Circular DNA in the human germline and its association with recombination

Henriksen, Rasmus Amund; Jenjaroenpun, Piroon; Sjøstrøm, Ida Borup; Jensen, Kristian Reveles; Prada-Luengo, Iñigo; Wongsurawat, Thidathip; Nookaew, Intawat; Regenberg, Birgitte

doi:10.1016/j.molcel.2021.11.027

Cited by 52 publications

(105 citation statements)

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“…This was also observed in several later studies, generally showing that smaller eccDNA can gradually increase in size over time by fusing with, for example, other eccDNA (Figure 1A). In several recent studies chimeric eccDNA, consisting of several noncontiguous chromosomal DNA segments, has been detected, which also supports an evolutionary process after the initial formation event [14][15][16][17]48,58].…”

Section: Evolutionsupporting

confidence: 57%

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Extrachromosomal circular DNA in cancer: history, current knowledge, and methods

et al. 2022

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Section: Evolutionsupporting

confidence: 57%

“…In several studies, long read sequencing methods have been applied to perform de novo assembly of eccDNA structures. This allows for more confident identification of repeat-containing and chimeric eccDNA; that is, those consisting of several noncontiguous genomic sequences [15,16,19,48,58] (Figure 3C).…”

Section: Trends In Geneticsmentioning

confidence: 99%

Extrachromosomal circular DNA in cancer: history, current knowledge, and methods

et al. 2022

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Section: Discussionmentioning

confidence: 99%

“…In recent years, more and more studies have shown that eccDNA is closely involved in the occurrence and development of several diseases such as cancer 9 13 . Turner, K. M. et al reported that eccDNA was found in nearly half of human cancers and its frequency varied by tumor type 9 13 . They also revealed that driver oncogenes in eccDNA were amplified commonly, which contributed to the transcription of oncogenes out of chromosomes 14 .…”

Section: Discussionmentioning

confidence: 99%

“…Extrachromosomal circular DNA (eccDNA) refers to the circular DNA derived from genomic DNA but free of chromosomes. Recent studies have shown that eccDNA is extensively expressed in different tissues and may be involved in varied physiological and pathological processes including immune, inflammation, aging and tumors 6-9 . However, the expression of eccDNA in cartilage tissue and its pathological significance in OA are still unknown.…”

Section: Introductionmentioning

confidence: 99%

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cir-DNA sequencing revealed the landscape of extrachromosomal circular DNA in articular cartilage and the potential roles in osteoarthritis

Kuang

Gao

et al. 2022

Preprint

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Objective: Extrachromosomal circular DNA (eccDNA) has been shown to be involved in several physiological and pathological processes including immunity, inflammation, aging and tumor. However, the expression of eccDNA in cartilage has been not reported until now. In this study, we aimed to investigated the landscape of eccDNA in articular cartilage and analyze the potential roles in Osteoarthritis (OA). Methods: The samples of articular cartilage were obtained from total knee arthroplasty (TKA) donors with OA. The mtDNAs (mitochondrial DNA) and the linear DNAs from chondrocytes of articular cartilage were removed. Then the eccDNAs were enriched for cir-DNA sequencing. After quality control evaluation, we systematically revealed the identified eccDNA data including size distribution, the size range and sequence pattern. Moreover, we explored and disscussed the potential roles of eccDNA in OA via motif analysis and GO/KEGG pathways analysis. Results: The chondrocytes from OA cartilage contained an abundance of eccDNAs, which was termed as OC-eccDNAs (OA Cartilage-derived eccDNA). The characteristics of OC-eccDNAs were tissue specific, including the distribution, the size range and sequence pattern. Moreover, the functional analysis indicated that eccDNA may be involved in the homeostasis maintenance of chondrocytes and participated in the process of OA. Conclutions: Our data firstly showed the landscape of eccDNA in articular cartilage, and preliminarily indicated the potential roles of eccDNA in OA.

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Circle‐Seq reveals genomic and disease‐specific hallmarks in urinary cell‐free extrachromosomal circular DNAs

Pan²,

Han

et al. 2022

Clinical & Translational Med

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Background Extrachromosomal circular deoxyribonucleic acid (eccDNA) is evolving as a valuable biomarker, while little is known about its presence in urine. Methods Here, we report the discovery and analysis of urinary cell‐free eccDNAs (ucf‐eccDNAs) in healthy controls and patients with advanced chronic kidney disease (CKD) by Circle‐Seq. Results Millions of unique ucf‐eccDNAs were identified and comprehensively characterised. The ucf‐eccDNAs are GC‐rich. Most ucf‐eccDNAs are less than 1000 bp and are enriched in four pronounced peaks at 207, 358, 553 and 732 bp. Analysis of the genomic distribution of ucf‐eccDNAs shows that eccDNAs are found on all chromosomes but enriched on chromosomes 17, 19 and 20 with a high density of protein‐coding genes, CpG islands, short interspersed transposable elements (SINEs) and simple repeat elements. Analysis of eccDNA junction sequences further suggests that microhomology and palindromic repeats might be involved in eccDNA formation. The ucf‐eccDNAs in CKD patients are significantly higher than those in healthy controls. Moreover, eccDNA with miRNA genes is highly enriched in CKD ucf‐eccDNA. Conclusions This work discovers and provides the first deep characterisation of ucf‐eccDNAs and suggests ucf‐eccDNA as a valuable noninnvasive biomarker for urogenital disorder diagnosis and monitoring.

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Circular DNA in the human germline and its association with recombination

Cited by 52 publications

References 50 publications

Extrachromosomal circular DNA in cancer: history, current knowledge, and methods

Extrachromosomal circular DNA in cancer: history, current knowledge, and methods

cir-DNA sequencing revealed the landscape of extrachromosomal circular DNA in articular cartilage and the potential roles in osteoarthritis

Circle‐Seq reveals genomic and disease‐specific hallmarks in urinary cell‐free extrachromosomal circular DNAs

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