eccDNA-pipe: an integrated pipeline for identification, analysis and visualization of extrachromosomal circular DNA from high-throughput sequencing data

Briefings in Bioinformatics, Год журнала: 2024, Номер 25(2)

Опубликована: Янв. 22, 2024

Abstract Extrachromosomal circular DNA (eccDNA) is currently attracting considerable attention from researchers due to its significant impact on tumor biogenesis. High-throughput sequencing (HTS) methods for eccDNA identification are continually evolving. However, an efficient pipeline the integrative and comprehensive analysis of obtained HTS data still lacking. Here, we introduce eccDNA-pipe, accessible software package that offers a user-friendly conducting starting raw data. This dataset includes various techniques such as whole-genome (WGS), Circle-seq Circulome-seq, through short-read or long-read sequencing. eccDNA-pipe presents solution both upstream downstream analysis, encompassing quality control in tasks length distribution differential genes enriched with visualization structures. Notably, automatically generates high-quality publication-ready plots. In summary, provides customized research.

Язык: Английский

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Comparative analysis of methodologies for detecting extrachromosomal circular DNA

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Окт. 24, 2024

Extrachromosomal circular DNA (eccDNA) is crucial in oncogene amplification, gene transcription regulation, and intratumor heterogeneity. While various analysis pipelines experimental methods have been developed for eccDNA identification, their detection efficiencies not systematically assessed. To address this, we evaluate the performance of 7 using seven simulated datasets, terms accuracy, identity, duplication rate, computational resource consumption. We also compare efficiency through twenty-one real sequencing datasets. Here, show that Circle-Map Circle_finder (bwa-mem-samblaster) outperform other short-read pipelines. However, exhibits notable redundancy its outcomes. CReSIL most effective pipeline long-read data at depths higher than 10X. Moreover, sequencing-based Circle-Seq shows superior detecting copy number-amplified over 10 kb length. These results offer valuable insights researchers choosing suitable research.

Язык: Английский

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Cell-cycle dependent DNA repair and replication unifies patterns of chromosome instability

Nature Communications, Год журнала: 2025, Номер 16(1)

Опубликована: Март 28, 2025

Chromosomal instability (CIN) is pervasive in human tumours and often leads to structural or numerical chromosomal aberrations. Somatic variants (SVs) are intimately related copy number alterations but the two types of variant studied independently. Additionally, despite numerous studies on detecting various SV patterns, there still no general quantitative models generation. To address this issue, we develop a computational cell-cycle model for generation SVs from end-joining repair replication after double-strand break formation. Our provides information relationship between breakage fusion bridge cycle, chromothripsis, seismic amplification, extra-chromosomal circular DNA. Given whole-genome sequencing data, also allows us infer important parameters with Bayesian inference. framework unifies disparate genomic patterns resulted CIN, null mutational SV, reveals deeper insights into impact genome rearrangement tumour evolution.

Язык: Английский

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Unveiling the mysteries of extrachromosomal circular DNA: from generation to clinical relevance in human cancers and health

Molecular Cancer, Год журнала: 2024, Номер 23(1)

Опубликована: Дек. 20, 2024

Extrachromosomal circular DNAs (eccDNAs) are a type of originating from but independent chromosomal DNAs. Nowadays, with the rapid development sequencing and bioinformatics, accuracy eccDNAs detection has significantly improved. This advancement consequently enhanced feasibility exploring biological characteristics functions eccDNAs. review elucidates potential mechanisms eccDNA generation, existing methods for their analysis, basic features. Furthermore, it focuses on in regulating gene expression under both physiological pathological conditions. Additionally, summarizes clinical implications human cancers health.

Язык: Английский

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Cell-cycle dependent DNA repair and replication unifies patterns of chromosome instability

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Янв. 4, 2024

Abstract Chromosomal instability (CIN) is pervasive in human tumours and often leads to structural or numerical chromosomal aberrations. Somatic variants (SVs) are intimately related copy number alterations but the two types of variant studied independently. In addition, despite numerous studies on detecting various SV patterns, there still no general quantitative models generation. To address this issue, we develop a computational cell-cycle model for generation SVs from end-joining repair replication after double strand break formation. Our provides information relationship between breakage fusion bridge cycle, chromothripsis, seismic amplification, extra-chromosomal circular DNA. Given single-cell whole-genome sequencing data, also allows us infer important parameters with Bayesian inference. framework unifies disparate genomic patterns resulted CIN, null mutational SV, reveals new insights into impact genome rearrangement tumour evolution.

Язык: Английский

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Characterization, biogenesis model, and current bioinformatics of human extrachromosomal circular DNA

Frontiers in Genetics, Год журнала: 2024, Номер 15

Опубликована: Апрель 29, 2024

Human extrachromosomal circular DNA, or eccDNA, has been the topic of extensive investigation in last decade due to its prominent regulatory role development disorders including cancer. With rapid advancement experimental, sequencing and computational technology, millions eccDNA records are now accessible. Unfortunately, literature databases only provide snippets this information, preventing us from fully understanding eccDNAs. Researchers frequently struggle with process selecting algorithms tools examine eccDNAs interest. To explain underlying formation mechanisms five basic classes eccDNAs, we categorized their characteristics functions summarized eight biogenesis theories. Most significantly, created a clear procedure help selection suitable techniques thoroughly examined most recent experimental bioinformatics methodologies data resources for identifying, measuring analyzing sequences. In conclusion, highlighted current obstacles prospective paths research, specifically discussing probable uses molecular diagnostics clinical prediction, an emphasis on potential contribution novel strategies.

Язык: Английский

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Bioinformatics advances in eccDNA identification and analysis

Oncogene, Год журнала: 2024, Номер 43(41), С. 3021 - 3036

Опубликована: Авг. 29, 2024

Язык: Английский

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Mobile circular DNAs regulating memory and communication in CNS neurons

Frontiers in Molecular Neuroscience, Год журнала: 2023, Номер 16

Опубликована: Дек. 6, 2023

Stimuli that stimulate neurons elicit transcription of immediate-early genes, a process which requires local sites chromosomal DNA to form double-strand breaks (DSBs) generated by topoisomerase IIb within few minutes, followed repair hours. Wakefulness, exploring novel environment, and contextual fear conditioning also turn-on synaptic genes requiring DSBs repair. It has been reported (in non-neuronal cells) extrachromosomal circular can at as the are repaired. I propose activated may generate DNAs during DSB sites, thus creating long-lasting "markers" activity pattern contain sequences from their origin regulate long-term gene expression. Although population is diverse overall associated with pathology, subclass small ("microDNAs," ∼100-400 bases long), largely derives unique genomic attractive features act stable, mobile expression in sequence-specific manner. Circular be templates for RNAs, particularly inhibitory siRNAs, RNAs other non-coding interact microRNAs. These translation involved plasticity, learning memory. Another possible fate inserted stably into chromosomes after new response subsequent activation events. Thus, insertions activity-induced tend inactivate them aid homeostatic regulation avoid over-excitation, well providing "counter" neuron's history. Moreover, release secretory exosomes transferred recipient cells Mobile packaged exosomes, released an activity-dependent manner, cells, where they regulatory possibly incorporated chromosomes. Finally, aging neurodegenerative diseases (including Alzheimer's disease) increase neurons. will become important future assess how pathology-associated relate DNAs, whether latter potentially contribute pathogenesis.

Язык: Английский

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Comparative analysis of methodologies for detecting extrachromosomal circular DNA

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Дек. 3, 2023

Abstract Extrachromosomal circular DNA (eccDNA) is crucial in oncogene amplification, gene transcription regulation, and intratumor heterogeneity. While various analysis pipelines experimental methods have been developed for eccDNA identification, their detection efficiencies not systematically assessed. To address this, we evaluated the performance of 7 using three simulated datasets, terms accuracy, similarity, duplication rate, computational resource consumption. We also compared efficiency through twenty-one real sequencing datasets. Our results identified Circle-Map CReSIL as most effective short-read long-read data, respectively. Moreover, third-generation sequencing-based Circle-Seq showed superior detecting copy number-amplified over 10 kb length. These offer valuable insights researchers choosing suitable research.

Язык: Английский

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scEccDNAdb: an integrated single-cell eccDNA resource for human and mouse

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июль 22, 2024

Abstract Extrachromosomal circular DNA (eccDNA), an extrachromosomal structured DNA, is extensively found in eukaryotes. Exploring eccDNA at the single-cell level contributes to understanding heterogeneity, evolution, development, and specific functions within cells. Nevertheless, high-throughput identification methods for are complex, currently mature widely applicable technologies lacking. Those factors have led a scarcity of resources studying level. Therefore, using available whole-genome sequencing (WGS) data, we constructed comprehensive database named scEccDNAdb ( https://lcbb.swjtu.edu.cn/scEccDNAdb/ ). Presently, comprises 3,195,464 entries from both disease/health human mouse samples, which provides annotations including oncogenes, typical enhancers, super-enhancers, CTCF binding sites, SNPs, chromatin accessibility, eQTLs, transcription factor motifs, SVs. Additionally, it nine online analysis visualization tools, facilitating generation publication-quality figures through upload customized files. Overall, represents first known us exploring analyzing data diverse cell types, tissues, species. Graphical abstract

Язык: Английский

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