Abstract
Cytosine C5 methylation is an important epigenetic control mechanism in a wide array of Eukaryotic organisms and generally carried out by proteins of C-5 DNA methyltransferase family (DNMTs). In several protozoans the status of this mechanism remains elusive, such as in Leishmania, the causative agent of the disease leishmaniasis in humans and a wide array of vertebrate animals. In this work, we show that the Leishmania donovani genome contains a C-5 DNA methyltransferase (DNMT) from the DNMT6 subfamily, of which the function is still unclear, and verified its expression at RNA level. We created viable overexpressor and knock-out lines of this enzyme and characterised their genome-wide methylation patterns using whole-genome bisulfite sequencing, together with promastigote and amastigote control lines. Interestingly, despite DNMT6 presence, we found that methylation levels were equal to or lower than 0.0003% at CpG sites, 0.0005% at CHG sites and 0.0126% at CHH sites at genome scale. As none of the methylated sites were retained after manual verification, we conclude that there is no evidence for DNA methylation in this species. A similar absence of DNA methylation was observed for the blood form of Trypanosoma brucei, another Trypanosomatid species. We demonstrate that this difference in DNA methylation between the parasite (no detectable DNA methylation) and the vertebrate host (DNA methylation), allows enrichment of parasite DNA using Methyl-CpG-binding domain columns, readily available in commercial kits. As such, we depleted methylated DNA from 1) mixes of Leishmania promastigote and amastigote DNA with human DNA and 2) THP-1 cells infected with Leishmania amastigotes. This resulted in 62x to 263x Leishmania:human enrichment, depending on the dilution and type of sample studied. These results open a promising avenue for including an unmethylated DNA enrichment step as a pre-enrichment before sequencing clinical samples.