Epigenetic regulation of serotype expression antagonizes transcriptome dynamics inParamecium tetraurelia

Abstract

Phenotypic variation of a single genotype is achieved by alterations in gene expression patterns. Regulation of such alterations depends on their time scale, where short-time adaptations differ from permanently established gene expression patterns maintained by epigenetic mechanisms. In the ciliate Paramecium, serotypes were described for an epigenetically controlled gene expression pattern of an individual multigene family. Paradoxically, individual serotypes can be triggered in Paramecium by alternating environments but are then stabilized by epigenetic mechanisms, thus raising the question to which extend their expression follows environmental stimuli. To characterize environmental adaptation in the context of epigenetically controlled serotype expression, we used RNA-seq to characterize transcriptomes of serotype pure cultures. The resulting vegetative transcriptome resource is first analysed for genes involved in the adaptive response to the altered environment. Secondly, we identified groups of genes that do not follow the adaptive response but show co-regulation with the epigenetically controlled serotype system, suggesting that their gene expression pattern becomes manifested by similar mechanisms. In our experimental set-up, serotype expression and the entire group of co-regulated genes were stable among environmental changes and only heat-shock genes altered expression of these gene groups. The data suggest that the maintenance of these gene expression patterns in a lineage represents epigenetically controlled robustness counteracting short-time adaptation processes.

Two sets of RNAi components are required for heterochromatin formationin transtriggered by truncated transgenes

“…In Paramecium , recent studies demonstrate another RNAi pathway involving the highly divergent RNA-dependent RNA polymerase RDR3 to control endogenous gene expression, suggestive of transcriptional control ( 22 , 23 ). Further, RNAseq analyses suggest that such epigenetic mechanisms contribute to transcriptional robustness of the transcriptomic landscape in P. tetraurelia , thus raising the question about the extent and the molecular details of this mechanism ( 24 ).…”

Automated analysis of small RNA datasets with RAPID

“…They show nuclear dimorphism, and have a wide range of phenotypes. These phenotypes depend on an epigenetically controlled, mutually exclusive expression of members of a multigene family called serotypes [6]. With a dimorphic nucleus and more than 11 serotypes, P.tetraurelia sRNAs are involved in regulatory mechanisms at the post-transcriptional, and epigenetic level [11,6,5].…”

Peer Review #1 of "Automated analysis of small RNA datasets with RAPID (v0.1)"

“…They show nuclear dimorphism, and have a wide range of phenotypes. These phenotypes depend on an epigenetically controlled, mutually exclusive expression of members of a multigene family called serotypes (Cheaib et al, 2015). With a dimorphic nucleus and more than 11 serotypes, P.tetraurelia sRNAs are involved in regulatory mechanisms at the post-transcriptional, and epigenetic level (Götz et al, 2016;Cheaib et al, 2015;Carradec et al, 2015).…”