5-methyl-cytosine and 5-hydroxy-methyl-cytosine in the genome of Biomphalaria glabrata, a snail intermediate host of Schistosoma mansoni

Abstract

BackgroundBiomphalaria glabrata is the mollusc intermediate host for Schistosoma mansoni, a digenean flatworm parasite that causes human intestinal schistosomiasis. An estimated 200 million people in 74 countries suffer from schistosomiasis, in terms of morbidity this is the most severe tropical disease after malaria. Epigenetic information informs on the status of gene activity that is heritable, for which changes are reversible and that is not based on the DNA sequence. Epigenetic mechanisms generate variability that provides a source for potentially heritable phenotypic variation and therefore could be involved in the adaptation to environmental constraint. Phenotypic variations are particularly important in host-parasite interactions in which both selective pressure and rate of evolution are high. In this context, epigenetic changes are expected to be major drivers of phenotypic plasticity and co-adaptation between host and parasite. Consequently, with characterization of the genomes of invertebrates that are parasite vectors or intermediate hosts, it is also essential to understand how the epigenetic machinery functions to better decipher the interplay between host and parasite.MethodsThe CpGo/e ratios were used as a proxy to investigate the occurrence of CpG methylation in B. glabrata coding regions. The presence of DNA methylation in B. glabrata was also confirmed by several experimental approaches: restriction enzymatic digestion with isoschizomers, bisulfite conversion based techniques and LC-MS/MS analysis.ResultsIn this work, we report that DNA methylation, which is one of the carriers of epigenetic information, occurs in B. glabrata; approximately 2% of cytosine nucleotides are methylated. We describe the methylation machinery of B. glabrata. Methylation occurs predominantly at CpG sites, present at high ratios in coding regions of genes associated with housekeeping functions. We also demonstrate by bisulfite treatment that methylation occurs in multiple copies of Nimbus, a transposable element.ConclusionsThis study details DNA methylation for the first time, one of the carriers of epigenetic information in B. glabrata. The general characteristics of DNA methylation that we observed in the B. glabrata genome conform to what epigenetic studies have reported from other invertebrate species.

Elucidating the molecular bases of epigenetic inheritance in non-model invertebrates: the case of the root-knot nematode Meloidogyne incognita

“…The levels of 5-methylcytosine (5-mC) and 5-hydroxy methylcytosine (5-hmC) were determined by liquid chromatography-mass spectrometry LC-MS/MS analysis as their deoxyribonucleosides as described in (Fneich et al, 2013). Neither 5-methyl-cytosine nor 5-hydrox-methyl-cytosine could be detected.…”

The mysterious presence of a 5-methylcytosine oxidase in theDrosophilagenome

“…23 This difference in results was attributed to a lack of specificity of the earlier applied methods in comparison to the highly selective and comprehensive whole genome bisulfite sequencing used in the latest publication. However there are numerous reported cases of insects, including ants, aphids, bees, flies, and beetles (Acyrthosiphon pisum, Aedes aegypti, Apis mellifera, Camponotus floridanus, Harpegnathos saltator, Nasonia vitripennis, Tribolium castaneum) having clearly detectable levels and specific patterns of 5mC, [24][25][26][27][28][29][30][31] which would mean that the absence of DNA methylation in Drosophila melanogaster would seemingly be unique within this class of animals. Particularly wellstudied cases can be found with honeybees and ants 25,32 whose epigenetic machinery has much more in common with mammals than that found in Drosophila.…”

Comparative immunogenomics of molluscs

“…The availability of non-coding intergenic genomic sequences further enables exploration of (immune-relevant) regulatory mechanisms involving transcription factors and nuclear receptors (Humphries and Harter, 2016; Kaur et al, 2015). Moreover, molluscs possess the machinery to employ methylation for epigenetic regulation of gene expression (Fneich et al, 2013; Geyer et al, 2011) and genome-wide analysis of C. gigas suggests that a nucleotide sequence composition is biased towards GC content in families of inducible genes (like stress and environmental response genes) to facilitate methylation for epigenetic control of gene expression (Gavery and Roberts, 2010). The genome sequences also provide targets to develop markers for linkage studies.…”