Our recent progress in epigenetic research using the model ciliate, Tetrahymena thermophila

Abstract

Epigenetic research focuses on heritable changes beyond the DNA sequence, which has led to a revolution in biological studies and benefits in many other fields. The well-known model ciliate, Tetrahymena thermophila offers a unique system for epigenetic studies due to its nuclear dimorphism and special mode of sexual reproduction (conjugation), as well as abundant genomic resources and genetic tools. In this paper, we summarize recent progress made by our research team and collaborators in understanding epigenetic mechanisms using Tetrahymena. This includes: (1) providing the first genome-wide base pair-resolution map of DNA N 6-methyladenine (6mA) and revealed it as an integral part of the chromatin landscape; (2) dissecting the relative contribution of cis-and trans-elements to nucleosome distribution by exploring the unique nuclear dimorphism of Tetrahymena; (3) demonstrating the epigenetic controls of RNAi-dependent Polycomb repression pathways on transposable elements, and (4) identifying a new histone monomethyltransferase, TXR1 (Tetrahymena Trithorax 1), that facilitates replication elongation through its substrate histone H3 lysine 27 monomethylation (H3K27me1).

Comparative Transcriptome Analyses during the Vegetative Cell Cycle in the Mono-Cellular Organism Pseudokeronopsis erythrina (Alveolata, Ciliophora)

“…Previous morphogenetic studies of ciliates [14,15,[70][71][72] have shown that many biological processes, including somatic cortex morphogenesis, stomatogenesis, and organelle morphogenesis, occur at stage D. Transcriptomes from the G and D stages ( Figure 4C) and RT-qPCR analyses revealed that phosphotransferase activity might be related to cortex modifications [73] as it was enriched during the D stage. Common amino acid residues typically phosphorylated by kinases include serine, threonine, and tyrosine.…”

“…Ciliates, a group of unicellular eukaryotes, have been used extensively as model organisms to study a broad range of topics due to dual genome architecture, unique macronuclear genome characters ( Figure 1), and complex morphology [14][15][16][17][18][19][20][21][22][23][24]. Recently, molecular events underlying the sexual cell cycle of the model ciliate Tetrahymena thermophila were examined.…”

“…Vegetative proliferation is asexual cell division in ciliates and occurs by binary fission. The vegetative cell cycle consists of three consecutive periods, i.e., growth (G), morphogenesis (S), and cell division (D) [14]. Two "sister cells"-the proter and the opisthe-are produced during the process of cell division, which occurs after duplication of organelles (cell morphogenesis).…”

“…Morphogenetic studies have revealed rich morphological patterns during the process [38][39][40]. This is due to a multitude of events that occur during that time including macronuclear amitosis, micronuclear mitosis, cortical stomatogenesis, somatic cortex morphogenesis, and cytokinesis [14]. Molecular mechanisms underlying vegetative cell division of ciliates are largely unknown, with the exception of a study showing that Ca 2+ /CaM, p85, and RAN have important roles in the progression of cell division in Tetrahymena [40,41].…”

Marine life science and technology (MLST): a new journal highlighting all aspects of marine biology and biotechnology research

“…The model microbial eukaryote Tetrahymena has facilitated numerous studies and benefited many fields. In our first paper, Cheng et al (2019) summarize their progress in understanding epigenetic mechanisms using Tetrahymena. This review reports their efforts to generate a high-resolution DNA N 6 -methyladenine (6 mA) map, evaluate the determinants for nucleosome distribution, demonstrate the roles of RNAi-dependent Polycomb repression pathways on transposable elements, and discover the functions of histone methylation in replication elongation.…”