Molecular Biology Reports, Год журнала: 2024, Номер 51(1)
Опубликована: Янв. 18, 2024
Язык: Английский
Trends in Genetics, Год журнала: 2024, Номер 40(5), С. 437 - 448
Опубликована: Фев. 29, 2024
Helitrons, classified as DNA transposons, employ rolling-circle intermediates for transposition. Distinguishing themselves from other they leave the original template element unaltered during transposition, which has led to their characterization 'peel-and-paste elements'. Helitrons possess ability capture and mobilize host genome fragments, with enormous consequences genomes. This review discusses current understanding of exploring origins, transposition mechanism, extensive repercussions activity on structure function. We also explore evolutionary conflicts stemming Helitron-transposed gene fragments elucidate domestication regulating responses environmental challenges. Looking ahead, further research in this evolving field promises bring interesting discoveries role shaping genomic landscapes.
Язык: Английский
Процитировано
18
Signal Transduction and Targeted Therapy, Год журнала: 2022, Номер 7(1)
Опубликована: Окт. 2, 2022
Abstract Extrachromosomal circular DNA (eccDNA), ranging in size from tens to millions of base pairs, is independent conventional chromosomes. Recently, eccDNAs have been considered an unanticipated major source somatic rearrangements, contributing genomic remodeling through chimeric circularization and reintegration into the linear genome. In addition, origin eccDNA be associated with essential chromatin-related events, including formation super-enhancers repair machineries. Moreover, our understanding properties functions has continuously greatly expanded. Emerging investigations demonstrate that serve as multifunctional molecules various organisms during diversified biological processes, such epigenetic remodeling, telomere trimming, regulation canonical signaling pathways. Importantly, its special distribution potentiates a measurable biomarker many diseases, especially cancers. The loss homeostasis facilitates tumor initiation, malignant progression, heterogeneous evolution An in-depth provides novel insights for precision cancer treatment. this review, we summarized discovery history eccDNA, discussed biogenesis, characteristics, eccDNA. emphasized role pathogenesis evolution. Therapeutically, potential clinical applications target aberrant multiple diseases.
Язык: Английский
Процитировано
59
Nature Communications, Год журнала: 2023, Номер 14(1)
Опубликована: Авг. 28, 2023
Abundant extrachromosomal circular DNA (eccDNA) is associated with transposable element (TE) activity. However, how the eccDNA compartment controlled by epigenetic regulations and what its impact on genome understudied. Here, using long reads, we sequence both of Arabidopsis thaliana mutant plants affected in methylation post-transcriptional gene silencing. We detect a high load TE-derived truncated chimeric forms. On genomic side, top full length TE neo-insertions, complex structural variations (SVs) notably at disease resistance cluster being natural hotspot SV. Finally, serendipitously identify large tandem duplications hypomethylated plants, suggesting that SVs could have been overlooked mutants. propose may alter repair pathways leading to instability accumulation SVs, least plants.
Язык: Английский
Процитировано
28
Molecular Biology and Evolution, Год журнала: 2024, Номер 41(3)
Опубликована: Фев. 2, 2024
Abstract Although both are salient features of genomes, at first glance ribosomal DNAs and transposable elements genetic with not much in common: whereas mainly viewed as housekeeping genes that uphold all prime genome functions, generally portrayed selfish disruptive. These opposing characteristics also mirrored other attributes: organization tandem (ribosomal DNAs) versus a dispersed manner (transposable elements); evolution concerted by diversification activity prolongs genomic stability shortens it elements). Re-visiting relevant instances which DNA–transposable element interactions have been reported, we note repeat types share least four structural functional hallmarks: (1) they repetitive shape genomes evolutionary timescales, (2) exchange motifs can enter co-evolution processes, (3) tightly controlled stress sensors playing key roles senescence/aging, (4) common epigenetic marks such DNA methylation histone modification. Here, give an overview the structural, functional, elements, discuss their interactions, highlight trends future directions move forward understanding associations.
Язык: Английский
Процитировано
10
Journal of Experimental Botany, Год журнала: 2025, Номер unknown
Опубликована: Янв. 10, 2025
Abstract Plants host a range of DNA elements capable self-replication. These molecules, usually associated to the activity transposable or viruses, are found integrated in genome form extrachromosomal DNA. The these can impact plasticity by variety mechanisms, including generation structural variants, shuffling regulatory coding sequences across genome, and endoduplication. This dynamically alter gene expression stability, ultimately affecting plant development response environmental changes. While activation is often considered deleterious their role creating variation important adaptation evolution. Moreover, mechanisms which mobile proliferate have been exploited for engineering, contributed understand how desirable traits be generated crops. In this review, we discuss origins roles element on biology, as well potential function current application biotechnology.
Язык: Английский
Процитировано
1
Briefings in Bioinformatics, Год журнала: 2022, Номер 23(6)
Опубликована: Окт. 4, 2022
Extrachromosomal circular DNA (eccDNA) of chromosomal origin is found in many eukaryotic species and cell types, including cancer, where eccDNAs with oncogenes drive tumorigenesis. Most studies eccDNA employ short-read sequencing for their identification. However, cannot resolve the complexity genomic repeats, which can lead to missing products. Long-read technologies provide an alternative constructing complete maps. We present a software suite, Construction-based Rolling-circle-amplification Sequence Identification Location (CReSIL), identify characterize from long-read sequences. CReSIL's performance identifying eccDNA, minimum F1 score 0.98, superior other bioinformatic tools based on simulated data. CReSIL provides useful features annotation, be used infer function Circos visualization architecture investigation. demonstrated capability several datasets, datasets enriched whole genome cells containing large In conclusion, suite versatile tool investigating complex simple cells.
Язык: Английский
Процитировано
27
Plants, Год журнала: 2023, Номер 12(11), С. 2178 - 2178
Опубликована: Май 30, 2023
Extrachromosomal circular DNAs (eccDNAs) are enigmatic DNA molecules that have been detected in a range of organisms. In plants, eccDNAs various genomic origins and may be derived from transposable elements. The structures individual eccDNA their dynamics response to stress poorly understood. this study, we showed nanopore sequencing is useful tool for the detection structural analysis molecules. Applying epigenetically stressed
Язык: Английский
Процитировано
11
Frontiers in Plant Science, Год журнала: 2025, Номер 15
Опубликована: Янв. 10, 2025
Cassava is an important root crop that produced by smallholder farmers across Sub-Saharan Africa. mosaic disease (CMD), which caused a group of cassava begomoviruses (CMBs), one the most devastating diseases cassava. A previous study showed SEGS-1 (sequences enhancing geminivirus symptoms), occur both in genome and as episomes during CMD, can increase CMD severity overcome host resistance. In this report, we examined effects exogenously applied on incidence CMB infection, symptom severity, viral DNA copy number five cultivars ranged from highly susceptible to resistant CMD. These studies revealed effect cultivar dependent. Susceptible developed severe with or without exogenous SEGS-1, while increased carrying CMD2 resistance, conferred single locus, but not CMD1 polygenic. Analysis infected plants absence some, all, form The presence endogenous TME14, cultivar, correlated severity. contrast, TME3, closely related did produce was more resistance than TME14. different capacities TME3 TME14 unlikely due sequence differences around their genomic loci. functional regions were mapped using sequences flanking episome junction, junction itself required for activity. All have genomes potential negatively impact development stable breeding programs.
Язык: Английский
Процитировано
0
Mobile DNA, Год журнала: 2025, Номер 16(1)
Опубликована: Апрель 16, 2025
Язык: Английский
Процитировано
0
Nature Communications, Год журнала: 2025, Номер 16(1)
Опубликована: Май 4, 2025
Abstract Extrachromosomal circular DNAs (eccDNAs) have been identified in various eukaryotic organisms and are known to play crucial roles genomic plasticity. However, crop plants, the role of eccDNAs responses environmental cues, particularly nutritional stresses, remains unexplored. Rice ( Oryza sativa ssp. japonica ), a vital for over half world’s population an excellent model plant studies, faces numerous challenges during growth. Therefore, we conduct comprehensive studies investigating distribution, sequence, potential rice stresses. We describe changes eccDNA landscape at developmental stages optimal also identify overlapping with genes ecGenes transposable elements ecTEs full-length repeat units ecRepeatUnits whose prevalence responds nitrogen (N) phosphorus (P) deficiency. analyze multiple-fragment propose TE-mediated homologous recombination mechanism as origin rice’s eccDNAs. provide evidence genome plasticity under stresses underscore significance their abundance specificity.
Язык: Английский
Процитировано
0