ena-STUDY-SAARLAND UNIVERSITY-06-04-2018-12:50:29:297-1695
Genome-wide small RNA profiling in Paramecium reveals complex endogenous gene regulation
Distinct exogenous RNAi pathways regulate gene expression during vegetative growth of Paramecium, but the role of these and other pathways in endogenous gene regulation is unknown. Here, we describe the first genome-wide profiling of endogenous siRNAs. We developed a pipeline to identify, characterize and quantify 2,602 siRNA producing clusters (SRCs). We find no evidence that SRCs produce miRNAs and no preference for strand specificity. Most SRCs overlap coding genes and some show siRNA phasing along the entire open reading frame, suggesting that the mRNA transcript serves as a source for siRNAs. The four investigated transcriptomic states (serotypes) can be differentiated by their SRC expression pattern indicating close relationship of mRNA and siRNAs. Integrative analysis of siRNA abundance and gene expression revealed that siRNAs are not strict silencers but rather fine tune gene expression. Feeding-induced Dcr1 and Dcl4 knockdowns reveal strong effects to most SRCs, particularly to phased SRCs. Knockdown of a siRNA-unrelated gene also showed strong effects, suggesting a sequence independent saturation of RNAi components due to small RNA feeding. Our data suggests that Paramecium uses a complex set of RNAi pathways to regulate a large number of genes allowing for flexible adaptation to the environment.
Distinct exogenous RNAi pathways regulate gene expression during vegetative growth of Paramecium, but the role of these and other pathways in endogenous gene regulation is unknown. Here, we describe the first genome-wide profiling of endogenous siRNAs. We developed a pipeline to identify, characterize and quantify 2,602 siRNA producing clusters (SRCs). We find no evidence that SRCs produce miRNAs and no preference for strand specificity. Most SRCs overlap coding genes and some show siRNA phasing along the entire open reading frame, suggesting that the mRNA transcript serves as a source for siRNAs. The four investigated transcriptomic states (serotypes) can be differentiated by their SRC expression pattern indicating close relationship of mRNA and siRNAs. Integrative analysis of siRNA abundance and gene expression revealed that siRNAs are not strict silencers but rather fine tune gene expression. Feeding-induced Dcr1 and Dcl4 knockdowns reveal strong effects to most SRCs, particularly to phased SRCs. Knockdown of a siRNA-unrelated gene also showed strong effects, suggesting a sequence independent saturation of RNAi components due to small RNA feeding. Our data suggests that Paramecium uses a complex set of RNAi pathways to regulate a large number of genes allowing for flexible adaptation to the environment.