Figure - available from: Frontiers in Oncology
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Formation mechanisms of ecDNA. (A) During chromothripsis, chromosomes are shattered and religated to form ecDNA.(B) Local religation of DNA can form ecDNA. (C) Breakage-fusion-bridge (BFB) cycles generate rearranged chromosomes and ecDNA. (D) Fork stalling and template switching can loop out to form ecDNA.
Source publication
Extrachromosomal DNA (ecDNA) is circular DNA that plays an important role in the development and heterogeneity of cancer. The rapid evolution of methods to detect ecDNA, including microscopic and sequencing approaches, has greatly enhanced our knowledge of the role of ecDNA in cancer development and evolution. Here, we review the molecular characte...
Citations
... It forms the hubs of eccDNA and interact with the chromosomal DNA for the oncogene regulation. It is the storage place for the DNA recombination [32]. To study the aging yeast as a model organism, the eccDNAs cause aging in the yeast cells by accumulating in old cells [33]. ...
Many years ago, scientists keenly absorbed and paid attention to the Cytoplasmic genes and nucleus Chromosomes. In this era, Scientists also focused on the nucleus chromosomes since 1965. There are a lot of things that are fortunately or unfortunately neglected by the scientific community one is eccDNA. Mostly in the eukaryotic cell exons and eccDNA is a not-rare process. When the sequencing techniques have come into view this is highly appreciated that this eccDNA is due to the repeats again and again in genomic sequence, new and fresh studies and scientists admit that this eccDNA is due to the different regions of the genome taking part to the eccDNA pool. This eccDNA may be extra but plays a role as a DNA in the cell. Sometimes this is very dangerous for the wheat and in some conditions, it is very may be helpful and show their gene expression in the different plants to control their mechanisms such as stress and adaptation, this may also show the phenotypic effect as well as genotypic effect. In this review, we discuss different approaches and technologies that facilitate eccDNA identification and early discoveries in the eccDNA in wheat.
... An extrachromosomal DNA molecule (EcDNAm) is circular DNA that plays an important role in the development and heterogeneity of cancer (13,24,25). However, the structure, composition and genomewide frequency of extrachromosomal DNA have not been extensively pro led. ...
Background
Lung cancer (LC) is a cancer with high mortality worldwide. Research on the distribution and nature of extrachromosomal DNA molecules (EcDNAm) in early LC is scarce.
Methods
After removing linear DNA and mitochondrial circular DNA, EcDNAm were extracted from two paired LC tissue samples and amplified using rolling circle amplification. High throughput extrachromosomal DNA or RNA sequencing and bioinformatics analysis were used to explore the distribution and nature of the EcDNAm. To learn more about the role of oncogenes with large EcDNAm sizes, gene onology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed.
Results
RNA sequencing results revealed the significant difference in some genes between tumor and corresponding normal samples. At the same time, obvious distinctions were observed between relapsed and non-relapsed tumor samples. The nature of the EcDNAm was comparable between LC samples and matched normal samples. Compared with the matched normal samples, the number of EcDNAm with longer size (EcDNA), which contained driver oncogenes, was relatively high. The majority of EcDNA in this study was mainly focused on the tumor samples. Enrichment analysis of the cancer samples revealed enrichment in biological processes, such as positive regulation of protein localization, axon development and in utero embryonic development.
Conclusions
This study demonstrated the universality of the distribution and described the nature of EcDNAm in early LC. Moreover, our work fills the investigation of the EcDNAm gap and future studies should focus on the application of EcDNA as a potential biomarker in patients with early LC.
... Due to the presence of tandem repeats, the copy number variation (CNV) in localized regions will generally be formed after virus integration, directly destroying the structure and stability of the genome (Akagi et al., 2014). Some scholars believe that the formation of this structure is the result of re-integration after a certain tandem amplification of the virus integration (Balaji et al., 2021;Zhou et al., 2022;Chen et al., 2023;Dong et al., 2023). Studies have shown that HPV integration can produce ecDNA and has the function of regulating transcription. ...
Background
The integration of human papillomavirus (HPV) is closely related to the occurrence of cervical cancer. However, little is known about the complete state of HPV integration into the host genome.
Methods
In this study, three HPV-positive cell lines, HeLa, SiHa, and CaSki, were subjected to NANOPORE long-read sequencing to detect HPV integration. Analysis of viral integration patterns using independently developed software (HPV-TSD) yielded multiple complete integration patterns for the three HPV cell lines.
Results
We found distinct differences between the integration patterns of HPV18 and HPV16. Furthermore, the integration characteristics of the viruses were significantly different, even though they all belonged to HPV16 integration. The HPV integration in the CaSki cells was relatively complex. The HPV18 integration status in HeLa cells was the dominant, whereas the percentage of integrated HPV 16 in SiHa and CaSki cells was significantly lower. In addition, the virus sequences in the HeLa cells were incomplete and existed in an integrated state. We also identified a large number of tandem repeats in HPV16 and HPV18 integration. Our study not only clarified the feasibility of high-throughput long-read sequencing in the study of HPV integration, but also explored a variety of HPV integration models, and confirmed that viral integration is an important form of HPV in cell lines.
Conclusion
Elucidating HPV integration patterns will provide critical guidance for developing a detection algorithm for HPV integration, as well as the application of virus integration in clinical practice and drug research and development.
