Abstract
5-methylcytosine DNA methylation regulates gene expression and developmental programming in a broad range of eukaryotes. However, its presence and potential roles in ciliates, complex single-celled eukaryotes with germline-somatic genome specialization via nuclear dimorphism, are largely uncharted. While canonical cytosine methyltransferases have not been discovered in published ciliate genomes, recent studies performed in the stichotrichous ciliate Oxytricha trifallax suggest de novo cytosine methylation during macronuclear development. In this study, we applied bisulfite genome sequencing, DNA mass spectrometry and antibody-based fluorescence detection to investigate the presence of DNA methylation in Paramecium tetraurelia. While the antibody-based methods suggest cytosine methylation, DNA mass spectrometry and bisulfite sequencing reveal that levels are actually below the limit of detection. Our results suggest that Paramecium does not utilize 5-methylcytosine DNA methylation as an integral part of its epigenetic arsenal.
Highlights
The C5 position of cytosine can get methylated by DNA methyltransferases (DNMTs) into methylcytosine (5mC) and is necessary for the maintenance of chromatin structure, gene expression, and many chromatin-related processes[1,2,3]. 5mC has been extensively studied for its role in biological processes such as genomic imprinting, X chromosome inactivation and has long been implicated in human disease[3,4,5,6,7,8]
Other eukaryotes such as S. pombe[20] and C. elegans[21] are devoid of cytosine methylation in their genome
Though there was no clear evidence of presence or absence of cytosine methylation in Paramecium, recent studies identified its presence in Stylonychia lemnae[48] and O. trifallax [30]
Summary
The C5 position of cytosine can get methylated by DNA methyltransferases (DNMTs) into methylcytosine (5mC) and is necessary for the maintenance of chromatin structure, gene expression, and many chromatin-related processes[1,2,3]. 5mC has been extensively studied for its role in biological processes such as genomic imprinting, X chromosome inactivation and has long been implicated in human disease[3,4,5,6,7,8]. The C5 position of cytosine can get methylated by DNA methyltransferases (DNMTs) into methylcytosine (5mC) and is necessary for the maintenance of chromatin structure, gene expression, and many chromatin-related processes[1,2,3]. DNA methylation is heritable and actively maintained by methyltransferases. It can be removed by the suppression of maintenance methyltransferases or by the action of specific demethylases. Cytosine methylation in motifs other than CpG and CNF has been shown in plants and Drosophila [18], [19]. Other eukaryotes such as S. pombe[20] and C. elegans[21] are devoid of cytosine methylation in their genome
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