Paramecium epigenetics in development and proliferation

Abstract

CILIATES, particularly Paramecium, served as model organisms in genetics and epigenetics long before the latter term was even used for the first time. From the historical point of view, ciliate genetics had its first's heydays from 1940 to 1960, when many important discoveries were made, resulting in a detailed description of epigenetic phenomena. As a result, most textbooks for undergraduates dedicated individual chapters to ciliate cell biology and genetics in the 1970s, but these chapters disappeared from textbooks in modern times (Preer, 1997).This situation has now changed (Boenigk, 2021). Ciliate epigenetic research experiences a renaissance, although this wording might not be entirely precise as research is not simply making a replica of the former work. We are now able to describe epigenetic phenomena discovered phenotypically in the early 1940s on the molecular level and identify small RNAs, histone modifications, and DNA modifications that are responsible for these phenomena. Still, genetics research is primarily based on yeast, C. elegans, Drosophila, zebrafish, and

Using digital PCR to predict ciliate abundance from ribosomal RNA gene copy numbers

“…One possible explanation for this observation is that when resources become scarce, ciliates undergo autogamy. During this meiotic event, GCN could exceed those during vegetative growth since fragments of the degraded former macronucleus can still be present for several cell cycles (Drews, Boenigk, & Simon, 2022). To the best of our knowledge, we in this study for the first time show that also after mitotic events daughter cells do not receive equal amounts of gene copies after cell division (Supporting Information S11: https://www.zenodo.org/doi/10.5281/zenodo.10820661).…”

“…This finding is especially relevant for studies that discuss potential mechanisms controlling gene dosage in ciliates. To ascertain that also the daughter cell that received fewer rRNA gene copies still has a sufficiently high number of copies, assumptions are that such high CNs could be an adaptation to the random segregation of DNA to the daughter cells after mitosis (Drews, Boenigk, & Simon, 2022). However, we want to highlight that further analyses of single cells after division are needed to validate our observation.…”

“…When the cell divides, the macronucleus elongates and separates the genes to the daughter cells presumably by chance (Ahsan et al, 2022). During this event as well as afterwards, DNA within the macronucleus is continuously replicated, resulting in high numbers of gene copies (Drews, Boenigk, & Simon, 2022; Drews, Salhab, et al, 2022). High rRNA gene copy numbers (GCN) can skew quantitative interpretations and can lead to an over‐ or underestimation of certain taxa.…”

Species-Specific Duplication of Surface Antigen Genes in Paramecium

“…We could have also missed SAg genes due to a combination of sequencing depth and heterogeneity of MAC chromosome ends. The MAC genome is newly developed from two haploid MIC genomes during a sexual process and this process always causes certain heterogeneity of the MAC chromosomes, as reviewed in [49]. One aspect of heterogeneity concerns the MAC chromosome ends; these may exist in different lengths, and the published scaffolds only represent the longest possible scaffolds, ignoring the shorter versions [50].…”

Inter-generational nuclear crosstalk links the control of gene expression to programmed genome rearrangements during theParameciumsexual cycle

“…At each sexual cycle, the old (parental) MAC is destroyed, and in the same cell, two new MACs develop from mitotic copies of the zygotic nucleus. MAC development has been extensively studied in ciliate models (8), including Paramecium (9). In Paramecium tetraurelia, two sexual processes have been described: conjugation between a pair of reactive partners with complementary mating types, and autogamy, a self-fertilization that takes place in a single cell.…”