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Karunanithi S, Oruganti V, Marker S, Rodriguez-Viana AM, Drews F, Pirritano M, Nordström K, Simon M, Schulz MH. Exogenous RNAi mechanisms contribute to transcriptome adaptation by phased siRNA clusters in Paramecium. Nucleic Acids Res 2019; 47:8036-8049. [PMID: 31251800 PMCID: PMC6735861 DOI: 10.1093/nar/gkz553] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 06/06/2019] [Accepted: 06/19/2019] [Indexed: 01/26/2023] Open
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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Affiliation(s)
- Sivarajan Karunanithi
- Cluster of Excellence, Multimodal Computing and Interaction, Saarland University and Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany.,Graduate School of Computer Science, Saarland Informatics Campus, 66123 Saarbrücken, Germany.,Institute for Cardiovascular Regeneration, Goethe-University Hospital, 60590 Frankfurt, Germany
| | - Vidya Oruganti
- Cluster of Excellence, Multimodal Computing and Interaction, Saarland University and Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
| | - Simone Marker
- Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, 66123 Saarbrücken, Germany
| | - Angela M Rodriguez-Viana
- Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, 66123 Saarbrücken, Germany
| | - Franziska Drews
- Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, 66123 Saarbrücken, Germany.,Molecular Cell Biology and Microbiology, Wuppertal University, 42097 Wuppertal, Germany
| | - Marcello Pirritano
- Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, 66123 Saarbrücken, Germany.,Molecular Cell Biology and Microbiology, Wuppertal University, 42097 Wuppertal, Germany
| | - Karl Nordström
- Genetics/Epigenetics, Centre for Human and Molecular Biology, Saarland University, 66123 Saarbrücken, Germany
| | - Martin Simon
- Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, 66123 Saarbrücken, Germany.,Molecular Cell Biology and Microbiology, Wuppertal University, 42097 Wuppertal, Germany
| | - Marcel H Schulz
- Cluster of Excellence, Multimodal Computing and Interaction, Saarland University and Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany.,Institute for Cardiovascular Regeneration, Goethe-University Hospital, 60590 Frankfurt, Germany
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Quintana JF, Babayan SA, Buck AH. Small RNAs and extracellular vesicles in filarial nematodes: From nematode development to diagnostics. Parasite Immunol 2017; 39. [PMID: 27748953 DOI: 10.1111/pim.12395] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/08/2016] [Accepted: 10/12/2016] [Indexed: 02/06/2023]
Abstract
Parasitic nematodes have evolved sophisticated mechanisms to communicate with their hosts in order to survive and successfully establish an infection. The transfer of RNA within extracellular vesicles (EVs) has recently been described as a mechanism that could contribute to this communication in filarial nematodes. It has been shown that these EVs are loaded with several types of RNAs, including microRNAs, leading to the hypothesis that parasites could actively use these molecules to manipulate host gene expression and to the exciting prospect that these pathways could result in new diagnostic and therapeutic strategies. Here, we review the literature on the diverse RNAi pathways that operate in nematodes and more specifically our current knowledge of extracellular RNA (exRNA) and EVs derived from filarial nematodes in vitro and within their hosts. We further detail some of the issues and questions related to the capacity of RNA-mediated communication to function in parasite-host interactions and the ability of exRNA to enable us to distinguish and detect different nematode parasites in their hosts.
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Affiliation(s)
- J F Quintana
- Institute of Immunology and Infection Research and Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - S A Babayan
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - A H Buck
- Institute of Immunology and Infection Research and Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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Design, simplified cloning, and in-silico analysis of multisite small interfering RNA-targeting cassettes. MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS 2016; 5:31-43. [PMID: 27844018 PMCID: PMC5019331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Multiple gene silencing is being required to target and tangle metabolic pathways in eukaryotes and researchers have to develop a subtle method for construction of RNA interference (RNAi) cassettes. Although, several vectors have been developed due to different screening and cloning strategies but still some potential limitations remain to be dissolved. Here, we worked out a simple cloning strategy to develop multisite small interfering RNA (siRNA) cassette from different genes by two cloning steps. In this method, effective siRNA sites in the target messenger RNAs (mRNAs) were determined using in silico analysis and consecutively arranged to reduce length of inverted repeats. Here, we used one-step (polymerase chain reaction) PCR by designed long primer sets covering the selected siRNA sites. Rapid screening, cost-effective and shorten procedure are advantages of this method compare to PCR classic cloning. Validity of constructs was confirmed by optimal centroid secondary structures with high stability in plants.
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