ArticleNucleic acids research2019
Exogenous RNAi mechanisms contribute to transcriptome adaptation by phased siRNA clusters in Paramecium.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 23 citations in OpenAlex.
- Subtle-seq reveals frequent ageing-associated chromosome fragmentation on nucleosome core DNA.Nucleic acids research · 2026Article
- Exogenous dsRNA made accessible to Dicer by two eukaryotic RNA-dependent RNA polymerases in Paramecium tetraurelia.Communications biology · 2026Article
- A histone methyltransferase-independent function of PRC2 controls small RNA dynamics during programmed DNA elimination in Paramecium.Nucleic acids research · 2025Article
- De Novo Genome Sequence Assembly of the RNAi-Tractable Paramecium bursaria 186b: An Endosymbiotic Model System.Genome biology and evolution · 2025Article
- Defining an optimal control for RNAi experiments with adult Schistosoma mansoni.Scientific reports · 2023Article
- Developmental mRNA clearance by PIWI-bound endo-siRNAs in Paramecium.Cell reports · 2023Article
- Species-Specific Duplication of Surface Antigen Genes inMicroorganisms · 2022Article
- The origin of RNA interference: Adaptive or neutral evolution?PLoS biology · 2022Article
- Article
- Emergent RNA-RNA interactions can promote stability in a facultative phototrophic endosymbiosis.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Characterization of the RNA-interference pathway as a tool for reverse genetic analysis in the nascent phototrophic endosymbiosis,Royal Society open science · 2021Article
- Toward fine-tuned metabolic networks in industrial microorganisms.Synthetic and systems biotechnology · 2020Article
- Feeding exogenous dsRNA interferes with endogenous sRNA accumulation in Paramecium.DNA research : an international journal for rapid publication of reports on genes and genomes · 2020Article
- The Obligate Symbiont "Frontiers in microbiology · 2020Article
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Authors and funding
9 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Extensive research has characterized distinct exogenous RNAi pathways interfering in gene expression during vegetative growth of the unicellular model ciliate Paramecium. However, role of RNAi in endogenous transcriptome regulation, and environmental adaptation is unknown. Here, we describe the first genome-wide profiling of endogenous sRNAs in context of different transcriptomic states (serotypes). We developed a pipeline to identify, and characterize 2602 siRNA producing clusters (SRCs). Our data show no evidence that SRCs produce miRNAs, and in contrast to other species, no preference for strand specificity of siRNAs. Interestingly, most SRCs overlap coding genes and a separate group show siRNA phasing along the entire open reading frame, suggesting that the mRNA transcript serves as a source for siRNAs. Integrative analysis of siRNA abundance and gene expression levels revealed surprisingly that mRNA and siRNA show negative as well as positive associations. Two RNA-dependent RNA Polymerase mutants, RDR1 and RDR2, show a drastic loss of siRNAs especially in phased SRCs accompanied with increased mRNA levels. Importantly, most SRCs depend on both RDRs, reminiscent to primary siRNAs in the RNAi against exogenous RNA, indicating mechanistic overlaps between exogenous and endogenous RNAi contributing to flexible transcriptome adaptation.
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