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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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Zhao Y, Yu L, Zhang S, Su X, Zhou X. Extrachromosomal circular DNA: Current status and future prospects. eLife 2022; 11:81412. [PMID: 36256570 PMCID: PMC9578701 DOI: 10.7554/elife.81412] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/05/2022] [Indexed: 11/25/2022] Open
Abstract
Extrachromosomal circular DNA (eccDNA) is a double-stranded DNA molecule found in various organisms, including humans. In the past few decades, the research on eccDNA has mainly focused on cancers and their associated diseases. Advancements in modern omics technologies have reinvigorated research on eccDNA and shed light on the role of these molecules in a range of diseases and normal cell phenotypes. In this review, we first summarize the formation of eccDNA and its modes of action in eukaryotic cells. We then outline eccDNA as a disease biomarker and reveal its regulatory mechanism. We finally discuss the future prospects of eccDNA, including basic research and clinical application. Thus, with the deepening of understanding and exploration of eccDNAs, they hold great promise in future biomedical research and clinical translational application.
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Affiliation(s)
- Yiheng Zhao
- Department of Cardiology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Linchan Yu
- Department of Cardiology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Shuchen Zhang
- Department of Cardiology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiangyu Su
- Department of Cardiology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiang Zhou
- Department of Cardiology, The Second Affiliated Hospital of Soochow University, Suzhou, China
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Mann L, Seibt KM, Weber B, Heitkam T. ECCsplorer: a pipeline to detect extrachromosomal circular DNA (eccDNA) from next-generation sequencing data. BMC Bioinformatics 2022; 23:40. [PMID: 35030991 PMCID: PMC8760651 DOI: 10.1186/s12859-021-04545-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/20/2021] [Indexed: 11/14/2022] Open
Abstract
Background Extrachromosomal circular DNAs (eccDNAs) are ring-like DNA structures physically separated from the chromosomes with 100 bp to several megabasepairs in size. Apart from carrying tandemly repeated DNA, eccDNAs may also harbor extra copies of genes or recently activated transposable elements. As eccDNAs occur in all eukaryotes investigated so far and likely play roles in stress, cancer, and aging, they have been prime targets in recent research—with their investigation limited by the scarcity of computational tools. Results Here, we present the ECCsplorer, a bioinformatics pipeline to detect eccDNAs in any kind of organism or tissue using next-generation sequencing techniques. Following Illumina-sequencing of amplified circular DNA (circSeq), the ECCsplorer enables an easy and automated discovery of eccDNA candidates. The data analysis encompasses two major procedures: first, read mapping to the reference genome allows the detection of informative read distributions including high coverage, discordant mapping, and split reads. Second, reference-free comparison of read clusters from amplified eccDNA against control sample data reveals specifically enriched DNA circles. Both software parts can be run separately or jointly, depending on the individual aim or data availability. To illustrate the wide applicability of our approach, we analyzed semi-artificial and published circSeq data from the model organisms Homo sapiens and Arabidopsis thaliana, and generated circSeq reads from the non-model crop plant Beta vulgaris. We clearly identified eccDNA candidates from all datasets, with and without reference genomes. The ECCsplorer pipeline specifically detected mitochondrial mini-circles and retrotransposon activation, showcasing the ECCsplorer’s sensitivity and specificity. Conclusion The ECCsplorer (available online at https://github.com/crimBubble/ECCsplorer) is a bioinformatics pipeline to detect eccDNAs in any kind of organism or tissue using next-generation sequencing data. The derived eccDNA targets are valuable for a wide range of downstream investigations—from analysis of cancer-related eccDNAs over organelle genomics to identification of active transposable elements. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04545-2.
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Affiliation(s)
- Ludwig Mann
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | - Kathrin M Seibt
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | - Beatrice Weber
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | - Tony Heitkam
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany.
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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: 1.0] [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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Feng W, Arrey G, Zole E, lv W, Liang X, Han P, Mohiyuddin M, Pilegaard H, Regenberg B. Targeted removal of mitochondrial DNA from mouse and human extrachromosomal circular DNA with CRISPR-Cas9. Comput Struct Biotechnol J 2022; 20:3059-3067. [PMID: 35782732 PMCID: PMC9233219 DOI: 10.1016/j.csbj.2022.06.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/10/2022] [Accepted: 06/12/2022] [Indexed: 11/12/2022] Open
Abstract
Extrachromosomal circular DNA (eccDNA) of chromosomal origin is common in eukaryotic cells. Amplification of oncogenes on large eccDNA (ecDNA) can drive biological processes such as tumorigenesis, and identification of eccDNA by sequencing after removal of chromosomal DNA is therefore important for understanding their impact on the expressed phenotype. However, the circular mitochondrial DNA (mtDNA) might challenge the detection of eccDNA because the average somatic cell has hundreds of copies of mtDNA. Here we show that 61.2–99.5% of reads from eccDNA-enriched samples correspond to mtDNA in mouse tissues. We have developed a method to selectively remove mtDNA from total circular DNA by CRISPR/Cas9 guided cleavage of mtDNA with one single-guide RNA (sgRNA) or two sgRNAs followed by exonuclease degradation of the linearized mtDNA. Sequencing revealed that mtDNA reads were 85.9% ± 12.6% removed from eccDNA of 9 investigated mouse tissues. CRISPR/Cas9 cleavage also efficiently removed mtDNA from a human HeLa cell line and colorectal cancer samples. We identified up to 14 times more, and also larger eccDNA in CRISPR/Cas9 treated colorectal cancer samples than in untreated samples. We foresee that the method can be applied to effectively remove mtDNA from any eukaryotic species to obtain higher eccDNA yields.
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Liang X, Chen H, Li L, An R, Komiyama M. Ring-Structured DNA and RNA as Key Players In Vivoand In Vitro. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200235] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| | - Hui Chen
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Lin Li
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
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Zhu J, Chen S, Zhang F, Wang L. Cell-Free eccDNAs: A New Type of Nucleic Acid Component for Liquid Biopsy? Mol Diagn Ther 2019; 22:515-522. [PMID: 29959693 DOI: 10.1007/s40291-018-0348-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Extrachromosomal circular DNAs (eccDNAs) are circular DNAs that are originated from chromosomes, but are independent from chromosomal DNA. The eccDNAs are commonly found in various tissues and cell types, and in both normal and diseased conditions. Due to their highly heterogeneous origins and being widely spread in nearly all eukaryotes, the eccDNAs are believed to reflect the genome's plasticity and instability. With the assistance of next-generation sequencing, more eccDNAs have been characterized at the molecular level. Recently, eccDNAs have been reported as cell-free DNAs in the circulation system. Importantly, these circulating eccDNAs have shown some evidence with disease associations, suggesting their potential utility as a new type of biomarker for disease detection, treatment assessment and progress surveillance. However, many challenges need to be addressed before implementing the eccDNAs as a new source of genetic material for liquid biopsy.
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Affiliation(s)
- Jing Zhu
- Laboratory of Medical Genetics, Harbin Medical University, 157 Baojian Road, Harbin, 150081, Heilongjiang, China.
| | - Siyu Chen
- Laboratory of Medical Genetics, Harbin Medical University, 157 Baojian Road, Harbin, 150081, Heilongjiang, China
| | - Fan Zhang
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, 150001, Heilongjiang, China
| | - Liang Wang
- Department of Pathology and MCW Cancer Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.
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Sequencing the extrachromosomal circular mobilome reveals retrotransposon activity in plants. PLoS Genet 2017; 13:e1006630. [PMID: 28212378 PMCID: PMC5338827 DOI: 10.1371/journal.pgen.1006630] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 03/06/2017] [Accepted: 02/10/2017] [Indexed: 11/19/2022] Open
Abstract
Retrotransposons are mobile genetic elements abundant in plant and animal genomes. While efficiently silenced by the epigenetic machinery, they can be reactivated upon stress or during development. Their level of transcription not reflecting their transposition ability, it is thus difficult to evaluate their contribution to the active mobilome. Here we applied a simple methodology based on the high throughput sequencing of extrachromosomal circular DNA (eccDNA) forms of active retrotransposons to characterize the repertoire of mobile retrotransposons in plants. This method successfully identified known active retrotransposons in both Arabidopsis and rice material where the epigenome is destabilized. When applying mobilome-seq to developmental stages in wild type rice, we identified PopRice as a highly active retrotransposon producing eccDNA forms in the wild type endosperm. The mobilome-seq strategy opens new routes for the characterization of a yet unexplored fraction of plant genomes.
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