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

---

Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil

Genome Research, Год журнала: 2024, Номер 34(9), С. 1355 - 1364

Опубликована: Авг. 7, 2024

Circular extrachromosomal DNA (ecDNA) is a form of oncogene amplification found across cancer types and associated with poor outcome in patients. ecDNA can be structurally complex contain rearranged sequences derived from multiple chromosome locations. As the structure impact regulation may indicate mechanisms its formation, disentangling it at high resolution sequencing data essential. Even though methods have been developed to identify reconstruct genome sequencing, remains challenging resolve structures, particular amplicons shared genomic footprints. We here introduce Decoil, computational method that combines breakpoint-graph approach LASSO regression deconvolve co-occurring elements overlapping footprints long-read nanopore sequencing. Decoil outperforms de novo assembly alignment-based simulated for both simple ecDNAs. Applying on whole-genome uncovered different topologies explored heterogeneity neuroblastoma tumors cell lines, indicating this improve structural analyses cancer.

Язык: Английский

---

Identification of eccDNA in Extracellular Vesicles Derived from Human Dermal Fibroblasts Through Nanopore Sequencing

International Journal of Molecular Sciences, Год журнала: 2025, Номер 26(9), С. 4144 - 4144

Опубликована: Апрель 27, 2025

Extrachromosomal circular DNAs (eccDNAs) are heterogeneous DNA molecules derived from genomic DNA, and believed to be involved in intercellular communication natural biological processes. Extracellular vesicles (EVs) membrane-bound particles released all cells, have been shown contain various classes of nucleic acids. EVs can play a role may used as biomarkers. This constitutes the first study demonstrate that healthy human dermal fibroblasts carry eccDNA. eccDNA their corresponding donor cells were isolated sequenced on Oxford Nanopore MinIon platform, followed by identification potential eccDNAs through four different bioinformatic pipelines, namely ecc_Finder, cyrcular-calling, CReSIL, Flec. Our main findings eccDNA; there is variability number identified same sample pipelines; across replicates. Additionally, characterized this research had (a) sequences small 306 base pairs large 28,958 samples, (b) uneven chromosomal distribution, (c) an average 49.7% harboring gene fragments. Future implications for novel include using framework method elucidate factors conditions influence skin aging process related biogenesis cells.

Язык: Английский

---

Advances in sequencing-based studies of microDNA and ecDNA: Databases, identification methods, and integration with single-cell analysis

Computational and Structural Biotechnology Journal, Год журнала: 2023, Номер 21, С. 3073 - 3080

Опубликована: Янв. 1, 2023

Язык: Английский

---

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

---

Adaptive dynamics of extrachromosomal circular DNA in rice under nutrient stress

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

Опубликована: Май 4, 2025

Abstract Extrachromosomal circular DNAs (eccDNAs) have been identified in various eukaryotic organisms and are known to play crucial roles genomic plasticity. However, crop plants, the role of eccDNAs responses environmental cues, particularly nutritional stresses, remains unexplored. Rice ( Oryza sativa ssp. japonica ), a vital for over half world’s population an excellent model plant studies, faces numerous challenges during growth. Therefore, we conduct comprehensive studies investigating distribution, sequence, potential rice stresses. We describe changes eccDNA landscape at developmental stages optimal also identify overlapping with genes ecGenes transposable elements ecTEs full-length repeat units ecRepeatUnits whose prevalence responds nitrogen (N) phosphorus (P) deficiency. analyze multiple-fragment propose TE-mediated homologous recombination mechanism as origin rice’s eccDNAs. provide evidence genome plasticity under stresses underscore significance their abundance specificity.

Язык: Английский

---

Characterization and identification of extrachromosomal circular DNA in cholangiocarcinoma

PLoS ONE, Год журнала: 2025, Номер 20(5), С. e0322173 - e0322173

Опубликована: Май 5, 2025

Extrachromosomal circular DNAs (eccDNAs) have gained attention as key players in cancer heterogeneity, potentially associated with elevated oncogene copy numbers many cancers. While the presence of eccDNA both normal and cells is confirmed, its influence on gene-level alterations remains largely unexplored. This study delves into genomic profiles cholangiocarcinoma (CCA), an aggressive biliary tract extensive heterogeneity diverse molecular alterations, using a modified long-read CircleSeq method. We reveal distinct characteristics CCA compared to non-tumor cells, focusing genic components chromosomal origins. Analysing read depth differences oncogene-containing eccDNA; we identified potential candidates that may be relevant for biology. Subsequent bioinformatics analysis was performed established CReSIL tool, revealing patterns these oncogenes, particularly genes RAS/BRAF pathway, suggesting functional role. These findings highlight remarkable origins CCA. establishes first profiling paves way further investigation contribution amplification disease progression.

Язык: Английский

---

FLED: a full-length eccDNA detector for long-reads sequencing data

Briefings in Bioinformatics, Год журнала: 2023, Номер 24(6)

Опубликована: Сен. 22, 2023

Abstract Reconstructing the full-length sequence of extrachromosomal circular DNA (eccDNA) from short sequencing reads has proved challenging given similarity eccDNAs and their corresponding linear DNAs. Previous methods were unable to achieve high-throughput detection eccDNAs. Herein, a novel algorithm was developed, called Full-Length eccDNA Detection (FLED), reconstruct based on strategy that combined rolling circle amplification nanopore long-reads technology. Seven human epithelial cancer cell line samples analyzed by FLED over 5000 identified per sample. The structures validated both Polymerase Chain Reaction (PCR) Sanger sequencing. Compared other published nanopore-based detectors, exhibited higher sensitivity. In lines, genes overlapped with regions enriched in cancer-related pathways cis-regulatory elements can be predicted upstream or downstream intact molecules, expressions these dysregulated tumor indicating regulatory potency biological processes. proposed method takes advantage long enables unbiased reconstruction sequences. is implemented using Python3 which freely available GitHub (https://github.com/FuyuLi/FLED).

Язык: Английский

---

Methods, bioinformatics tools and databases in ecDNA research: An overview

Computers in Biology and Medicine, Год журнала: 2023, Номер 167, С. 107680 - 107680

Опубликована: Ноя. 10, 2023

Язык: Английский

---

Molecular characterization and functional roles of circulating cell-free extrachromosomal circular DNA

Clinica Chimica Acta, Год журнала: 2024, Номер 556, С. 117822 - 117822

Опубликована: Фев. 5, 2024

Язык: Английский

---