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Transposons, so-called jumping genes, are a threat to genomes, so plants work hard to prevent them from mobilizing and re-inserting into the genome. Spirodela polyrhiza, the most ancient member of the duckweed family, uses an understudied epigenetic mechanism to mark old transposons without DNA methylation, as researchers in the group of Arturo Marí-Ordóñez at the Gregor Mendel Institute of Molecular Plant Biology (GMI) of the Austrian Academy of Sciences show in a new study, published on March 5th in Genome Research.
A constant cat-and-mouse game is unfolding in all eukaryotic cells: Transposons, also known as jumping genes because they can move around the genome, threaten the cell’s genome by causing mutations and rearrangements. To defend their genomes, plants silence transposons by compacting the transposon-containing DNA, rendering it inaccessible to the cellular machinery. To compact the DNA, plants use various epigenetic marks, including DNA methylation and modifications of the histone proteins that organize and package the DNA. These two marks reinforce each other to ensure robust and stable transposon silencing. Over generations, silenced transposons accumulate mutations, and eventually transposons become fragmented. These “old” – or degenerate – transposons are no longer able to jump and cause damage to the genome, but their accumulation and repetitive nature can still cause genomic rearrangements. To prevent rearrangements, degenerate transposons are also kept under control by DNA methylation and histone modification– the mechanisms used to silence them in the first place.
However, researchers in Arturo Marí-Ordóñez’s group at the Gregor Mendel Institute of Molecular Plant Biology (GMI) of the Austrian Academy of Sciences now show that Spirodela polyrhiza – the oldest member of the duckweed family – does not mark “old”, degenerate transposons with DNA methylation, but instead uses an understudied epigenetic mark that, in Spirodela, is maintained independent of DNA methylation – contrary to other plants. Their findings expand upon the conventional models of transposon regulation and underline the importance of studying a variety of diverse model organisms.
Simple yet effective
Duckweeds – tiny plants that float in ponds and lagoons – have evolved to become increasingly simple and to reproduce through fast, clonal expansion instead of sexual reproduction. This evolutionary path has caused Spirodela polyrhiza, the species studied by Marí-Ordóñez, to lose key genes involved in various processes, allowing researchers to study the genetic consequences of developmental reductionism.
Although Spirodela has a genome of similar size and with similar transposon content as Arabidopsis thaliana – a widely used model plant – researchers have observed remarkably low levels of methylation in the Spirodela genome. Yet, despite these low methylation levels, Spirodela manages to keep transposons in check, showing that flowering plants can regulate transposons even without DNA methylation.
By comparing Spirodela to Arabidopsis, the researchers found that Spirodela lacks some of the proteins required for DNA methylation in other plants. Despite this, Mari-Ordonez and his team show that Spirodela does use DNA methylation and histone modifications to silence recently integrated, intact transposons – all the marks used by other plants. However, in Spirodela, as transposons degenerate, they lose all silencing marks but one – an understudied type of histone modification, also associated to transposon silencing, remains. “We’ve shown for the first time that some flowering plants can maintain heterochromatin marks even without DNA methylation,” explained Arturo Marí-Ordóñez. “This unique epigenetic landscape may be linked to Spirodela’s reproductive strategy, which relies on rapid clonal propagation.”
Tiny plants, enormous potential
The team’s findings suggest Spirodela focuses on silencing potentially active transposons – a clear threat to genome integrity – over fragmented transposons. The researchers now aim to uncover how Spirodela maintains epigenetic marks on degenerate transposons without DNA methylation. “The specific role of this epigenetic mark remains unknown but could be relevant to understanding how other duckweeds and plants deal with transposons, giving us one more piece to solve to puzzle of genome defense in plants,” said Arturo Marí-Ordóñez.
Beyond transposon research, duckweeds have recently emerged as a powerful biotechnological tool. Their simple lifestyle and rapid expansion make duckweeds an ideal platform for the sustainable production of pharmaceuticals, biofuels and even food. Understanding duckweeds’ genetic architecture will be key to optimizing genetic engineering strategies and unlocking their full potential in biotechnology.
Sylvia Weinzettl
Dr. Bohr-Gasse 3, 1030 Wien
T: +43 1 79044 – 4403
Mail: sylvia.weinzettl@gmi.oeaw.ac.at
gmi.oeaw.ac.at
Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza. Rodolphe Dombey, Daniel Buendía-Ávila, Verónica Barragán-Borrero, Laura Diezma-Navas, Arturo Ponce-Mañe, José Mario Vargas-Guerrero, Rana Elias, Arturo Marí-Ordóñez. doi: 10.1101/gr.279532.124.
https://www.oeaw.ac.at/gmi/detail/news/duckweed-differentially-marks-old-and-new...
Spirodela polyrhiza, the most ancient duckweed, differentially marks new and old transposons.
Adam Cooper / GMI
Adam Cooper / GMI
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Spirodela polyrhiza, the most ancient duckweed, differentially marks new and old transposons.
Adam Cooper / GMI
Adam Cooper / GMI
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