Extrachromosomal circular DNA and structural variants highlight genome instability in Arabidopsis epigenetic mutants

In an article published in August in Nature Communications, LGDP researchers demonstrate a new and crucial role for the epigenome in protecting the genome against structural variants, and open up new avenues for understanding the interaction between these circular shapes and genome stability in other biological systems.

"The genome, like all biological objects, is subject to a subtle balance between stability and adaptability. Transposable elements are mobile elements that participate in genome evolution, but can also cause harmful mutations. The epigenome helps maintain genome stability by preventing the activity of these transposable elements. During their activity, transposable elements generate circular forms of extrachromosomal DNA (ecDNA), but their impact on the genome is unknown.

We have developed a method called mobilome-seq for full-length sequencing of cDNA using Nanopore technology. By analyzing cDNAs and the genome of plants mutant for major epigenetic regulatory pathways in Arabidopsis thaliana, we were able to show that these plants accumulated a large quantity of cDNAs corresponding to DNA transposons and retrotransposons.

What's more, the cDNA population is much more diverse than expected, with half of the cDNAs being truncated and others chimeric. Unexpectedly, we have also shown that the genome of these plants contains important structural variants, such as gene duplications, which appear spontaneously in a single generation in the laboratory.

One locus in particular, involved in pathogen resistance, is deleted or duplicated in these plants, suggesting that there are "hotspots" of structural variation in the genome."

extrachomosomal

See also

Panpan Zhang, Assane Mbodj, Abirami Soundiramourtty, Christel Llauro, Alain Ghesquière, Mathieu Ingouff, R. Keith Slotkin, Frédéric Pontvianne, Marco Catoni, Marie Mirouze 
Nature Communications, 14, Article number: 5236 (2023) https://doi.org/10.1038/s41467-023-41023-0
Extrachromosomal circular DNA and structural variants highlight genome instability in Arabidopsis epigenetic mutants