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SABOT Francois

  • DIADE Unit, IRD, Montpellier, France
  • Bioinformatics, Evolutionary genomics, Population genomics, Structural genomics, Viruses and transposable elements
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PhD in molecular biology HDR in pangenomics

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18 Feb 2021
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Traces of transposable element in genome dark matter co-opted by flowering gene regulation networks

Recommended by based on reviews by Josep Casacuberta and 1 anonymous reviewer

Using small fragments to discover old TE remnants: the Duster approach empowers the TE detection

Transposable elements are the raw material of the dark matter of the genome, the foundation of the next generation of genes and regulation networks". This sentence could be the essence of the paper of Baud et al. (2021). Transposable elements (TEs) are endogenous mobile genetic elements found in almost all genomes, which were discovered in 1948 by Barbara McClintock (awarded in 1983 the only unshared Medicine Nobel Prize so far). TEs are present everywhere, from a single isolated copy for some elements to more than millions for others, such as Alu. They are founders of major gene lineages (HET-A, TART and telomerases, RAG1/RAG2 proteins from mammals immune system; Diwash et al, 2017), and even of retroviruses (Xiong & Eickbush, 1988). However, most TEs appear as selfish elements that replicate, land in a new genomic region, then start to decay and finally disappear in the midst of the genome, turning into genomic ‘dark matter’ (Vitte et al, 2007). The mutations (single point, deletion, recombination, and so on) that occur during this slow death erase some of their most notable features and signature sequences, rendering them completely unrecognizable after a few million years. Numerous TE detection tools have tried to optimize their detection (Goerner-Potvin & Bourque, 2018), but further improvement is definitely challenging. This is what Baud et al. (2021) accomplished in their paper. They used a simple, elegant and efficient k-mer based approach to find small signatures that, when accumulated, allow identifying very old TEs. Using this method, called Duster, they improved the amount of annotated TEs in the model plant Arabidopsis thaliana by 20%, pushing the part of this genome occupied by TEs up from 40 to almost 50%. They further observed that these very old Duster-specific TEs (i.e., TEs that are only detected by Duster) are, among other properties, close to genes (much more than recent TEs), not targeted by small RNA pathways, and highly associated with conserved regions across the rosid family. In addition, they are highly associated with flowering or stress response genes, and may be involved through exaptation in the evolution of responses to environmental changes. TEs are not just selfish elements: more and more studies have shown their key role in the evolution of their hosts, and tools such as Duster will help us better understand their impact.
 

References

Baud, A., Wan, M., Nouaud, D., Francillonne, N., Anxolabéhère, D. and Quesneville, H. (2021). Traces of transposable elements in genome dark matter co-opted by flowering gene regulation networks. bioRxiv, 547877, ver. 5 peer-reviewed and recommended by PCI Genomics.doi: https://doi.org/10.1101/547877
 
Bourque, G., Burns, K.H., Gehring, M. et al. (2018) Ten things you should know about transposable elements. Genome Biology 19:199. doi: https://doi.org/10.1186/s13059-018-1577-z
 
Goerner-Potvin, P., Bourque, G. Computational tools to unmask transposable elements. Nature Reviews Genetics 19:688–704 (2018) https://doi.org/10.1038/s41576-018-0050-x
 
Jangam, D., Feschotte, C. and Betrán, E. (2017) Transposable element domestication as an adaptation to evolutionary conflicts. Trends in Genetics 33:817-831. doi: https://doi.org/10.1016/j.tig.2017.07.011
 
Vitte, C., Panaud, O. and Quesneville, H. (2007) LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifications followed by rapid DNA loss. BMC Genomics 8:218. doi: https://doi.org/10.1186/1471-2164-8-218
 
Xiong, Y. and Eickbush, T. H. (1988) Similarity of reverse transcriptase-like sequences of viruses, transposable elements, and mitochondrial introns. Molecular Biology and Evolution 5: 675–690. doi: https://doi.org/10.1093/oxfordjournals.molbev.a040521

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SABOT Francois

  • DIADE Unit, IRD, Montpellier, France
  • Bioinformatics, Evolutionary genomics, Population genomics, Structural genomics, Viruses and transposable elements
  • recommender

Recommendation:  1

Reviews:  0

Educational and work
PhD in molecular biology HDR in pangenomics