Transposable elements and circular DNAs

Mourier, Tobias

doi:10.1080/2159256x.2016.1240748

Cited by 9 publications

(4 citation statements)

References 43 publications

(38 reference statements)

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“…In many model organisms, such as Drosophila , yeast, and human cell lines, large segmental deletions were previously found to be facilitated by ectopic recombination between tandemly arrayed repeat sequences (59, 60). This mechanism is particularly interesting in the context of HGT, as these recombination events often result in the formation of circular extrachromosomal DNA (61, 62).…”

Section: Discussionmentioning

confidence: 99%

Transposon-Mediated Horizontal Transfer of the Host-Specific Virulence Protein ToxA between Three Fungal Wheat Pathogens

McDonald

Taranto

Hill

et al. 2019

mBio

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Most known examples of horizontal gene transfer (HGT) between eukaryotes are ancient. These events are identified primarily using phylogenetic methods on coding regions alone. Only rarely are there examples of HGT where noncoding DNA is also reported. The gene encoding the wheat virulence protein ToxA and the surrounding 14 kb is one of these rare examples. ToxA has been horizontally transferred between three fungal wheat pathogens (Parastagonospora nodorum, Pyrenophora tritici-repentis, and Bipolaris sorokiniana) as part of a conserved ∼14 kb element which contains coding and noncoding regions. Here we used long-read sequencing to define the extent of HGT between these three fungal species. Construction of near-chromosomal-level assemblies enabled identification of terminal inverted repeats on either end of the 14 kb region, typical of a type II DNA transposon. This is the first description of ToxA with complete transposon features, which we call ToxhAT. In all three species, ToxhAT resides in a large (140-to-250 kb) transposon-rich genomic island which is absent in isolates that do not carry the gene (annotated here as toxa−). We demonstrate that the horizontal transfer of ToxhAT between P. tritici-repentis and P. nodorum occurred as part of a large (∼80 kb) HGT which is now undergoing extensive decay. In B. sorokiniana, in contrast, ToxhAT and its resident genomic island are mobile within the genome. Together, these data provide insight into the noncoding regions that facilitate HGT between eukaryotes and into the genomic processes which mask the extent of HGT between these species. IMPORTANCE This work dissects the tripartite horizontal transfer of ToxA, a gene that has a direct negative impact on global wheat yields. Defining the extent of horizontally transferred DNA is important because it can provide clues to the mechanisms that facilitate HGT. Our analysis of ToxA and its surrounding 14 kb suggests that this gene was horizontally transferred in two independent events, with one event likely facilitated by a type II DNA transposon. These horizontal transfer events are now in various processes of decay in each species due to the repeated insertion of new transposons and subsequent rounds of targeted mutation by a fungal genome defense mechanism known as repeat induced point mutation. This work highlights the role that HGT plays in the evolution of host adaptation in eukaryotic pathogens. It also increases the growing body of evidence indicating that transposons facilitate adaptive HGT events between fungi present in similar environments and hosts.

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Section: Discussionmentioning

confidence: 99%

Transposon-Mediated Horizontal Transfer of the Host-Specific Virulence Protein ToxA between Three Fungal Wheat Pathogens

McDonald

Taranto

Hill

et al. 2019

mBio

View full text Add to dashboard Cite

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“…The consistency between eccDNAs generated through recombination events within the genome and their recombination junctions supports the possibility that retrotransposable elements may move around the genome through DNA circularization [ 52 ]. EccDNAs from DNA circularization result in gene copy number variations when circles contain genes and origins of replication [ 53 ], which contributes to additional gain of novel functions. For example, a previous study revealed the eccDNA-based amplification and transmission of herbicide resistance in the crop weed Amaranthus palmeri [ 54 ].…”

Section: Biogenesis and Replication Of Eccdnamentioning

confidence: 99%

Small extrachromosomal circular DNA (eccDNA): major functions in evolution and cancer

et al. 2021

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Extrachromosomal circular DNA (eccDNA) refers to a type of circular DNA that originate from but are likely independent of chromosomes. Due to technological advancements, eccDNAs have recently emerged as multifunctional molecules with numerous characteristics. The unique topological structure and genetic characteristics of eccDNAs shed new light on the monitoring, early diagnosis, treatment, and prediction of cancer. EccDNAs are commonly observed in both normal and cancer cells and function via different mechanisms in the stress response to exogenous and endogenous stimuli, aging, and carcinogenesis and in drug resistance during cancer treatment. The structural diversity of eccDNAs contributes to the function and numerical diversity of eccDNAs and thereby endows eccDNAs with powerful roles in evolution and in cancer initiation and progression by driving genetic plasticity and heterogeneity from extrachromosomal sites, which has been an ignored function in evolution in recent decades. EccDNAs show great potential in cancer, and we summarize the features, biogenesis, evaluated functions, functional mechanisms, related methods, and clinical utility of eccDNAs with a focus on their role in evolution and cancer.

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“…EccDNAs are produced in both physiological and pathological conditions. For eccDNAs in normal cells, like the eccDNAs containing transposable elements and the extrachromosomal ribosomal DNA circles in yeast (4, 41, 42), their presence may be related to genome plasticity during development and aging (25). In pathological conditions, eccDNAs are found to play roles in human diseases and disease treatments, especially for larger eccDNAs (episomes and DMs) with their functions being better characterized.…”

Section: Implications Of Eccdnas In Human Diseases and Treatmentsmentioning

confidence: 99%

Cell-Free eccDNAs: A New Type of Nucleic Acid Component for Liquid Biopsy?

et al. 2018

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Extrachromosomal circular DNAs (eccDNAs) are circular DNAs that are originated from chromosomes, but are independent from chromosomal DNA. The eccDNAs are commonly found in various tissues and cell types, and in both normal and diseased conditions. Due to their highly heterogeneous origins and being widely spread in nearly all eukaryotes, the eccDNAs are believed to reflect the genome's plasticity and instability. With the assistance of next-generation sequencing, more eccDNAs have been characterized at the molecular level. Recently, eccDNAs have been reported as cell-free DNAs in the circulation system. Importantly, these circulating eccDNAs have shown some evidence with disease associations, suggesting their potential utility as a new type of biomarker for disease detection, treatment assessment and progress surveillance. However, many challenges need to be addressed before implementing the eccDNAs as a new source of genetic material for liquid biopsy.

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Transposable elements and circular DNAs

Cited by 9 publications

References 43 publications

Transposon-Mediated Horizontal Transfer of the Host-Specific Virulence Protein ToxA between Three Fungal Wheat Pathogens

Transposon-Mediated Horizontal Transfer of the Host-Specific Virulence Protein ToxA between Three Fungal Wheat Pathogens

Small extrachromosomal circular DNA (eccDNA): major functions in evolution and cancer

Cell-Free eccDNAs: A New Type of Nucleic Acid Component for Liquid Biopsy?

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