eccDNA sequencing and eccDNA synthesis

1. About eccDNA
1.1 The Introduction of eccDNA
eccDNA (extrachromosomal circular DNA) refers to circular DNA structures found outside of chromosomes in eukaryotic cells, excluding mitochondrial and chloroplast DNA. It was discovered in 1964, earlier than the widely known mitochondrial DNA and bacterial plasmid DNA. However, at the time, it did not attract much attention from the scientific community, as it was considered merely useless junk fragments outside of chromosomes. Recent research has shown that eccDNA often accumulates during tumorigenesis and aging, playing a unique role in these processes.

In 2021, Professor Zhang Yi published a study in Nature, concluding that eccDNA originates randomly from chromosomal genomic DNA without specific positions or sequences. The study also revealed that eccDNA is a circularized product of apoptotic DNA fragments mediated by Lig3 and possesses a strong ability to stimulate innate immune responses.

1.2 Functional Exploration of eccDNA
The functions of eccDNA are being extensively studied. While not yet fully understood, it has been discovered that eccDNA may play potentially important roles in several biological processes:

1.2.1.Oncogene Amplification and Cancer Development:
Oncogenes carried by eccDNA may play a key role in cancer development. This includes the amplification of oncogenes such as EGFR and MYC, promoting abnormal cell proliferation.

1.2.2.Genetic Stability and Gene Copy Number Variation:
The presence of eccDNA is related to gene copy number variations and genetic stability, potentially leading to genomic polymorphisms within cells.

1.2.3.Cell Stress Response and Environmental Adaptation:
The formation of eccDNA may be an adaptive response of cells to stress and environmental changes, participating in the survival mechanisms of cells.

1.2.4.Cell Evolution and Genetic Diversity:
The presence of eccDNA may increase genetic diversity within cells, contributing to cell evolution and enhancing adaptability to complex environments.

1.2.5.Cell Cycle Regulation:
eccDNA may be involved in the regulation of the cell cycle, particularly during cell division and proliferation stages, potentially exerting regulatory effects.

2.1 About Circle-seq
Circle-Seq, also known as circular DNA sequencing, is a powerful tool for detecting eccDNA. This technique is based on plasmid extraction,
enzymatic digestion, and high-throughput sequencing. It involves three major steps for eccDNA enrichment: cell lysis and column purification, removal of linear DNA, and rolling circle amplification. Combined with high-throughput sequencing, Circle-Seq obtains the sequence information of eccDNA.
Circle-Seq can detect all eccDNA in various species samples with high detection rates and good accuracy. Sample types include tissues, cells, serum, plasma, and urine. Species covered include humans, mice, rats, Arabidopsis, fruit flies, yeast, and African clawed frogs, among various other animals and plants.
More info.: https://www.tubegene.cc/eccDNAsequencing.html

2.2 The cooperation process of Circle-seq：
Sign Contract and half payment--->Send samples and start experiment--->Issue experiment report and pay the balance--->Issue data analysis report and sequencing data.

3.1 The technical background of circular DNA synthesis/eccDNAsynthesis
Recent studies have shown that eccDNA is present in most tumor tissues and often carries tumor driver genes.Its enrichment typically promotes the amplification of oncogenes,increasing their plasticity and instability.Therefore, eccDNA may play a significant role in the evolution of tumor cells.
This discovery has quickly garnered attention from the scientific community.

In 2018, researchers such as Moller, H. D.,isolated over 100,000 eccDNA molecules from the muscle and blood cells of healthy individuals. Most of these molecules carry genes or gene fragments,typically ranging from 100 bp to 10 kb in length.This study suggests that eccDNA may be widespread.

In recent years,the development and application of high-throughput sequencing technology and related bioinformatics analysis software have provided a more in-depth understanding of eccDNA at the whole-genome level.However,functional validation of individual eccDNA of interest still requires synthesis and overexpression at the cellular level.TubeGene holds patented technology for eccDNA synthesis, enabling the rapid and efficient synthesis of eccDNA of the desired size. Currently, we can stably and efficiently synthesize eccDNA up to 5 kb in length for downstream cell function validation.

3.2 eccDNA synthesis example
TubeGene synthesized six types of eccDNA, each approximately 1 kb in length, using LAMA technology. Restriction endonuclease digestion was performed to identify linear fragments and eccDNA circular products, showing no residual linear fragments in the synthesized eccDNA, indicating that all products were circular DNA.
more info.: www.tubegene.cc/eccDNAsynthesis.html
3.3 The cooperation process of eccDNA synthesis
Sign Contract and half payment--->Provide eccDNA sequence, start experiment--->Issue experiment report and pay the balance--->Express the synthesized eccDNA.

http://www.tubegene.com
www.tubegene.cn

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About TubeGene
TubeGene was founded by postdoctoral researchers and PhDs from renowned universities, such as Peking University,University of Chinese Academy of Sciences, and University of Michigan. Our team members possess extensive industry research experience.

The company focuses primarily on research, development, and services related to eccDNA technologies. We currently offer a range of core technical support services in the eccDNA field, including eccDNA synthesis technology for downstream cellular functional validation, ecc RBD technology, and circle-seq for eccDNA sequencing research.

TubeGene boasts a professional team of experimentalists and analysts who ensure efficient delivery of high-quality eccDNA experimental services.
We not only provide standardized eccDNA technical services but also offer personalized in-depth data analysis and research support tailored to project requirements.

We have provided eccDNA-related services to prestigious domestic research institutions such as Peking Union Medical College Hospital, Third Hospital of Peking University, Wuhan University, and Sun Yat-sen University. Accumulating rich experience in eccDNA sequencing analysis and synthesis, we have contributed to numerous high-impact eccDNA research papers.

TubeGene maintains rigorous quality control standards with a comprehensive delivery quality control system, overseeing each process stage to ensure strict control over every experimental step. We have achieved 100% satisfaction and praise from our collaborating clients.

Looking ahead, TubeGene remains committed to advancing eccDNA technologies through continuous research and service innovation,
dedicated to supporting your research endeavors.

High-performance computing platform
The TubeGene high-performance computing platform (HPC) uses a highly efficient combination of Sugon computing nodes and NAS storage. It boasts high computing power, large total memory, and strong total storage capacity. As the company grows, the computing platform will continue to expand to ensure efficient data processing and secure data storage.

Mastering the core technologies of eccDNA research
TubeGene is one of the important companies to offer eccDNA synthesis technology services, enabling the rapid and efficient synthesis of eccDNA of the required size for downstream cellular functional validation.

TubeGene is a key service provider in China
that has mastered eccDNA sequencing technology, and we have provided eccDNA sequencing services to numerous renowned universities, hospitals,
and research institutes across the country.

TubeGene can provide eccRBD technology support services, assisting in your product development.

This release was published on openPR.