangapichart
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Gerard Arrey
- Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Charles M Burnham
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Maria C Tümmler
- Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jesus Delgado-Calle
- Department of Physiology and Cell Biology, College of Medicine, Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Birgitte Regenberg
- Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
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Zhao Y, Yu L, Zhang S, Su X, Zhou X. Extrachromosomal circular DNA: Current status and future prospects. eLife 2022; 11:81412. [PMID: 36256570 PMCID: PMC9578701 DOI: 10.7554/elife.81412] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/05/2022] [Indexed: 11/25/2022] Open
Abstract
Extrachromosomal circular DNA (eccDNA) is a double-stranded DNA molecule found in various organisms, including humans. In the past few decades, the research on eccDNA has mainly focused on cancers and their associated diseases. Advancements in modern omics technologies have reinvigorated research on eccDNA and shed light on the role of these molecules in a range of diseases and normal cell phenotypes. In this review, we first summarize the formation of eccDNA and its modes of action in eukaryotic cells. We then outline eccDNA as a disease biomarker and reveal its regulatory mechanism. We finally discuss the future prospects of eccDNA, including basic research and clinical application. Thus, with the deepening of understanding and exploration of eccDNAs, they hold great promise in future biomedical research and clinical translational application.
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Affiliation(s)
- Yiheng Zhao
- Department of Cardiology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Linchan Yu
- Department of Cardiology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Shuchen Zhang
- Department of Cardiology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiangyu Su
- Department of Cardiology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiang Zhou
- Department of Cardiology, The Second Affiliated Hospital of Soochow University, Suzhou, China
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35
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Extrachromosomal circular DNA: biogenesis, structure, functions and diseases. Signal Transduct Target Ther 2022; 7:342. [PMID: 36184613 PMCID: PMC9527254 DOI: 10.1038/s41392-022-01176-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 08/14/2022] [Accepted: 09/01/2022] [Indexed: 11/08/2022] Open
Abstract
Extrachromosomal circular DNA (eccDNA), ranging in size from tens to millions of base pairs, is independent of conventional chromosomes. Recently, eccDNAs have been considered an unanticipated major source of somatic rearrangements, contributing to genomic remodeling through chimeric circularization and reintegration of circular DNA into the linear genome. In addition, the origin of eccDNA is considered to be associated with essential chromatin-related events, including the formation of super-enhancers and DNA repair machineries. Moreover, our understanding of the properties and functions of eccDNA has continuously and greatly expanded. Emerging investigations demonstrate that eccDNAs serve as multifunctional molecules in various organisms during diversified biological processes, such as epigenetic remodeling, telomere trimming, and the regulation of canonical signaling pathways. Importantly, its special distribution potentiates eccDNA as a measurable biomarker in many diseases, especially cancers. The loss of eccDNA homeostasis facilitates tumor initiation, malignant progression, and heterogeneous evolution in many cancers. An in-depth understanding of eccDNA provides novel insights for precision cancer treatment. In this review, we summarized the discovery history of eccDNA, discussed the biogenesis, characteristics, and functions of eccDNA. Moreover, we emphasized the role of eccDNA during tumor pathogenesis and malignant evolution. Therapeutically, we summarized potential clinical applications that target aberrant eccDNA in multiple diseases.
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36
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Peng H, Mirouze M, Bucher E. Extrachromosomal circular DNA: A neglected nucleic acid molecule in plants. CURRENT OPINION IN PLANT BIOLOGY 2022; 69:102263. [PMID: 35872391 DOI: 10.1016/j.pbi.2022.102263] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 06/15/2022] [Accepted: 06/19/2022] [Indexed: 06/15/2023]
Abstract
Throughout the years, most plant genomic studies were focused on nuclear chromosomes. Extrachromosomal circular DNA (eccDNA) has largely been neglected for decades since its discovery in 1965. While initial research showed that eccDNAs can originate from highly repetitive sequences, recent findings show that many regions of the genome can contribute to the eccDNA pool. Currently, the biological functions of eccDNAs, if any, are a mystery but recent studies have indicated that they can be regulated by different genomic loci and contribute to stress response and adaptation. In this review, we outline current relevant technological developments facilitating eccDNA identification and the latest discoveries about eccDNAs in plants. Finally, we explore the probable functions and future research directions that could be undertaken with respect to different eccDNA sources.
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Affiliation(s)
- Haoran Peng
- Crop Genome Dynamics Group, Agroscope Changins, 1260, Nyon, Switzerland; Department of Botany and Plant Biology, Section of Biology, Faculty of Science, University of Geneva, 1211, Geneva, Switzerland
| | - Marie Mirouze
- Institut de Recherche pour le Développement (IRD), EMR269 MANGO, Université de Perpignan, 66860 Perpignan, France; Laboratory of Plant Genome and Development, Université de Perpignan, 66860, Perpignan, France.
| | - Etienne Bucher
- Crop Genome Dynamics Group, Agroscope Changins, 1260, Nyon, Switzerland.
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Matthey-Doret C, Colp MJ, Escoll P, Thierry A, Moreau P, Curtis B, Sahr T, Sarrasin M, Gray MW, Lang BF, Archibald JM, Buchrieser C, Koszul R. Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection-related chromatin reorganization. Genome Res 2022; 32:1698-1710. [PMID: 36109147 PMCID: PMC9528979 DOI: 10.1101/gr.276375.121] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 07/25/2022] [Indexed: 11/24/2022]
Abstract
The unicellular amoeba Acanthamoeba castellanii is ubiquitous in aquatic environments, where it preys on bacteria. The organism also hosts bacterial endosymbionts, some of which are parasitic, including human pathogens such as Chlamydia and Legionella spp. Here we report complete, high-quality genome sequences for two extensively studied A. castellanii strains, Neff and C3. Combining long- and short-read data with Hi-C, we generated near chromosome-level assemblies for both strains with 90% of the genome contained in 29 scaffolds for the Neff strain and 31 for the C3 strain. Comparative genomics revealed strain-specific functional enrichment, most notably genes related to signal transduction in the C3 strain and to viral replication in Neff. Furthermore, we characterized the spatial organization of the A. castellanii genome and showed that it is reorganized during infection by Legionella pneumophila Infection-dependent chromatin loops were found to be enriched in genes for signal transduction and phosphorylation processes. In genomic regions where chromatin organization changed during Legionella infection, we found functional enrichment for genes associated with metabolism, organelle assembly, and cytoskeleton organization. Given Legionella infection is known to alter its host's cell cycle, to exploit the host's organelles, and to modulate the host's metabolism in its favor, these changes in chromatin organization may partly be related to mechanisms of host control during Legionella infection.
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Affiliation(s)
- Cyril Matthey-Doret
- Institut Pasteur, CNRS UMR 3525, Université de Paris, Unité Régulation Spatiale des Génomes, F-75015 Paris, France
- Collège Doctoral, Sorbonne Université, F-75005 Paris, France
| | - Morgan J Colp
- Department of Biochemistry and Molecular Biology and Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Pedro Escoll
- Institut Pasteur, Université de Paris, Biologie des Bactéries Intracellulaires and CNRS UMR 6047, F-75015 Paris, France
| | - Agnès Thierry
- Institut Pasteur, CNRS UMR 3525, Université de Paris, Unité Régulation Spatiale des Génomes, F-75015 Paris, France
| | - Pierrick Moreau
- Institut Pasteur, CNRS UMR 3525, Université de Paris, Unité Régulation Spatiale des Génomes, F-75015 Paris, France
| | - Bruce Curtis
- Department of Biochemistry and Molecular Biology and Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Tobias Sahr
- Institut Pasteur, Université de Paris, Biologie des Bactéries Intracellulaires and CNRS UMR 6047, F-75015 Paris, France
| | - Matt Sarrasin
- Robert Cedergren Centre for Bioinformatics and Genomics, Département de Biochimie, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Michael W Gray
- Department of Biochemistry and Molecular Biology and Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - B Franz Lang
- Robert Cedergren Centre for Bioinformatics and Genomics, Département de Biochimie, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - John M Archibald
- Department of Biochemistry and Molecular Biology and Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Carmen Buchrieser
- Institut Pasteur, Université de Paris, Biologie des Bactéries Intracellulaires and CNRS UMR 6047, F-75015 Paris, France
| | - Romain Koszul
- Institut Pasteur, CNRS UMR 3525, Université de Paris, Unité Régulation Spatiale des Génomes, F-75015 Paris, France
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