Abstract
Transposable elements (TEs) are mobile genetic elements that constitute a major part of eukaryotic genomes. Host genomes have developed epigenetic mechanisms to control and prevent their proliferation. While efficiently silenced by the epigenetic machinery, they can be reactivated upon stress or at precise developmental stages. However, available methods to detect TE activity are often limited to transcriptional level or more adapted to small genomes. Today, only few TEs are known to be active and specific mechanisms controlling TEs are not well defined.
To address this question during my phD, we developed a strategy of high throughput sequencing that detects extrachromosomal circular DNA (eccDNA) forms which reflect TE activity and genome stability. We characterised mobilomes from different organisms defined as all eccDNA in a cell.
Our mobilome-seq technique successfully identified active TEs especially in asian rice Oryza sativa. We identified an active retrotransposon PopRice in endosperm tissue from different rice varieties. Interestingly and for the first time in plants, we detected somatic insertions from genome- wide resequencing. We combined our mobilome-seq results with a GWAS analysis to propose new PopRice regulation mechanisms.
In a second step, we applied our mobilome seq technique to different animal and plant organisms showing mobilome specificities from each species. Our work in collaboration with different labs help contributed to define role of RNA polymerase II in the control of TEs in O. sativa and have revealed a link between presence of eccDNA from virus and immune response in Drosophila melanogaster.
Altogether, our mobilome-sequencing method opens the possibility to explore unexplored genomic compartment. Future mobilome analysis represents new possibilities to improve our understanding of dynamics of genomes.