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

ABSTRACT: 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.

ORGANISM(S): Mus musculus

PROVIDER: GSE216956 | GEO | 2023/12/31

REPOSITORIES: GEO

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Genome-wide characterization of extrachromosomal circular DNA and its functional role in colon cancer carcinogenesis and progression [Circle-Map]

Project description:Extrachromosomal circular DNAs (eccDNAs) are defined as distinct genomic entities of circular and mobile DNA molecules, but their molecular functions in and impact on breast cancer (BC) are rarely known. This study used Circle-seq to analyze eccDNAs from 19 BC tissues and 17 adjacent normal tissues. We found that eccDNAs are present on all chromosomes and enriched in seven eccDNA hotspot genes (HSGs) associated with the BC pathway. Several eccDNAs harboring entire genes (eccGenes) and eccDNAs harboring miRNAs (eccMIRs) were identified and linked to cancer-relevant pathways. Synthetic eccMIR6748, eccMIR6508, and eccMIR3142 elevated miRNA expression in MCF-7 cells, with eccMIR6748 promoting BC cell migration and invasion by upregulating miR-6748, which suppresses tumor suppressor candidate factor 5 (TUSC5) at the post-transcriptional level. eccMIR6748 also influences BC progression via the p38 mitogenactivated protein kinase (MAPK) signaling pathway. These findings suggest that eccDNAs, which contain functional genomic segments, play a role in BC initiation and progression, offering a dynamic source of genomic plasticity and potential as biomarkers and therapeutic targets.

2026-06-16 | GSE335080 | GEO

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.

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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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Circle-seq revealing eccDNA profiling of human bone marrow mesenchymal stem cells

Project description:Extrachromosomal circular DNAs (eccDNAs) have been discovered in various species and play a significant role in cancer development However, our understanding of eccDNAs in normal cells is limited. Here, we conducted eccDNA sequencing by Circle-seq in undifferentiated human bone marrow mesenchymal stem cells (uhBMSCs) and their differentiation into osteoblasts (OBs), chondrocytes (CCs), and adipocytes (ACs) to gain knowledge about eccDNAs in cell differentiation,

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

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

| PRJNA896237 | ENA

Characterizing Age-Related Extrachromosomal Circular DNA in Mouse Liver: Potential Biomarker for Liver Aging [ChIP-Seq]

Project description:Background: Extrachromosomal circular deoxyribonucleic acid (eccDNA) is progressively being recognized as a useful biomarker, however, its presence in the liver remains relatively understudied. Methods: Through the application of Circle-Seq, this research reports on the identification and subsequent analysis of eccDNAs in both young and aging livers of the house mouse species. As a complement, RNA-Seq tests were conducted, and results subjected to a combined analysis with the initial Circle-Seq findings. Results: In total, Hundreds of thousands of unique eccDNAs were identified and methodically characterized. The eccDNAs detected were predominantly GC-rich. The majority of eccDNAs were under the size of 10000 base pairs, accumulating predominantly in two distinct peaks. The genomic distribution analysis of the eccDNAs revealed their presence across all chromosomes, concentrating on the 5’UTR and CpG islands. Analysis of the junction sequences infer that microhomology and palindromic repeats may contribute to eccDNA formation. The frequency of eccDNAs in aged mice exceeded that of their youthful counterparts. In addition, there was a noticeable positive correlation between the substantial production of eccDNA and the transcription of its corresponding mRNA, all of which were reported as senescence-related genes. Conclusions: This research offers the inaugural comprehensive characterisation of aging-related eccDNAs in the liver. It underscores the potential of eccDNA as a valuable biomarker for liver aging.

2026-02-26 | GSE289754 | GEO

Whole-genome sequencing of Extrachromosomal circular DNA (eccDNA) of cerebrospinal fluid of Medulloblastoma

Project description:Background: Medulloblastoma (MB) is one of the malignant tumors of the central nervous system (CNS) with a poor prognosis and lack of effective detection. Extrachromosomal circular DNA (eccDNA) has been reported to be closely related to CNS tumors. However, there is still a gap in eccDNA of MB.Methods: Genomic features of eccDNAs were identified in MB tissues and matched cerebrospinal fluid (CSF) using a circle-map, compared with normal. The nucleotides on both sides of the eccDNAs breakpoint were analyzed to investigate the mechanisms of eccDNAs formation. Bioinformatics analysis combined with the GEO database identified reliable features of eccDNA-related genes in MB. Lasso Cox regression model, univariate and multivariate Cox regression analysis, time-dependent ROC, and Kaplan–Meier curve were used to assess the potential diagnostic and prognostic value of the Hub genes.Results: 35179 eccDNAs were identified, with the majority less than 1000 base pairs (bp). The distribution of eccDNAs on the genome was closely related to gene density. EccDNAs in CSF exhibited phase parallelism with matched MB tissues and were shown differently in tumors and normal. Ten core genes were identified in combination with GEO and showed reliable diagnostic and prognostic value in independent datasets through univariate and multivariate Cox regression. Nomogram included Hub-gene signatures was established and showed clinical benefit.Conclusions: This study described the characteristics and formation mechanism of eccDNAs in MB and CSF. The role of eccDNA in MB was revealed, and eccDNA-associated hub genes in CSF could be used as diagnostic and prognostic biomarkers for MB.

2022-10-20 | GSE205178 | GEO