Egg-specific expression of protein with DNA methyltransferase activity in the biocarcinogenic liver fluke Clonorchis sinensis

Abstract

Despite recent reports regarding the biology of cytosine methylation in Schistosoma mansoni, the impact of the regulatory machinery remains unclear in diverse platyhelminthes. This ambiguity is reinforced by discoveries of DNA methyltransferase 2 (DNMT2)-only organisms and the substrate specificity of DNMT2 preferential to RNA molecules. Here, we characterized a novel DNA methyltransferase, named CsDNMT2, in a liver fluke Clonorchis sinensis. The protein exhibited structural properties conserved in other members of the DNMT2 family. The native and recombinant CsDNMT2 exhibited considerable enzymatic activity on DNA. The spatiotemporal expression of CsDNMT2 mirrored that of 5-methylcytosine (5 mC), both of which were elevated in the C. sinensis eggs. However, CsDNMT2 and 5 mC were marginally detected in other histological regions of C. sinensis adults including ovaries and seminal receptacle. The methylation site seemed not related to genomic loci occupied by progenies of an active long-terminal-repeat retrotransposon. Taken together, our data strongly suggest that C. sinensis has preserved the functional DNA methylation machinery and that DNMT2 acts as a genuine alternative to DNMT1/DNMT3 to methylate DNA in the DNMT2-only organism. The epigenetic regulation would target functional genes primarily involved in the formation and/or maturation of eggs, rather than retrotransposons.

Genome-wide identification of histone lysine methyltransferases and their implications in the epigenetic regulation of eggshell formation-related genes in a trematode parasite Clonorchis sinensis

“…Since DNMT2 was shown to be an RNA methyltransferase [ 30 ] and platyhelminths belong to the so-called DNMT2-only organisms [ 10 ], the presence of DNA methylation-related epigenetic machinery and/or its practical implications in gene regulation have been highly disputable for a long time in the lower animals. However, recent studies have provided multiple evidences revealing that the epigenetic machinery effectively operates in the lower animal group [ 14 , 21 , 31 ]. In addition to the previously described 5-methylcytosines [ 21 ], this study showed that methylated histone variants are intimately involved in the epigenetic regulation of C. sinensis genes.…”

“…However, recent studies have provided multiple evidences revealing that the epigenetic machinery effectively operates in the lower animal group [ 14 , 21 , 31 ]. In addition to the previously described 5-methylcytosines [ 21 ], this study showed that methylated histone variants are intimately involved in the epigenetic regulation of C. sinensis genes. For the differential histone methylation, genes encoding most of the HKMT family members, which have been widely identified across animal taxa, are preserved in the liver fluke and other platyhelminth genomes, while some genes were specifically expanded in a series of donor organisms.…”

“…The high gene dosages were in contrast to that of DNMT gene. Platyhelminth genomes preserved only a single DNMT2 homolog but no DNMT1 or DNMT3 homologs [ 21 ].…”

“…Most multicellular eukaryotes express 3 DNMTs that generate (DNMT3a and DNMT3b) and maintain (DNMT1) the genome-wide 5mC methylomes. However, the genomes of C. sinensis and other platyhelminths encode only a single DNMT protein homologous to the mammalian DNMT2 [ 21 ] and the DNMT2-like protein seems to provide enzymatic activity responsible for the generation and/or maintenance of DNA methylomes [ 21 , 31 ]. This situation is highly contrasted to the well-preserved HKMT dosages in these invertebrates ( Figs.…”

“…Reversible modification of the chromatin structure induced by methylated DNA and/or histones may be a strong candidate for the epigenetic gene regulation. We have previously reported the structural and biochemical properties of a DNMT homolog in C. sinensis [ 21 ]. In this study, we analyzed HKMT proteins by screening the entire C. sinensis genome.…”