A comparative study of genome organization and epigenetic mechanisms in model ciliates, with an emphasis on Tetrahymena, Paramecium and Oxytricha.

As a group of unicellular eukaryotes, ciliates offer a unique system to explore epigenetic regulation, mostly due to their nuclear dualism. Ciliates launched a successful radiation after their early evolutionary branching, therefore harboring an unexpectedly rich pool of diverse biological functions and mechanisms. In this review, we compare distinct features of different ciliates in mating type determination, genome organization, DNA methylation, and removal of internal eliminated sequences (IES), with emphasis on Tetrahymena, Paramecium and Oxytricha. Firstly, we review studies on mating type determination in Paramecium, one of the foundational phenomena that defined the field of epigenetics, and compare this process with that in Tetrahymena. Secondly, we showcase the high diversity in genome structure of several ciliates, such as genome size, gene copy numbers, genome rearrangement, etc. Thirdly, we present a brief description of features and potential functions of 5-methylcytosine (5mC) and N6-methyladenine (6mA) in ciliates so far studied. Fourthly, we describe both the initial and the continuously optimized scan RNA (scnRNA) model for IES elimination in Tetrahymena and contrast it with that in Paramecium and Oxytricha. Finally, we discuss the importance of integrative approaches to the study of epigenetic diversity in ciliates and provide possible directions for future research.