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Extrachromosomal circular DNAs are ubiquitous in mouse hearts and function as enhancers to promote chromosomal transcription [Circle-seq]

ABSTRACT: Extrachromosomal circular DNAs are ubiquitous in mouse hearts and function as enhancers to promote chromosomal transcription [Circle-seq]

PROVIDER: PRJNA896237 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22114383_1.fastq.gz	Fastqsanger.gz
	SRR22114383_2.fastq.gz	Fastqsanger.gz
	SRR22114384_1.fastq.gz	Fastqsanger.gz
	SRR22114384_2.fastq.gz	Fastqsanger.gz
	SRR22114385_1.fastq.gz	Fastqsanger.gz

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Extrachromosomal circular DNAs are ubiquitous in mouse hearts and function as enhancers to promote chromosomal transcription [Circle-seq]

Project description:To systematically analyzed the genome-wide characterization of potential eccDNAs in mouse heart tissues, we peformed Circle-seq in embryonic, neonatal and adult mouse heart tissues.

2023-12-31 | GSE216956 | GEO

Extrachromosomal circular DNAs are ubiquitous in mouse hearts and function as enhancers to promote chromosomal transcription [RNA-seq]

Project description:Extrachromosomal circular DNAs are ubiquitous in mouse hearts and function as enhancers to promote chromosomal transcription [RNA-seq]

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Engineered extrachromosomal circular DNAs promote tumorigenesis (WGS)

Project description:Engineered extrachromosomal circular DNAs promote tumorigenesis (WGS)

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Engineered extrachromosomal circular DNAs promote tumorigenesis (WGS)

Project description:Focal gene amplifications are among the most common cancer-associated mutations, but their evolution and contribution to tumorigenesis have proven challenging to recapitulate in primary cells and model organisms. Here we describe a general strategy to engineer large (>1 Mbp) focal amplifications mediated by extrachromosomal circular DNAs (ecDNAs) in a spatiotemporally controlled manner in cells and in genetically engineered mice. By coupling ecDNA formation with expression of selectable markers, we track the dynamics of ecDNA-containing cells under physiological conditions and in the presence of specific selective pressures. We also apply this approach to generate mice harboring Cre-inducible Myc- and Mdm2-containing ecDNAs analogous to those occurring in human cancers. We show that the engineered ecDNAs spontaneously accumulate in primary cells derived from these animals, promoting their proliferation, immortalization, and transformation. Finally, we demonstrate the ability of Mdm2-containing ecDNAs to promote tumor formation in an autochthonous mouse model of hepatocellular carcinoma.

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Circle-Seq for extrachromosomal circular DNA in PLC-PRF-5 cells after treatment with 25OHD

Project description:It has been verified that extrachromosomal circular DNA (ecDNA) has important clinical significance, and the formation process of ecDNA, its immunogenicity, and its other functions have also been described. However, the balancing mechanism by which cells respond to ecDNA, i.e., how ecDNA degrades within cells, is unclear. Here, by using Circle-Seq method conducted on PLC-PRF-5 HCC Cells, ecDNA was purified and the samples were used for DNA Library Preparation and Next Generation Paired-End Sequencing using Illumina MiSeq Technology, We found that some ecDNAs disappeared after VD treatment compared with the DMSO group, and these disappearing ecDNA were related to EMT, proliferation, cell cycle, focal adhesion and other malignant behaviors. Moreover, Circle-seq peaks narrowed after VD treatment, and the coverage over the whole gene was significantly reduced, suggesting that ecDNA after VD treatment carried smaller DNA fragments, which may cause them not to function as a whole gene. Importantly, we demonstrate that VD can cause a continuous and steady decrease in ecDNA in HCC cells.

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Single-cell Circle-seq unveils diversity and cell specificity of circular DNA in single cells

Project description:Circular DNAs have been reported for decades and have been linked to tumorigenesis in humans. Previous sequencing-based genomic approaches capture circular DNA and average their readout over millions of cells, thereby losing insight into intercellular variation. Here, we introduce single-cell Circle-seq and show that the occurrence of most circular DNA species is stochastic, with some oncogene-containing large circular DNAs observed relatively frequently among different single cells. Despite this stochasticity, circular DNA is cell type-specific, which is concordant with H3K9me3 and H3K4me3 chromatin modification specificity of the corresponding cell lines. Moreover, we identify a cell type-specific circular DNA signature in cancer cells, which, we believe holds potential for early cancer diagnosis. In sum, our novel method single-cell Circle-seq dissects the randomness and cell type-specificity of circular DNAs at the single-cell level and uncovers the potential clinical application of circular DNA.

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Primary Neuroblastoma Circle-seq

Project description:We generated Circle-seq data for primary neuroblastoma to describe the landscape of extrachromosomal circular DNA in neuroblastoma.

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Extrachromosomal circular DNAs are ubiquitous in mouse hearts and function as enhancers to promote chromosomal transcription [RNA-seq]

Project description:To exaimine the transcription levels among embryonic, neonatal and adult mouse heart tissues, we performed the whole transcriptome sequencing.

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Neuroblastoma Cell Line Circle-seq

Project description:We generated Circle-seq data for 12 neuroblastoma cell lines to describe the landscape of extrachromosomal circular DNA in neuroblastoma.

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Characterization of extrachromosomal circular DNA for human dilated cardiomyopathy

Project description:Extrachromosomal circular DNAs (eccDNAs) are prevalent in different tumors, and have been shown to be important oncogenic drivers. While recent studies have found many eccDNAs in non-tumor cells, to date, the nature and characteristics of eccDNAs in human heart failure are rarely known. In this study, we provided a comprehensive analysis of eccDNAs in human heart failure caused by dilated cardiomyopathy (DCM). Using the Circle-Seq method, we identified the expression profile of eccDNAs in heart samples from DCM patients and healthy controls. Most eccDNAs were less than 1kb and enriched in two peaks. Analysis of the genomic distribution of eccDNAs revealed that eccDNAs were derived from all chromosomes and half of these eccDNAs carried at least one gene or gene fragment. Most eccDNAs originated from 5’UTR, 3’UTR, CpG island, long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs). In addition, eccDNAs were more enriched on gene-rich chromosomes 17 and 19. In conclusion, our work delineated the eccDNAs profiling of human healthy heart and DCM and explored potential functions of eccDNAs in the development of DCM.

2024-12-31 | GSE241568 | GEO

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