Deciphering extrachromosomal circular DNA in Arabidopsis

Wang, Keyi; Tian, Hui; Wang, Lequn; Lin, Wei; Tan, Yacong; Zhang, Ziting; Sun, Kai; Yin, Meng; Wei, Qinggong; Guo, Baohua; Han, Jinyu; Zhang, Peiru; Han, Li; Liu, Yulong; Zhao, Hongwei; Sun, Xiaoyong

doi:10.1016/j.csbj.2021.01.043

Cited by 36 publications

(54 citation statements)

References 20 publications

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“…We were first interested in comparing the circularome of M. oryzae to those of other previously characterized organisms. To compare these datasets across different organisms, we gathered sequencing data from several previous studies 11, 27, 28, 32 and reanalyzed them using our pipeline (Supplemental Data Files 3-18). This analysis revealed a very large number of eccDNA forming regions in M. oryzae compared to other previously sequenced organisms (Figure 1B).…”

Section: Resultsmentioning

confidence: 99%

“…Supplemental Data File 12. List of eccDNA forming regions called using Illumina circularome sequencing data for A. thaliana flower tissue published by Wang et al 32 . The first column describes the sample the eccDNA was called with, the next three columns represent the genomic coordinates of the eccDNA forming region, and the last column represents the number of junction split reads used to call the eccDNA forming region.…”

Section: Supplemental Data Filesmentioning

confidence: 99%

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The extrachromosomal circular DNAs of the rice blast pathogenMagnaporthe oryzaecontain a wide variety of LTR retrotransposons, genes, and effectors

Joubert

Krasileva

2021

Preprint

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One of the ways genomes respond to stress is by shedding extrachromosomal circular DNAs (eccDNAs). EccDNAs can contain genes and dramatically increase their copy number. They can also reinsert into the genome, generating structural variation. They have been shown to provide a source of phenotypic and genotypic plasticity in several species. However, whole-circularome studies have so far been limited to a few model organisms. Fungal plant pathogens are a serious threat to global food security in part because of their rapid adaptation to disease prevention strategies. Understanding the mechanisms fungal pathogens use to escape disease control is paramount to curbing their threat. We present a whole circularome sequencing study of the rice blast pathogen Magnaporthe oryzae. We find that M. oryzae has a highly diverse circularome containing many genes and showing evidence of large LTR retrotransposon activity. We find that genes enriched on eccDNAs in M. oryzae occur in genomic regions prone to presence-absence variation and that disease associated genes are frequently on eccDNAs. Finally, we find that a subset of genes is never present on eccDNAs, which indicates that the presence of these genes on eccDNAs is selected against.

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Section: Resultsmentioning

confidence: 99%

Section: Supplemental Data Filesmentioning

confidence: 99%

The extrachromosomal circular DNAs of the rice blast pathogenMagnaporthe oryzaecontain a wide variety of LTR retrotransposons, genes, and effectors

Joubert

Krasileva

2021

Preprint

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“…Sizes of cancer related eccDNA have been reported to range from several hundred base pairs to 600 kb encoded with functional oncogenes and their various regulatory elements [16,17]. In plants, eccDNAs have been reported in Arabidopsis [18,19], Oryza, Pisum, Secale, Triticum,…”

Section: Introductionmentioning

confidence: 99%

“…and Vicia [20,21] with sizes that range from 1 kb to 50kb. These eccDNAs contain coding sequences commonly found within the nucleus such as ribosomal genes, tRNAs, and transposons [19,22,23]. EccDNAs are thought to arise from linear chromosomes through repeat-mediated intrachromosomal homologous recombination that results in the 'looping-out' of circular structures.…”

Section: Introductionmentioning

confidence: 99%

“…The copyright holder for this preprint this version posted November 20, 2021. ; https://doi.org/10.1101/2021.11. 19.469340 doi: bioRxiv preprint rice, have shown that defective RNA polymerase II (Pol II) activity and simultaneous inhibition of DNA methylation leads to the activation of retrotransposons which can induce eccDNA formation upon stress [11]. These studies suggest a possible relationship among epigenetic status, regulation of transposon bursts, and genomic focal amplifications.…”

Section: Introductionmentioning

confidence: 99%

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Sequence characterization of eccDNA content in glyphosate sensitive and resistant Palmer amaranth from geographically distant populations

Camposano

Saski

Molin

2021

Preprint

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The discovery of non-chromosomal circular DNA offers new directions in linking genome structure with function in plant biology. Glyphosate resistance through EPSPS gene copy amplification in Palmer amaranth was due to an autonomously replicating extra-chromosomal circular DNA mechanism (eccDNA). CIDER-Seq analysis of geographically distant glyphosate sensitive (GS) and resistant (GR) Palmer Amaranth (Amaranthus palmeri) revealed the presence of numerous small extra-chromosomal circular DNAs varying in size and with degrees of repetitive content, coding sequence, and motifs associated with autonomous replication. In GS biotypes, only a small portion of these aligned to the 399 kb eccDNA replicon, the vehicle underlying gene amplification and genetic resistance to the herbicide glyphosate. The aligned eccDNAs from GS were separated from one another by large gaps in sequence. In GR biotypes, the eccDNAs were present in both abundance and diversity to assemble into a nearly complete eccDNA replicon. Mean sizes of eccDNAs were similar in both biotypes and were around 5kb with larger eccDNAs near 25kb. Gene content for eccDNAs ranged from 0 to 3 with functions that include ribosomal proteins, transport, metabolism, and general stress response genetic elements. Repeat content among smaller eccDNAs indicate a potential for recombination into larger structures. Genomic hotspots were also identified in the Palmer amaranth genome with a disposition for gene focal amplifications as eccDNA. The presence of eccDNA may serve as a reservoir of genetic heterogeneity in this species and may be functionally important for survival.

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Small extrachromosomal circular DNAs as biomarkers for multi‐cancer diagnosis and monitoring

Luo,

Zhang,

Cui

et al. 2023

Clinical & Translational Med

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BackgroundSmall extrachromosomal circular DNAs (eccDNAs) have the potential to be cancer biomarkers. However, the formation mechanisms and functions of small eccDNAs selected in carcinogenesis are not clear, and whether the small eccDNA profile in the plasma of cancer patients represents that in cancer tissues remains to be elucidated.MethodsA novel sequencing workflow based on the nanopore sequencing platform was used to sequence naturally existing full‐length small eccDNAs in tissues and plasma collected from 25 cancer patients (including prostate cancer, hepatocellular carcinoma and colorectal cancer), and from an independent validation cohort (including 7 cancer plasma and 14 healthy plasma).ResultsCompared with those in non‐cancer tissues, small eccDNAs detected in cancer tissues had a significantly larger number and size (P = 0.040 and 2.2e‐16, respectively), along with more even distribution and different formation mechanisms. Although small eccDNAs had different general characteristics and genomic annotation between cancer tissues and the paired plasma, they had similar formation mechanisms and cancer‐related functions. Small eccDNAs originated from some specific genes had great multi‐cancer diagnostic value in tissues (AUC ≥ 0.8) and plasma (AUC > 0.9), especially increasing the accuracy of multi‐cancer prediction of CEA/CA19‐9 levels. The high multi‐cancer diagnostic value of small eccDNAs originated from ALK&ETV6 could be extrapolated from tissues (AUC = 0.804) to plasma and showed high positive predictive value (100%) and negative predictive value (82.35%) in a validation cohort.ConclusionsAs independent and stable circular DNA molecules, small eccDNAs in both tissues and plasma can be used as ideal biomarkers for cost‐effective multi‐cancer diagnosis and monitoring.

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Deciphering extrachromosomal circular DNA in Arabidopsis

Abstract: Graphical abstract

Cited by 36 publications

References 20 publications

The extrachromosomal circular DNAs of the rice blast pathogenMagnaporthe oryzaecontain a wide variety of LTR retrotransposons, genes, and effectors

The extrachromosomal circular DNAs of the rice blast pathogenMagnaporthe oryzaecontain a wide variety of LTR retrotransposons, genes, and effectors

Sequence characterization of eccDNA content in glyphosate sensitive and resistant Palmer amaranth from geographically distant populations

Small extrachromosomal circular DNAs as biomarkers for multi‐cancer diagnosis and monitoring

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