Abstract
Transposable elements are in a constant arms race with the silencing mechanisms of their host genomes. One silencing mechanism commonly used by many eukaryotes is dependent on cytosine methylation, a covalent modification of DNA deposited by C5 cytosine methyltransferases (DNMTs). Here, we report how two distantly related eukaryotic lineages, dinoflagellates and charophytes, have independently incorporated DNMTs into the coding regions of distinct retrotransposon classes. Concomitantly, we show that dinoflagellates of the genus Symbiodinium have evolved cytosine methylation patterns unlike any other eukaryote, with most of the genome methylated at CG dinucleotides. Finally, we demonstrate the ability of retrotransposon DNMTs to methylate CGs de novo, suggesting that retrotransposons could self-methylate retrotranscribed DNA. Together, this is an example of how retrotransposons incorporate host-derived genes involved in DNA methylation. In some cases, this event could have implications for the composition and regulation of the host epigenomic environment.
Highlights
Transposable elements are in a constant arms race with the silencing mechanisms of their host genomes
One of the most recent reports from this alleged deposited by C5 cytosine methyltransferases (DNMTs)-retrotransposon association comes from the genome of the dinoflagellate Symbiodinium kawagutii[7], a member of a genus that plays a key role as coral symbionts[8, 9]
Here, we report an unprecedented example of divergent retrotransposons that have recruited host genes involved in cytosine methylation in two distantly related lineages of eukaryotes
Summary
Transposable elements are in a constant arms race with the silencing mechanisms of their host genomes. We report how two distantly related eukaryotic lineages, dinoflagellates and charophytes, have independently incorporated DNMTs into the coding regions of distinct retrotransposon classes. We demonstrate the ability of retrotransposon DNMTs to methylate CGs de novo, suggesting that retrotransposons could self-methylate retrotranscribed DNA Together, this is an example of how retrotransposons incorporate host-derived genes involved in DNA methylation. Given the disparity of lineages that share this trait, mC-dependent transposable element silencing has been suggested as one of the original roles of mC in eukaryotes, together with active gene body methylation[1, 2]. We characterise how cytosine-specific DNMTs have been incorporated into distinct classes of retrotransposons independently We assess their functional activity and profile the epigenomic characteristics of their algal hosts that belong to the charophyte and dinoflagellate lineages
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