Analyses of chromosome copy number and expression level of four genes in the ciliate Chilodonella uncinata reveal a complex pattern that suggests epigenetic regulation

Abstract

Chilodonella uncinata, like all ciliates, contains two distinct nuclei in every cell: a germline micronucleus and a somatic macronucleus. The macronucleus develops from the zygotic nucleus through a series of chromosomal rearrangements. Macronuclear development in C. uncinata yields a nucleus with highly amplified gene-sized chromosomes. The macronucleus is transcriptionally active during vegetative growth while there is no expression in the micronucleus except during a brief period following conjugation. Gene family evolution in ciliates occurs through complex processes including gene duplication and an alternative processing of scrambled genes. Here we use quantitative PCR to compare relative expression levels of eight genes (SSU-rDNA, Actin, α-Tubulin and five β-Tubulin sequences) to their abundance as macronuclear chromosomes. We show that three strains of the morphospecies C. uncinata share similar patterns across all loci. For example, we find an inverse correlation among five β-tubulin genes whereby the more abundant macronuclear chromosomes have lower levels of expression compared to less abundant chromosomes. We discuss implication of ours finding, which suggest an epigenetic mechanism maintains chromosome copy number in C. uncinata.

Chromosome Copy Number Variation and Control in the Ciliate Chilodonella uncinata

“…The observed differences in copy number could be due to either independent control of amplification of each chromosome during development of the MAC or accumulated differences due to lack of regulation during segregation. The fact that our results correspond well with previous estimates of chromosome copy number in this species [41]–[43] suggests that the overall differences between chromosomes are due to differential amplification. Likewise, as expected based on the high copy number of the rDNA-containing chromosome in other ciliates, we also find this chromosome at a high copy number, supporting the role of differential chromosome amplification during development [22], [44].…”

Nanochromosome Copy Number Does not Correlate with RNA Levels Though Patterns are Conserved between Strains of the Ciliate Morphospecies Chilodonella uncinata

“…We observed similar patterns of copy numbers of three essential genes (SSU, actin and α-tubulin) and three Hap gene family members between two strains of C. uncinata (Table 1; Figure 1). In addition, the pattern of three essential gene copy numbers are stable compared to that quantified two years ago (Bellec and Katz 2012), which corresponds with the recent report that gene copy numbers in C. uncinata do not change under a stochastic process during vegetative growth (Spring et al 2013). This is different from spirotrichous ciliates where copy number patterns are not conserved in closely related species or even between two subpopulations of one strain (Xu et al 2012).…”

“…In Oxytricha trifallax (CI: Spirotrichea), the copy numbers of 11 MAC chromosomes are moderately correlated to gene expression levels, though the pattern is not conserved in closely related species or even between two subpopulations of one strain (Xu et al 2012). In contrast, a recent study in Chilodonella uncinata revealed that members of the β-tubulin gene family that are abundant in the macronucleus tend to be expressed at low levels, while rarer gene family members are expressed at higher levels (Bellec and Katz 2012). …”

“…are generated using a combination of unique and shared micronuclear regions, Gao et al 2014). Two of the three rarely expressed β-tubulin members (Bellec and Katz 2012) are also generated from alternatively processing of micronuclear loci (Katz and Kovner 2010), suggesting that alternatively processed gene family members may be expressed at low levels during vegetative growth of C. uncinata . Finally, the low expression of members of Hap and Pkc may indicate that they are cell-cycle dependent and repressed during vegetative growth, as has been seen for gene family members in other ciliates.…”

Insights into transgenerational epigenetics from studies of ciliates

“…Copy number of chromosomes in the macronucleus is another epigenetically controlled phenomenon in ciliates with extensively processed, gene-sized macronuclear chromosomes (Bellec and Katz, 2012; Xu et al, 2012). Ciliates with multigene macronuclear chromosomes, such as Paramecium and Tetrahymena , have roughly even copy numbers of all chromosomes in their macronuclei (Xu et al, 2012).…”