Periodic Patterns of Adenosine DNA Methylation in the Ciliate O. trifallax

Abstract

DNA methylation is a highly conserved epigenetic regulatory mechanism, and is essential to the development of most eukaryotic organisms. Though chemically stable and reliably inherited, de novo methylation allows an organism to adapt its expression levels in response to its environment. Consequently, changes in methylation patterns have been linked to aging, obesity, and Alzheimers, as well as cancer. Though there are three common types of methylation, the vast majority of the current research has focused on cytosine methylation, with recent exciting discoveries in gene body methylation and nucleosome interactions. Adenosine DNA methylation, however, while also prevalent, has been largely neglected. In this study we examined the role of adenosine methylation in the ciliate Oxytricha trifallax, a unicellular organism with many chromosomes, most containing only one gene. The unique genomic structure of this organism has allowed us to identify a periodic pattern of adenosine methylation sites. Using a methylated DNA immunoprecipitation, we found that approximately one third of O. trifallax chromosomes have methylation sites detectable by a statistically significant peak in read density, with a weak relationship between the number of sites and the length of the chromosome, as well as the number of coding DNA sequences present. Around the methylation sites, we detected periodic increases in methylation densities every 190-200 base pairs, a pattern which was sensitive to the direction of transcription of nearby coding DNA sequences. Methylation peaks were preferentially located in coding DNA sequences, and enriched in genes involved in biosynthetic pathways and organelles. We also looked at dynamic methylation patterns during encystment, and found a general decrease in methylation levels. In addition, the top genes preferentially methylated during encystment did not overlap with the top processes of vegetative cells, enriching instead for functions associated with translation.