Merkulov Pavel, Egorova Ekaterina, Kirov Ilya
Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia.
All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia.
Plants (Basel). 2023 May 30;12(11):2178. doi: 10.3390/plants12112178.
Extrachromosomal circular DNAs (eccDNAs) are enigmatic DNA molecules that have been detected in a range of organisms. In plants, eccDNAs have various genomic origins and may be derived from transposable elements. The structures of individual eccDNA molecules and their dynamics in response to stress are poorly understood. In this study, we showed that nanopore sequencing is a useful tool for the detection and structural analysis of eccDNA molecules. Applying nanopore sequencing to the eccDNA molecules of epigenetically stressed plants grown under various stress treatments (heat, abscisic acid, and flagellin), we showed that TE-derived eccDNA quantity and structure vary dramatically between individual TEs. Epigenetic stress alone did not cause eccDNA up-regulation, whereas its combination with heat stress triggered the generation of full-length and various truncated eccDNAs of the element. We showed that the ratio between full-length and truncated eccDNAs is TE- and condition-dependent. Our work paves the way for further elucidation of the structural features of eccDNAs and their connections with various biological processes, such as eccDNA transcription and eccDNA-mediated TE silencing.
染色体外环状DNA（eccDNA）是在多种生物体中都被检测到的神秘DNA分子。在植物中，eccDNA有多种基因组来源，可能源自转座元件。单个eccDNA分子的结构及其对应激的动态响应还知之甚少。在本研究中，我们表明纳米孔测序是检测和分析eccDNA分子结构的有用工具。将纳米孔测序应用于在各种应激处理（热、脱落酸和鞭毛蛋白）下生长的表观遗传应激植物的eccDNA分子，我们发现源自转座元件的eccDNA数量和结构在各个转座元件之间差异巨大。仅表观遗传应激不会导致eccDNA上调，而其与热应激相结合会触发该元件全长和各种截短的eccDNA的产生。我们表明全长和截短的eccDNA之间的比例取决于转座元件和条件。我们的工作为进一步阐明eccDNA的结构特征及其与各种生物学过程的联系（如eccDNA转录和eccDNA介导的转座元件沉默）铺平了道路。
