Institut de Recherche pour le Développement (IRD), Laboratory of Plant Genome and Development, Perpignan, France.
EMR269 MANGO (CNRS/IRD/UPVD), Laboratory of Plant Genome and Development, Perpignan, France.
Nat Commun. 2023 Aug 28;14(1):5236. doi: 10.1038/s41467-023-41023-0.
Abundant extrachromosomal circular DNA (eccDNA) is associated with transposable element (TE) activity. However, how the eccDNA compartment is controlled by epigenetic regulations and what is its impact on the genome is understudied. Here, using long reads, we sequence both the eccDNA compartment and the genome of Arabidopsis thaliana mutant plants affected in DNA methylation and post-transcriptional gene silencing. We detect a high load of TE-derived eccDNA with truncated and chimeric forms. On the genomic side, on top of truncated and full length TE neo-insertions, we detect complex structural variations (SVs) notably at a disease resistance cluster being a natural hotspot of SV. Finally, we serendipitously identify large tandem duplications in hypomethylated plants, suggesting that SVs could have been overlooked in epigenetic mutants. We propose that a high eccDNA load may alter DNA repair pathways leading to genome instability and the accumulation of SVs, at least in plants.
大量的染色体外环状 DNA（eccDNA）与转座元件（TE）的活性有关。然而，eccDNA 区室如何受到表观遗传调控的控制，以及它对基因组的影响还在研究中。在这里，我们使用长读长对拟南芥突变体植物的 eccDNA 区室和基因组进行测序，这些突变体植物在 DNA 甲基化和转录后基因沉默方面受到影响。我们检测到大量具有截断和嵌合形式的 TE 衍生的 eccDNA。在基因组方面，除了截断和全长 TE 新插入之外，我们还检测到复杂的结构变异（SV），特别是在一个疾病抗性簇中，这是 SV 的自然热点。最后，我们偶然在低甲基化植物中发现了大量串联重复，这表明在表观遗传突变体中，SV 可能被忽视了。我们提出，高 eccDNA 负荷可能会改变 DNA 修复途径，导致基因组不稳定和 SV 的积累，至少在植物中是这样。
