1
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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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2
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Song Y, Yu K, Guo Y, Cao Y, Xu C, Ma L, Zhang Z, Liu Y, Yin J, Hu Z, Shen S, Xu H, Zhang X, Niu S, Cui Y, Lin J. Integration Analysis of Circle-Sequencing and Transcriptome Reveals Extrachromosomal Circular DNA Is Involved in the Regulation of Vascular Cambium Annual Cycle in Chinese Pine. PLANT, CELL & ENVIRONMENT 2025. [PMID: 40205707 DOI: 10.1111/pce.15549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2024] [Revised: 03/29/2025] [Accepted: 03/31/2025] [Indexed: 04/11/2025]
Abstract
Extrachromosomal circular DNA (eccDNA) has been reported to play important roles in regulating genome replication, immune response and cellular communications in humans and animals. Recently, the presence of eccDNA has also recently been discovered in Arabidopsis, Amaranthus palmeri and Oryza sativa. Nevertheless, whether eccDNA exists and has roles in woody plants remains enigmatic. Here, we conducted a comprehensive analysis of morphological imaging, transcriptome and eccDNA expression profiles during different development stages of vascular cambium in Chinese pine (Pinus tabuliformis (P. tabuliformis)). It was found that eccDNA existed in the different development stages of vascular cambium and derived from each chromosome of P. tabuliformis. Further analysis revealed that eccDNA was not entirely random but rather exhibited a certain preference in exon regions. We also identified a high frequency of AA/AT/TT/TA dinucleotide repeats at the junctions of eccDNA and found that the length distribution of eccDNA was clustered between 158 and 316 bp. Notably, integration analysis revealed that differentially expressed eccDNAs and their annotated genes exhibited more significant dynamic changes in the dormant stage as compared with other stages. Taken together, our results provide new insights into the important mechanisms by which eccDNA influences vascular cambium development, enhancing our understanding of its role in tree plasticity.
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Affiliation(s)
- Yushuang Song
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, China
| | - Keji Yu
- Center for Viticulture and Enology, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, China
| | - Yayu Guo
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, China
| | - Yuan Cao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Changwen Xu
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, China
| | - Lingyu Ma
- Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, China
| | - Zhun Zhang
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, China
| | - Yiqun Liu
- College of Life Science, Peking University, Beijing, China
| | - Jinhuan Yin
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, China
| | - Zijian Hu
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, China
| | - Shiya Shen
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, China
| | - Huimin Xu
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xi Zhang
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, China
| | - Shihui Niu
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, China
| | - Yaning Cui
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, China
| | - Jinxing Lin
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, China
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3
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Carvalho-Moore P, Borgato EA, Cutti L, Porri A, Meiners I, Lerchl J, Norsworthy JK, Patterson EL. A rearranged Amaranthus palmeri extrachromosomal circular DNA confers resistance to glyphosate and glufosinate. THE PLANT CELL 2025; 37:koaf069. [PMID: 40152451 PMCID: PMC11985328 DOI: 10.1093/plcell/koaf069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2025] [Revised: 02/07/2025] [Accepted: 02/22/2025] [Indexed: 03/29/2025]
Abstract
Some herbicide-resistant weeds become resistant by generating additional copies of specific loci. For example, amplification of the locus encoding chloroplastic glutamine synthetase (GS2) produces herbicide resistance in the glufosinate-resistant Palmer amaranth (Amaranthus palmeri) accession MSR2. Previously, overamplification of the glyphosate-resistant gene encoding 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) in Palmer amaranth was determined to be driven by an extrachromosomal circular DNA (eccDNA). Here, we describe a rearranged eccDNA that confers resistance to both glyphosate and glufosinate ammonium due to the coduplication of the native chromosomal regions that contain the genes that encode for these herbicides target proteins. In addition to EPSPS, the replicon carries 2 GS2 isoforms (GS2.1 and GS2.2) and other genes. MSR2 samples harbored eccDNA carrying only EPSPS coexisting with eccDNAs harboring both EPSPS and GS2. A second glufosinate-resistant Palmer amaranth accession (MSR1) showed distinct GS2.1 and GS2.2 amplification patterns from MSR2, suggesting the existence of diverse replicons in Palmer amaranth. EPSPS copy number was correlated with both GS2 isoforms copy number in MSR2, further supporting the coexistence of these genes in the same replicon. These findings shed light on the complexity of eccDNA formation in plant systems, with the collection and accumulation of extra pieces of DNA.
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Affiliation(s)
- Pâmela Carvalho-Moore
- Crop, Soil and Environmental Science Department, University of Arkansas, Fayetteville, AR 72703, USA
| | - Ednaldo A Borgato
- Agronomy Department, West Florida Research and Education Center, University of Florida, Jay, FL 32565, USA
| | - Luan Cutti
- Department of Plant, Soil, and Microbial Science, Michigan State University, East Lansing, MI 48823, USA
| | - Aimone Porri
- Global Research & Development Agricultural Solutions, BASF SE, Ludwigshafen 67063, Germany
| | - Ingo Meiners
- Agricultural Solutions North America, BASF Corporation, Research Triangle Park, NC 27709, USA
| | - Jens Lerchl
- Global Research & Development Agricultural Solutions, BASF SE, Ludwigshafen 67063, Germany
| | - Jason K Norsworthy
- Crop, Soil and Environmental Science Department, University of Arkansas, Fayetteville, AR 72703, USA
| | - Eric L Patterson
- Department of Plant, Soil, and Microbial Science, Michigan State University, East Lansing, MI 48823, USA
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4
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Qiu GH, Fu M, Zheng X, Huang C. Protection of the genome and the central exome by peripheral non-coding DNA against DNA damage in health, ageing and age-related diseases. Biol Rev Camb Philos Soc 2025; 100:508-529. [PMID: 39327815 DOI: 10.1111/brv.13151] [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: 09/26/2023] [Revised: 09/15/2024] [Accepted: 09/18/2024] [Indexed: 09/28/2024]
Abstract
DNA in eukaryotic genomes is under constant assault from both exogenous and endogenous sources, leading to DNA damage, which is considered a major molecular driver of ageing. Fortunately, the genome and the central exome are safeguarded against these attacks by abundant peripheral non-coding DNA. Non-coding DNA codes for small non-coding RNAs that inactivate foreign nucleic acids in the cytoplasm and physically blocks these attacks in the nucleus. Damage to non-coding DNA produced during such blockage is removed in the form of extrachromosomal circular DNA (eccDNA) through nucleic pore complexes. Consequently, non-coding DNA serves as a line of defence for the exome against DNA damage. The total amount of non-coding DNA/heterochromatin declines with age, resulting in a decrease in both physical blockage and eccDNA exclusion, and thus an increase in the accumulation of DNA damage in the nucleus during ageing and in age-related diseases. Here, we summarize recent evidence supporting a protective role of non-coding DNA in healthy and pathological states and argue that DNA damage is the proximate cause of ageing and age-related genetic diseases. Strategies aimed at strengthening the protective role of non-coding DNA/heterochromatin could potentially offer better systematic protection for the dynamic genome and the exome against diverse assaults, reduce the burden of DNA damage to the exome, and thus slow ageing, counteract age-related genetic diseases and promote a healthier life for individuals.
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Affiliation(s)
- Guo-Hua Qiu
- College of Life Sciences, Longyan University, Longyan, 364012, People's Republic of China
- Fujian Provincial Key Laboratory of Preventive Veterinary Medicine and Biotechnology, Engineering Research Center for the Prevention and Control of Animal-Origin Zoonosis, Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Province Universities, Longyan, People's Republic of China
| | - Mingjun Fu
- College of Life Sciences, Longyan University, Longyan, 364012, People's Republic of China
- Fujian Provincial Key Laboratory of Preventive Veterinary Medicine and Biotechnology, Engineering Research Center for the Prevention and Control of Animal-Origin Zoonosis, Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Province Universities, Longyan, People's Republic of China
| | - Xintian Zheng
- College of Life Sciences, Longyan University, Longyan, 364012, People's Republic of China
- Fujian Provincial Key Laboratory of Preventive Veterinary Medicine and Biotechnology, Engineering Research Center for the Prevention and Control of Animal-Origin Zoonosis, Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Province Universities, Longyan, People's Republic of China
| | - Cuiqin Huang
- College of Life Sciences, Longyan University, Longyan, 364012, People's Republic of China
- Fujian Provincial Key Laboratory of Preventive Veterinary Medicine and Biotechnology, Engineering Research Center for the Prevention and Control of Animal-Origin Zoonosis, Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Province Universities, Longyan, People's Republic of China
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5
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Eugen-Olsen RB, Hariprakash J, Oestergaard V, Regenberg B. Molecular mechanisms of extrachromosomal circular DNA formation. Nucleic Acids Res 2025; 53:gkaf122. [PMID: 40037708 PMCID: PMC11879418 DOI: 10.1093/nar/gkaf122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 01/26/2025] [Accepted: 02/06/2025] [Indexed: 03/06/2025] Open
Abstract
Recent research reveals that eukaryotic genomes form circular DNA from all parts of their genome, some large enough to carry whole genes. In organisms like yeast and in human cancers, it is often observed that extrachromosomal circular DNA (eccDNA) benefits the individual cell by providing resources for rapid cellular growth. However, our comprehension of eccDNA remains incomplete, primarily due to their transient nature. Early studies suggest they arise when DNA breaks and is subsequently repaired incorrectly. In this review, we provide an overview of the evidence for molecular mechanisms that lead to eccDNA formation in human cancers and yeast, focusing on nonhomologous end joining, alternative end joining, and homologous recombination repair pathways. Furthermore, we present hypotheses in the form of molecular eccDNA formation models and consider cellular conditions which may affect eccDNA generation. Finally, we discuss the framework for future experimental evidence.
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Affiliation(s)
- Rasmus A B Eugen-Olsen
- Department of Biology, University of Copenhagen, Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Judith M Hariprakash
- Department of Biology, University of Copenhagen, Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Vibe H Oestergaard
- Department of Biology, University of Copenhagen, Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Birgitte Regenberg
- Department of Biology, University of Copenhagen, Copenhagen, DK-2200 Copenhagen N, Denmark
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6
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He S, Bing J, Zhong Y, Zheng X, Zhou Z, Wang Y, Hu J, Sun X. PlantCircRNA: a comprehensive database for plant circular RNAs. Nucleic Acids Res 2025; 53:D1595-D1605. [PMID: 39189447 PMCID: PMC11701686 DOI: 10.1093/nar/gkae709] [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: 06/07/2024] [Revised: 07/11/2024] [Accepted: 08/02/2024] [Indexed: 08/28/2024] Open
Abstract
Circular RNAs (circRNAs) represent recently discovered novel regulatory non-coding RNAs. While they are present in many eukaryotes, there has been limited research on plant circRNAs. We developed PlantCircRNA (https://plant.deepbiology.cn/PlantCircRNA/) to fill this gap. The two most important features of PlantCircRNA are (i) it incorporates circRNAs from 94 plant species based on 39 245 RNA-sequencing samples and (ii) it imports the original AtCircDB and CropCircDB databases. We manually curated all circRNAs from published articles, and imported them into the database. Furthermore, we added detailed information of tissue as well as abiotic stresses to the database. To help users understand these circRNAs, the database includes a detection score to measure their consistency and a naming system following the guidelines recently proposed for eukaryotes. Finally, we developed a comprehensive platform for users to visualize, analyze, and download data regarding specific circRNAs. This resource will serve as a home for plant circRNAs and provide the community with unprecedented insights into these mysterious molecule.
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Affiliation(s)
- Shutian He
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Jianhao Bing
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Yang Zhong
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Xiaoyang Zheng
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Ziyu Zhou
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Yifei Wang
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Jiming Hu
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Xiaoyong Sun
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
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7
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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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8
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Abbasi AF, Asim MN, Ahmed S, Dengel A. Long extrachromosomal circular DNA identification by fusing sequence-derived features of physicochemical properties and nucleotide distribution patterns. Sci Rep 2024; 14:9466. [PMID: 38658614 PMCID: PMC11043385 DOI: 10.1038/s41598-024-57457-5] [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: 09/19/2023] [Accepted: 03/18/2024] [Indexed: 04/26/2024] Open
Abstract
Long extrachromosomal circular DNA (leccDNA) regulates several biological processes such as genomic instability, gene amplification, and oncogenesis. The identification of leccDNA holds significant importance to investigate its potential associations with cancer, autoimmune, cardiovascular, and neurological diseases. In addition, understanding these associations can provide valuable insights about disease mechanisms and potential therapeutic approaches. Conventionally, wet lab-based methods are utilized to identify leccDNA, which are hindered by the need for prior knowledge, and resource-intensive processes, potentially limiting their broader applicability. To empower the process of leccDNA identification across multiple species, the paper in hand presents the very first computational predictor. The proposed iLEC-DNA predictor makes use of SVM classifier along with sequence-derived nucleotide distribution patterns and physicochemical properties-based features. In addition, the study introduces a set of 12 benchmark leccDNA datasets related to three species, namely Homo sapiens (HM), Arabidopsis Thaliana (AT), and Saccharomyces cerevisiae (SC/YS). It performs large-scale experimentation across 12 benchmark datasets under different experimental settings using the proposed predictor, more than 140 baseline predictors, and 858 encoder ensembles. The proposed predictor outperforms baseline predictors and encoder ensembles across diverse leccDNA datasets by producing average performance values of 81.09%, 62.2% and 81.08% in terms of ACC, MCC and AUC-ROC across all the datasets. The source code of the proposed and baseline predictors is available at https://github.com/FAhtisham/Extrachrosmosomal-DNA-Prediction . To facilitate the scientific community, a web application for leccDNA identification is available at https://sds_genetic_analysis.opendfki.de/iLEC_DNA/.
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Affiliation(s)
- Ahtisham Fazeel Abbasi
- Department of Computer Science, Rhineland-Palatinate Technical University of Kaiserslautern-Landau, 67663, Kaiserslautern, Germany.
- German Research Center for Artificial Intelligence GmbH, 67663, Kaiserslautern, Germany.
| | - Muhammad Nabeel Asim
- German Research Center for Artificial Intelligence GmbH, 67663, Kaiserslautern, Germany.
| | - Sheraz Ahmed
- German Research Center for Artificial Intelligence GmbH, 67663, Kaiserslautern, Germany
| | - Andreas Dengel
- Department of Computer Science, Rhineland-Palatinate Technical University of Kaiserslautern-Landau, 67663, Kaiserslautern, Germany
- German Research Center for Artificial Intelligence GmbH, 67663, Kaiserslautern, Germany
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9
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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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10
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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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11
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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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12
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Kirov I. Toward Transgene-Free Transposon-Mediated Biological Mutagenesis for Plant Breeding. Int J Mol Sci 2023; 24:17054. [PMID: 38069377 PMCID: PMC10706983 DOI: 10.3390/ijms242317054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
Genetic diversity is a key factor for plant breeding. The birth of novel genic and genomic variants is also crucial for plant adaptation in nature. Therefore, the genomes of almost all living organisms possess natural mutagenic mechanisms. Transposable elements (TEs) are a major mutagenic force driving genetic diversity in wild plants and modern crops. The relatively rare TE transposition activity during the thousand-year crop domestication process has led to the phenotypic diversity of many cultivated species. The utilization of TE mutagenesis by artificial and transient acceleration of their activity in a controlled mode is an attractive foundation for a novel type of mutagenesis called TE-mediated biological mutagenesis. Here, I focus on TEs as mutagenic sources for plant breeding and discuss existing and emerging transgene-free approaches for TE activation in plants. Furthermore, I also review the non-randomness of TE insertions in a plant genome and the molecular and epigenetic factors involved in shaping TE insertion preferences. Additionally, I discuss the molecular mechanisms that prevent TE transpositions in germline plant cells (e.g., meiocytes, pollen, egg and embryo cells, and shoot apical meristem), thereby reducing the chances of TE insertion inheritance. Knowledge of these mechanisms can expand the TE activation toolbox using novel gene targeting approaches. Finally, the challenges and future perspectives of plant populations with induced novel TE insertions (iTE plant collections) are discussed.
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Affiliation(s)
- Ilya Kirov
- All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia;
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
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Zhu M, Tong X, Qiu Q, Pan J, Wei S, Ding Y, Feng Y, Hu X, Gong C. Identification and characterization of extrachromosomal circular DNA in the silk gland of Bombyx mori. INSECT SCIENCE 2023; 30:1565-1578. [PMID: 36826848 DOI: 10.1111/1744-7917.13191] [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: 09/19/2022] [Revised: 01/30/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
The silk gland cells of silkworm are special cells which only replicate DNA in the nucleus without cell division throughout the larval stage. The extrachromosomal circular DNAs (eccDNAs) have not yet been reported in the silk gland of silkworms. Herein, we have explored the characterization of eccDNAs in the posterior silk gland of silkworms. A total of 35 346 eccDNAs were identified with sizes ranging from 30 to 13 569 549 bp. Motif analysis revealed that dual direct repeats are flanking the 5' and 3' breaking points of eccDNA. The sequences exceeding 1 kb length in eccDNAs present palindromic sequence characteristics flanking the 5' and 3' breaking points of the eccDNA. These motifs might support possible models for eccDNA generation. Genomic annotation of the eccDNA population revealed that most eccDNAs (58.6%) were derived from intergenic regions, whereas full or partial genes were carried by 41.4% of eccDNAs. It was found that silk protein genes fib-H, fib-L, and P25, as well as the transcription factors SGF and sage, which play an important regulatory role in silk protein synthesis, could be carried by eccDNAs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses showed that the genes carried by eccDNAs were mainly associated with the development and metabolism-related signaling pathways. Moreover, it was found that eccDNAfib-L could promote the transcription of fib-L gene. Overall, the results of the present study not only provide a novel perspective on the mechanism of silk gland development and silk protein synthesis but also complement previously reported genome-scale eccDNA data supporting that eccDNAs are common in eukaryotes.
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Affiliation(s)
- Min Zhu
- School of Biology & Basic Medical Science, Soochow University, Suzhou, China
| | - Xinyu Tong
- School of Biology & Basic Medical Science, Soochow University, Suzhou, China
| | - Qunnan Qiu
- School of Biology & Basic Medical Science, Soochow University, Suzhou, China
| | - Jun Pan
- School of Biology & Basic Medical Science, Soochow University, Suzhou, China
| | - Shulin Wei
- School of Biology & Basic Medical Science, Soochow University, Suzhou, China
| | - Yuming Ding
- School of Biology & Basic Medical Science, Soochow University, Suzhou, China
| | - Yongjie Feng
- School of Biology & Basic Medical Science, Soochow University, Suzhou, China
| | - Xiaolong Hu
- School of Biology & Basic Medical Science, Soochow University, Suzhou, China
- Institute of Agricultural Biotechnology and Ecological Research, Soochow University, Suzhou, China
| | - Chengliang Gong
- School of Biology & Basic Medical Science, Soochow University, Suzhou, China
- Institute of Agricultural Biotechnology and Ecological Research, Soochow University, Suzhou, China
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14
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Luo X, Zhang L, Cui J, An Q, Li H, Zhang Z, Sun G, Huang W, Li Y, Li C, Jia W, Zou L, Zhao G, Xiao F. Small extrachromosomal circular DNAs as biomarkers for multi-cancer diagnosis and monitoring. Clin Transl Med 2023; 13:e1393. [PMID: 37649244 PMCID: PMC10468585 DOI: 10.1002/ctm2.1393] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 08/15/2023] [Accepted: 08/21/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND Small extrachromosomal circular DNAs (eccDNAs) have the potential to be cancer biomarkers. However, the formation mechanisms and functions of small eccDNAs selected in carcinogenesis are not clear, and whether the small eccDNA profile in the plasma of cancer patients represents that in cancer tissues remains to be elucidated. METHODS A novel sequencing workflow based on the nanopore sequencing platform was used to sequence naturally existing full-length small eccDNAs in tissues and plasma collected from 25 cancer patients (including prostate cancer, hepatocellular carcinoma and colorectal cancer), and from an independent validation cohort (including 7 cancer plasma and 14 healthy plasma). RESULTS Compared with those in non-cancer tissues, small eccDNAs detected in cancer tissues had a significantly larger number and size (P = 0.040 and 2.2e-16, respectively), along with more even distribution and different formation mechanisms. Although small eccDNAs had different general characteristics and genomic annotation between cancer tissues and the paired plasma, they had similar formation mechanisms and cancer-related functions. Small eccDNAs originated from some specific genes had great multi-cancer diagnostic value in tissues (AUC ≥ 0.8) and plasma (AUC > 0.9), especially increasing the accuracy of multi-cancer prediction of CEA/CA19-9 levels. The high multi-cancer diagnostic value of small eccDNAs originated from ALK&ETV6 could be extrapolated from tissues (AUC = 0.804) to plasma and showed high positive predictive value (100%) and negative predictive value (82.35%) in a validation cohort. CONCLUSIONS As independent and stable circular DNA molecules, small eccDNAs in both tissues and plasma can be used as ideal biomarkers for cost-effective multi-cancer diagnosis and monitoring.
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Affiliation(s)
- Xuanmei Luo
- Peking University Fifth School of Clinical MedicineBeijing HospitalNational Center of GerontologyBeijingChina
- The Key Laboratory of GeriatricsBeijing Institute of GeriatricsInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing HospitalNational Center of Gerontology of National Health CommissionBeijingChina
| | - Lili Zhang
- Clinical BiobankBeijing HospitalNational Center of GerontologyNational Health CommissionInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Jian Cui
- Department of General SurgeryBeijing HospitalBeijingChina
| | - Qi An
- Department of General SurgeryBeijing HospitalBeijingChina
| | - Hexin Li
- Clinical BiobankBeijing HospitalNational Center of GerontologyNational Health CommissionInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Zaifeng Zhang
- The Key Laboratory of GeriatricsBeijing Institute of GeriatricsInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing HospitalNational Center of Gerontology of National Health CommissionBeijingChina
| | - Gaoyuan Sun
- Clinical BiobankBeijing HospitalNational Center of GerontologyNational Health CommissionInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Wei Huang
- The Key Laboratory of GeriatricsBeijing Institute of GeriatricsInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing HospitalNational Center of Gerontology of National Health CommissionBeijingChina
| | - Yifei Li
- Clinical BiobankBeijing HospitalNational Center of GerontologyNational Health CommissionInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Chang Li
- Peking University Fifth School of Clinical MedicineBeijing HospitalNational Center of GerontologyBeijingChina
- The Key Laboratory of GeriatricsBeijing Institute of GeriatricsInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing HospitalNational Center of Gerontology of National Health CommissionBeijingChina
| | - Wenzhuo Jia
- Department of General SurgeryBeijing HospitalBeijingChina
- National Center of GerontologyInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Lihui Zou
- The Key Laboratory of GeriatricsBeijing Institute of GeriatricsInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing HospitalNational Center of Gerontology of National Health CommissionBeijingChina
| | - Gang Zhao
- Department of General SurgeryBeijing HospitalBeijingChina
- National Center of GerontologyInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Fei Xiao
- Peking University Fifth School of Clinical MedicineBeijing HospitalNational Center of GerontologyBeijingChina
- The Key Laboratory of GeriatricsBeijing Institute of GeriatricsInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing HospitalNational Center of Gerontology of National Health CommissionBeijingChina
- Clinical BiobankBeijing HospitalNational Center of GerontologyNational Health CommissionInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
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15
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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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16
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Ullah I, Dunwell JM. Bioinformatic, genetic and molecular analysis of several badnavirus sequences integrated in the genomes of diverse cocoa ( Theobroma cacao L.) germplasm. Saudi J Biol Sci 2023; 30:103648. [PMID: 37131491 PMCID: PMC10149277 DOI: 10.1016/j.sjbs.2023.103648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/14/2023] [Accepted: 03/31/2023] [Indexed: 05/04/2023] Open
Abstract
Endogenous viral elements (EVEs) are integrations of whole or partial viral genomes into the host genome, where they act as host alleles. They exist in a wide range of plant species including Theobroma cacao, the source of chocolate. Because of the international transfer of cacao germplasm, it is important to discriminate between the presence of these inserts and any episomal viruses that may be present in the material. This study was designed to survey a wide range of cacao germplasm, to assess the number, length, orientation, and precise location of the inserts and to identify any effect on the transcription of the gene into which they are inserted. Using a combination of bioinformatic, genetic and molecular approaches, we cloned and sequenced a series of different inserts, including one full-length virus sequence. We also identified, for the first time, an inhibitory effect of the insert on the expression of host genes. Such information is of practical importance in determining the regulation of germplasm transfer and of fundamental relevance to aiding an understanding of the role that such inserts may have on the performance of the host plant.
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17
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Guo J, Zhang Z, Li Q, Chang X, Liu X. TeCD: The eccDNA Collection Database for extrachromosomal circular DNA. BMC Genomics 2023; 24:47. [PMID: 36707765 PMCID: PMC9881285 DOI: 10.1186/s12864-023-09135-5] [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: 05/04/2022] [Accepted: 01/13/2023] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Extrachromosomal circular DNA (eccDNA) is a kind of DNA that widely exists in eukaryotic cells. Studies in recent years have shown that eccDNA is often enriched during tumors and aging, and participates in the development of cell physiological activities in a special way, so people have paid more and more attention to the eccDNA, and it has also become a critical new topic in modern biological research. DESCRIPTION We built a database to collect eccDNA, including animals, plants and fungi, and provide researchers with an eccDNA retrieval platform. The collected eccDNAs were processed in a uniform format and classified according to the species to which it belongs and the chromosome of the source. Each eccDNA record contained sequence length, start and end sites on the corresponding chromosome, order of the bases, genomic elements such as genes and transposons, and other information in the respective sequencing experiment. All the data were stored into the TeCD (The eccDNA Collection Database) and the BLAST (Basic Local Alignment Search Tool) sequence alignment function was also added into the database for analyzing the potential eccDNA sequences. CONCLUSION We built TeCD, a platform for users to search and obtain eccDNA data, and analyzed the possible potential functions of eccDNA. These findings may provide a basis and direction for researchers to further explore the biological significance of eccDNA in the future.
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Affiliation(s)
- Jing Guo
- grid.410726.60000 0004 1797 8419Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310013 China ,grid.410726.60000 0004 1797 8419Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310013 China ,grid.464226.00000 0004 1760 7263Institute of Statistics and Applied Mathematics, Anhui University of Finance & Economics, Bengbu, 233030 China ,grid.27255.370000 0004 1761 1174School of Mathematics and Statistics, Shandong University, Weihai, 264209 Shandong China
| | - Ze Zhang
- grid.410726.60000 0004 1797 8419Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310013 China ,grid.410726.60000 0004 1797 8419Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310013 China ,grid.410726.60000 0004 1797 8419School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310013 China
| | - Qingcui Li
- grid.410726.60000 0004 1797 8419School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310013 China
| | - Xiao Chang
- grid.464226.00000 0004 1760 7263Institute of Statistics and Applied Mathematics, Anhui University of Finance & Economics, Bengbu, 233030 China
| | - Xiaoping Liu
- grid.410726.60000 0004 1797 8419Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310013 China ,grid.410726.60000 0004 1797 8419Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310013 China ,grid.27255.370000 0004 1761 1174School of Mathematics and Statistics, Shandong University, Weihai, 264209 Shandong China
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18
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Chitwood DG, Wang Q, Klaubert SR, Green K, Wu CH, Harcum SW, Saski CA. Microevolutionary dynamics of eccDNA in Chinese hamster ovary cells grown in fed-batch cultures under control and lactate-stressed conditions. Sci Rep 2023; 13:1200. [PMID: 36681715 PMCID: PMC9862248 DOI: 10.1038/s41598-023-27962-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/10/2023] [Indexed: 01/22/2023] Open
Abstract
Chinese hamster ovary (CHO) cell lines are widely used to manufacture biopharmaceuticals. However, CHO cells are not an optimal expression host due to the intrinsic plasticity of the CHO genome. Genome plasticity can lead to chromosomal rearrangements, transgene exclusion, and phenotypic drift. A poorly understood genomic element of CHO cell line instability is extrachromosomal circular DNA (eccDNA) in gene expression and regulation. EccDNA can facilitate ultra-high gene expression and are found within many eukaryotes including humans, yeast, and plants. EccDNA confers genetic heterogeneity, providing selective advantages to individual cells in response to dynamic environments. In CHO cell cultures, maintaining genetic homogeneity is critical to ensuring consistent productivity and product quality. Understanding eccDNA structure, function, and microevolutionary dynamics under various culture conditions could reveal potential engineering targets for cell line optimization. In this study, eccDNA sequences were investigated at the beginning and end of two-week fed-batch cultures in an ambr®250 bioreactor under control and lactate-stressed conditions. This work characterized structure and function of eccDNA in a CHO-K1 clone. Gene annotation identified 1551 unique eccDNA genes including cancer driver genes and genes involved in protein production. Furthermore, RNA-seq data is integrated to identify transcriptionally active eccDNA genes.
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Affiliation(s)
- Dylan G Chitwood
- Department of Bioengineering, Clemson University, Clemson, SC, USA
| | - Qinghua Wang
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Stephanie R Klaubert
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, USA
| | - Kiana Green
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Cathy H Wu
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Sarah W Harcum
- Department of Bioengineering, Clemson University, Clemson, SC, USA
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, USA
| | - Christopher A Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, 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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20
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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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21
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Li F, Yang L, Han J, Han X, Peng L, Du Y, Xia H, Yang L, Zhou Y. Characterization of extrachromosomal circular DNA in cattle using 676 whole genome sequencing datasets. Anim Genet 2022; 53:761-768. [PMID: 36226728 DOI: 10.1111/age.13269] [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: 09/22/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 11/28/2022]
Abstract
Extrachromosomal circular DNA (eccDNA) is an important fraction of the genome. Recent studies proved that eccDNA plays important roles in genetic variation, aging and environmental adaptation, which have drawn wide attention. However, the characteristics of eccDNA in cattle remain unclear. Here, we studied eccDNAs from 676 cattle of 58 breeds using whole genome sequencing datasets. In total, 47 355 high-confidence eccDNAs were identified and covered 4.6% of the cattle autosomes in length. Similarly to other species, the cattle eccDNA preferentially located in the genic and repeat sequences. Cattle eccDNAs contained complete sequences of 661 genes, which were significantly (p < 0.05) enriched in immunity-related functions. The eccDNA was further proved to have inverted repeats on the boundaries, which contained a high proportion of A/T and ranged from 4 to 17 bp. Interestingly, we successfully separated animals according to their geographical distributions and their tissues where DNA was isolated. This implied possible roles for eccDNA in cattle selection and tissue development. Our study supplies basic knowledges on eccDNAs in cattle, which will promote understanding of extrachromosomal DNA.
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Affiliation(s)
- Fan Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Lv Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Jiazheng Han
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Xiaotao Han
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Lingwei Peng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Yuqin Du
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Han Xia
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Liguo Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,National Center for International Research on Animal Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan, China.,Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Wuhan, China
| | - Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,National Center for International Research on Animal Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan, China.,Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Wuhan, China
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22
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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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23
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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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24
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Sequence characterization of eccDNA content in glyphosate sensitive and resistant Palmer amaranth from geographically distant populations. PLoS One 2022; 17:e0260906. [PMID: 36103503 PMCID: PMC9473621 DOI: 10.1371/journal.pone.0260906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 08/30/2022] [Indexed: 11/19/2022] Open
Abstract
The discovery of non-chromosomal circular DNA offers new directions in linking genome structure with function in plant biology. Glyphosate resistance through EPSPS gene copy amplification in Palmer amaranth was due to an autonomously replicating extra-chromosomal circular DNA mechanism (eccDNA). CIDER-Seq analysis of geographically distant glyphosate sensitive (GS) and resistant (GR) Palmer Amaranth (Amaranthus palmeri) revealed the presence of numerous small extra-chromosomal circular DNAs varying in size and with degrees of repetitive content, coding sequence, and motifs associated with autonomous replication. In GS biotypes, only a small portion of these aligned to the 399 kb eccDNA replicon, the vehicle underlying gene amplification and genetic resistance to the herbicide glyphosate. The aligned eccDNAs from GS were separated from one another by large gaps in sequence. In GR biotypes, the eccDNAs were present in both abundance and diversity to assemble into a nearly complete eccDNA replicon. Mean sizes of eccDNAs were similar in both biotypes and were around 5kb with larger eccDNAs near 25kb. Gene content for eccDNAs ranged from 0 to 3 with functions that include ribosomal proteins, transport, metabolism, and general stress response genetic elements. Repeat content among smaller eccDNAs indicate a potential for recombination into larger structures. Genomic hotspots were also identified in the Palmer amaranth genome with a disposition for gene focal amplifications as eccDNA. The presence of eccDNA may serve as a reservoir of genetic heterogeneity in this species and may be functionally important for survival.
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25
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Kwolek K, Kędzierska P, Hankiewicz M, Mirouze M, Panaud O, Grzebelus D, Macko‐Podgórni A. Diverse and mobile: eccDNA-based identification of carrot low-copy-number LTR retrotransposons active in callus cultures. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1811-1828. [PMID: 35426957 PMCID: PMC9324142 DOI: 10.1111/tpj.15773] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/15/2022] [Accepted: 03/29/2022] [Indexed: 05/28/2023]
Abstract
Long terminal repeat retrotransposons (LTR-RTs) are mobilized via an RNA intermediate using a 'copy and paste' mechanism, and account for the majority of repetitive DNA in plant genomes. As a side effect of mobilization, the formation of LTR-RT-derived extrachromosomal circular DNAs (eccDNAs) occurs. Thus, high-throughput sequencing of eccDNA can be used to identify active LTR-RTs in plant genomes. Despite the release of a reference genome assembly, carrot LTR-RTs have not yet been thoroughly characterized. LTR-RTs are abundant and diverse in the carrot genome. We identified 5976 carrot LTR-RTs, 2053 and 1660 of which were attributed to Copia and Gypsy superfamilies, respectively. They were further classified into lineages, families and subfamilies. More diverse LTR-RT lineages, i.e. lineages comprising many low-copy-number subfamilies, were more frequently associated with genic regions. Certain LTR-RT lineages have been recently active in Daucus carota. In particular, low-copy-number LTR-RT subfamilies, e.g. those belonging to the DcAle lineage, have significantly contributed to carrot genome diversity as a result of continuing activity. We utilized eccDNA sequencing to identify and characterize two DcAle subfamilies, Alex1 and Alex3, active in carrot callus. We documented 14 and 32 de novo insertions of Alex1 and Alex3, respectively, which were positioned in non-repetitive regions.
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Affiliation(s)
- Kornelia Kwolek
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and HorticultureUniversity of Agriculture in Krakow31 120KrakowPoland
| | - Patrycja Kędzierska
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and HorticultureUniversity of Agriculture in Krakow31 120KrakowPoland
| | - Magdalena Hankiewicz
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and HorticultureUniversity of Agriculture in Krakow31 120KrakowPoland
| | - Marie Mirouze
- Laboratoire Génome et Développement des Plantes, UMR 5096 CNRS/UPVDUniversité de PerpignanVia Domitia, 52 Avenue Paul Alduy66 860Perpignan CedexFrance
- IRD, EMR IRD‐CNRS‐UPVD ‘MANGO’Université de PerpignanPerpignanFrance
| | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes, UMR 5096 CNRS/UPVDUniversité de PerpignanVia Domitia, 52 Avenue Paul Alduy66 860Perpignan CedexFrance
| | - Dariusz Grzebelus
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and HorticultureUniversity of Agriculture in Krakow31 120KrakowPoland
| | - Alicja Macko‐Podgórni
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and HorticultureUniversity of Agriculture in Krakow31 120KrakowPoland
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26
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Lv W, Pan X, Han P, Wang Z, Feng W, Xing X, Wang Q, Qu K, Zeng Y, Zhang C, Xu Z, Li Y, Zheng T, Lin L, Liu C, Liu X, Li H, Henriksen RA, Bolund L, Lin L, Jin X, Yang H, Zhang X, Yin T, Regenberg B, He F, Luo Y. Circle-Seq reveals genomic and disease-specific hallmarks in urinary cell-free extrachromosomal circular DNAs. Clin Transl Med 2022; 12:e817. [PMID: 35474296 PMCID: PMC9042798 DOI: 10.1002/ctm2.817] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/08/2022] [Accepted: 03/29/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Extrachromosomal circular deoxyribonucleic acid (eccDNA) is evolving as a valuable biomarker, while little is known about its presence in urine. METHODS Here, we report the discovery and analysis of urinary cell-free eccDNAs (ucf-eccDNAs) in healthy controls and patients with advanced chronic kidney disease (CKD) by Circle-Seq. RESULTS Millions of unique ucf-eccDNAs were identified and comprehensively characterised. The ucf-eccDNAs are GC-rich. Most ucf-eccDNAs are less than 1000 bp and are enriched in four pronounced peaks at 207, 358, 553 and 732 bp. Analysis of the genomic distribution of ucf-eccDNAs shows that eccDNAs are found on all chromosomes but enriched on chromosomes 17, 19 and 20 with a high density of protein-coding genes, CpG islands, short interspersed transposable elements (SINEs) and simple repeat elements. Analysis of eccDNA junction sequences further suggests that microhomology and palindromic repeats might be involved in eccDNA formation. The ucf-eccDNAs in CKD patients are significantly higher than those in healthy controls. Moreover, eccDNA with miRNA genes is highly enriched in CKD ucf-eccDNA. CONCLUSIONS This work discovers and provides the first deep characterisation of ucf-eccDNAs and suggests ucf-eccDNA as a valuable noninnvasive biomarker for urogenital disorder diagnosis and monitoring.
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Affiliation(s)
- Wei Lv
- College of Life Sciences, University of Chinese Academy of Science, Beijing, China.,IBMC-BGI Center, the Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Xiaoguang Pan
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
| | - Peng Han
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China.,Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ziyu Wang
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China.,Department of Biochemistry and Molecular Biology, School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Weijia Feng
- Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xue Xing
- Department of Nephrology, Tongji Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qingqing Wang
- College of Life Sciences, University of Chinese Academy of Science, Beijing, China.,Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Kunli Qu
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China.,Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yuchen Zeng
- IBMC-BGI Center, the Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China.,College of Life Sciences, Tianjin University, Tianjin, China
| | - Cailin Zhang
- Department of Nephrology, Tongji Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhe Xu
- College of Life Sciences, University of Chinese Academy of Science, Beijing, China.,Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
| | - Yi Li
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Tianyu Zheng
- College of Life Sciences, University of Chinese Academy of Science, Beijing, China.,Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
| | - Ling Lin
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
| | - Chengxun Liu
- College of Life Sciences, University of Chinese Academy of Science, Beijing, China.,Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
| | - Xuemei Liu
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
| | - Hanbo Li
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
| | - Rasmus Amund Henriksen
- Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Section for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Lars Bolund
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China.,BGI-Shenzhen, Shenzhen, China.,Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Lin Lin
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.,Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Xin Jin
- BGI-Shenzhen, Shenzhen, China
| | - Huanming Yang
- College of Life Sciences, University of Chinese Academy of Science, Beijing, China.,IBMC-BGI Center, the Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China.,Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China.,Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen, China
| | - Xiuqing Zhang
- College of Life Sciences, University of Chinese Academy of Science, Beijing, China.,IBMC-BGI Center, the Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China.,BGI-Shenzhen, Shenzhen, China
| | - Tailang Yin
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Birgitte Regenberg
- Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Fan He
- Department of Nephrology, Tongji Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yonglun Luo
- IBMC-BGI Center, the Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China.,Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China.,BGI-Shenzhen, Shenzhen, China.,Department of Biomedicine, Aarhus University, Aarhus, Denmark.,Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
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27
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Zhu M, Pan J, Tong X, Qiu Q, Zhang X, Zhang Y, Sun S, Feng Y, Xue R, Cao G, Hu X, Gong C. BmCPV-Derived Circular DNA vcDNA-S7 Mediated by Bombyx mori Reverse Transcriptase (RT) Regulates BmCPV Infection. Front Immunol 2022; 13:861007. [PMID: 35371040 PMCID: PMC8964962 DOI: 10.3389/fimmu.2022.861007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/21/2022] [Indexed: 12/05/2022] Open
Abstract
Circular DNAs derived from single-stranded RNA viruses play important roles in counteracting viral infection. However, whether double-stranded RNA viruses generate functional circular DNAs is still unknown. Using circDNA sequencing, divergent PCR, DNA in situ hybridization and rolling circular amplification, we presently confirmed that in silkworm, Bombyx mori cytoplasmic polyhedrosis virus (BmCPV), a double-stranded RNA virus belonging to cypovirus, is prone to produce a BmCPV-derived circular DNA termed as vcDNA-S7. We have also found that vcDNA-S7 formation is mediated by endogenous reverse transcriptase (RT), and the proliferation of BmCPV can be inhibited by vcDNA-S7 in vitro and in vivo. Moreover, we have discovered that the silkworm RNAi immune pathway is activated by vcDNA-S7, while viral small interfering RNAs (vsiRNAs) derived from transcribed RNA by vcDNA-S7 can be detected by small RNA deep sequencing. These results suggest that BmCPV-derived vcDNA-S7, mediated by RT, can serve as a template for the biogenesis of antiviral siRNAs, which may lead to the repression of BmCPV infection. To our knowledge, this is the first demonstration that a circular DNA, produced by double stranded RNA viruses, is capable of regulating virus infection.
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Affiliation(s)
- Min Zhu
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China
| | - Jun Pan
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China
| | - Xinyu Tong
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China
| | - Qunnan Qiu
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China
| | - Xing Zhang
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China
| | - Yaxin Zhang
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China
| | - Sufei Sun
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China
| | - Yongjie Feng
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China
| | - Renyu Xue
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China
| | - Guangli Cao
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China
| | - Xiaolong Hu
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China.,Institute of Agricultural Biotechnology and Ecological Research, Soochow University, Suzhou, China
| | - Chengliang Gong
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China.,Institute of Agricultural Biotechnology and Ecological Research, Soochow University, Suzhou, China
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28
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Yang H, He J, Huang S, Yang H, Yi Q, Tao Y, Chen M, Zhang X, Qi H. Identification and Characterization of Extrachromosomal Circular DNA in Human Placentas With Fetal Growth Restriction. Front Immunol 2022; 12:780779. [PMID: 34992600 PMCID: PMC8724250 DOI: 10.3389/fimmu.2021.780779] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/29/2021] [Indexed: 12/13/2022] Open
Abstract
Many studies have confirmed that extrachromosomal circular DNAs (eccDNAs/ecDNAs) exist in tumor and normal cells independently of the chromosome and are essential for oncogene plasticity and drug resistance. Studies have confirmed that there are many eccDNAs/ecDNAs in maternal plasma derived from the fetus. Fetal growth restriction (FGR) is a pregnancy-related disease associated with high newborn morbidity and mortality. However, the characteristics and nature of eccDNAs/ecDNAs in FGR are poorly understood. This study aims to deconstruct the properties and potential functions of eccDNAs/ecDNAs in FGR. We performed circle-seq to identify the expression profile of eccDNAs/ecDNAs, analyzed by bioinformatics, and verified by real-time Polymerase Chain Reaction (PCR) combined with southern blot in FGR compared with the normal groups. A total of 45,131 eccDNAs/ecDNAs (including 2,118 unique ones) were identified, which had significantly higher abundance in FRG group than in normal group, and was bimodal in length, peaking at ~146bp and ~340bp, respectively. Gestational age may be one independent factor affecting the production of eccDNAs/ecDNAs, most of which come from genomic regions with high gene density, with a 4~12bp repeat around the junction, and their origin had a certain genetic preference. In addition, some of the host-genes overlapped with non-coding RNAs (ncRNAs) partially or even completely. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that host-genes on the differentially expressed eccDNAs/ecDNAs (DEEECs/DEECs) were mainly enriched in immune-related functions and pathways. The presence of some ecDNAs were verified, and whose variability were consistent with the circle-seq results. We identified and characterized eccDNAs/ecDNAs in placentas with FGR, and elucidated the formation mechanisms and the networks with ncRNAs, which provide a new vision for the screening of new biomarkers and therapeutic targets for FGR.
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Affiliation(s)
- Huan Yang
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Department of Obstetrics, Chongqing University Three Gorges Hospital, Chongqing, China.,Chongqing Key Laboratory of Maternal and Fetal Medicine, Chongqing Medical University, Chongqing, China.,China-Canada-New Zealand Joint International Research Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Jie He
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Maternal and Fetal Medicine, Chongqing Medical University, Chongqing, China.,China-Canada-New Zealand Joint International Research Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Shuai Huang
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Maternal and Fetal Medicine, Chongqing Medical University, Chongqing, China.,China-Canada-New Zealand Joint International Research Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Hongbing Yang
- Department of Obstetrics, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Qingjie Yi
- Department of Obstetrics, Chongqing University Three Gorges Hospital, Chongqing, China.,Department of Epidemiology and Health Statistics, School of Public Health and Management, Chongqing Medical University, Chongqing, China
| | - Yuelan Tao
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Maternal and Fetal Medicine, Chongqing Medical University, Chongqing, China.,China-Canada-New Zealand Joint International Research Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Miaomiao Chen
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Maternal and Fetal Medicine, Chongqing Medical University, Chongqing, China.,China-Canada-New Zealand Joint International Research Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Xuemei Zhang
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Maternal and Fetal Medicine, Chongqing Medical University, Chongqing, China.,China-Canada-New Zealand Joint International Research Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Hongbo Qi
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Maternal and Fetal Medicine, Chongqing Medical University, Chongqing, China.,China-Canada-New Zealand Joint International Research Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
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29
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Zuo S, Yi Y, Wang C, Li X, Zhou M, Peng Q, Zhou J, Yang Y, He Q. Extrachromosomal Circular DNA (eccDNA): From Chaos to Function. Front Cell Dev Biol 2022; 9:792555. [PMID: 35083218 PMCID: PMC8785647 DOI: 10.3389/fcell.2021.792555] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 12/16/2021] [Indexed: 11/15/2022] Open
Abstract
Extrachromosomal circular DNA (eccDNA) is a type of double-stranded circular DNA that is derived and free from chromosomes. It has a strong heterogeneity in sequence, length, and origin and has been identified in both normal and cancer cells. Although many studies suggested its potential roles in various physiological and pathological procedures including aging, telomere and rDNA maintenance, drug resistance, and tumorigenesis, the functional relevance of eccDNA remains to be elucidated. Recently, due to technological advancements, accumulated evidence highlighted that eccDNA plays an important role in cancers by regulating the expression of oncogenes, chromosome accessibility, genome replication, immune response, and cellular communications. Here, we review the features, biogenesis, physiological functions, potential functions in cancer, and research methods of eccDNAs with a focus on some open problems in the field and provide a perspective on how eccDNAs evolve specific functions out of the chaos in cells.
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Affiliation(s)
- Shanru Zuo
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, China.,The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, Changsha, China
| | - Yihu Yi
- Department of Orthopaedics, Wuhan Union Hospital, Wuhan, China
| | - Chen Wang
- Department of Obstetrics and Gynecology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Xueguang Li
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, Changsha, China
| | - Mingqing Zhou
- Zhongshan Hospital Affiliated to Sun Yat-Sen University, Zhongshan People's Hospital, Zhongshan, China
| | - Qiyao Peng
- Institute of Chinese Medicine, Hunan Academy of Traditional Chinese Medicine and Innovation Centre for Science and Technology, Hunan University of Chinese Medicine, Changsa, China.,Chongqing Key Laboratory for Pharmaceutical Metabolism Research, College of Pharmacy, College of Traditional Chinese Medicine, Chongqing Medical University, Chongqing, China
| | - Junhua Zhou
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, Changsha, China
| | - Yide Yang
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, Changsha, China
| | - Quanyuan He
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, Changsha, China
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30
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Koo DH, Sathishraj R, Friebe B, Gill BS. Deciphering the Mechanism of Glyphosate Resistance in Amaranthus palmeri by Cytogenomics. Cytogenet Genome Res 2022; 161:578-584. [PMID: 35021177 DOI: 10.1159/000521409] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 12/07/2021] [Indexed: 11/19/2022] Open
Abstract
In agriculture, various chemicals are used to control the weeds. Out of which, glyphosate is an important herbicide invariably used in the cultivation of glyphosate-resistant crops to control weeds. Overuse of glyphosate results in the evolution of glyphosate-resistant weeds. Evolution of glyphosate resistance (GR) in Amaranthus palmeri (AP) is a serious concern in the USA. Investigation of the mechanism of GR in AP identified different resistance mechanisms of which 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene amplification is predominant. Molecular analysis of GR AP identified the presence of a 5- to >160-fold increase in copies of the EPSPS gene than in a glyphosate-susceptible (GS) population. This increased copy number of the EPSPS gene increased the genome size ranging from 3.5 to 11.8%, depending on the copy number compared to the genome size of GS AP. FISH analysis using a 399-kb EPSPS cassette derived from bacterial artificial chromosomes (BACs) as probes identified that amplified EPSPS copies in GR AP exist in extrachromosomal circular DNA (eccDNA) in addition to the native copy in the chromosome. The EPSPS gene-containing eccDNA having a size of ∼400 kb is termed EPSPS-eccDNA and showed somatic mosacism in size and copy number. EPSPS-eccDNA has a genetic mechanism to tether randomly to mitotic or meiotic chromosomes during cell division or gamete formation and is inherited to daughter cells or progeny generating copy number variation. These eccDNAs are stable genetic elements that can replicate and exist independently. The genomic characterization of the EPSPS locus, along with the flanking regions, identified the presence of a complex array of repeats and mobile genetic elements. The cytogenomics approach in understanding the biology of EPSPS-eccDNA sheds light on various characteristics of EPSPS-eccDNA that favor GR in AP.
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Affiliation(s)
- Dal-Hoe Koo
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA
| | - Rajendran Sathishraj
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA
| | - Bernd Friebe
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA
| | - Bikram S Gill
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA
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