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Grentzinger T, Oberlin S, Schott G, Handler D, Svozil J, Barragan-Borrero V, Humbert A, Duharcourt S, Brennecke J, Voinnet O. A universal method for the rapid isolation of all known classes of functional silencing small RNAs. Nucleic Acids Res 2020; 48:e79. [PMID: 32496553 PMCID: PMC7641303 DOI: 10.1093/nar/gkaa472] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 05/05/2020] [Accepted: 05/25/2020] [Indexed: 01/30/2023] Open
Abstract
Diverse classes of silencing small (s)RNAs operate via ARGONAUTE-family proteins within RNA-induced-silencing-complexes (RISCs). Here, we have streamlined various embodiments of a Q-sepharose-based RISC-purification method that relies on conserved biochemical properties of all ARGONAUTEs. We show, in multiple benchmarking assays, that the resulting 15-min benchtop extraction procedure allows simultaneous purification of all known classes of RISC-associated sRNAs without prior knowledge of the samples-intrinsic ARGONAUTE repertoires. Optimized under a user-friendly format, the method – coined ‘TraPR’ for Trans-kingdom, rapid, affordable Purification of RISCs – operates irrespectively of the organism, tissue, cell type or bio-fluid of interest, and scales to minute amounts of input material. The method is highly suited for direct profiling of silencing sRNAs, with TraPR-generated sequencing libraries outperforming those obtained via gold-standard procedures that require immunoprecipitations and/or lengthy polyacrylamide gel-selection. TraPR considerably improves the quality and consistency of silencing sRNA sample preparation including from notoriously difficult-to-handle tissues/bio-fluids such as starchy storage roots or mammalian plasma, and regardless of RNA contaminants or RNA degradation status of samples.
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Affiliation(s)
- Thomas Grentzinger
- Department of Biology, Swiss Federal Institute of Technology (ETH), Zürich, 8092, Switzerland
| | - Stefan Oberlin
- Department of Biology, Swiss Federal Institute of Technology (ETH), Zürich, 8092, Switzerland
| | - Gregory Schott
- Department of Biology, Swiss Federal Institute of Technology (ETH), Zürich, 8092, Switzerland
| | - Dominik Handler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, 1030, Austria
| | - Julia Svozil
- Department of Biology, Swiss Federal Institute of Technology (ETH), Zürich, 8092, Switzerland
| | | | - Adeline Humbert
- Institut Jacques Monod, Université de Paris, CNRS, Paris, 75013, France
| | - Sandra Duharcourt
- Institut Jacques Monod, Université de Paris, CNRS, Paris, 75013, France
| | - Julius Brennecke
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, 1030, Austria
| | - Olivier Voinnet
- Department of Biology, Swiss Federal Institute of Technology (ETH), Zürich, 8092, Switzerland
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Lerat E, Fablet M, Modolo L, Lopez-Maestre H, Vieira C. TEtools facilitates big data expression analysis of transposable elements and reveals an antagonism between their activity and that of piRNA genes. Nucleic Acids Res 2018; 45:e17. [PMID: 28204592 PMCID: PMC5389681 DOI: 10.1093/nar/gkw953] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 09/29/2016] [Accepted: 10/11/2016] [Indexed: 11/24/2022] Open
Abstract
Over recent decades, substantial efforts have been made to understand the interactions between host genomes and transposable elements (TEs). The impact of TEs on the regulation of host genes is well known, with TEs acting as platforms of regulatory sequences. Nevertheless, due to their repetitive nature it is considerably hard to integrate TE analysis into genome-wide studies. Here, we developed a specific tool for the analysis of TE expression: TEtools. This tool takes into account the TE sequence diversity of the genome, it can be applied to unannotated or unassembled genomes and is freely available under the GPL3 (https://github.com/l-modolo/TEtools). TEtools performs the mapping of RNA-seq data obtained from classical mRNAs or small RNAs onto a list of TE sequences and performs differential expression analyses with statistical relevance. Using this tool, we analyzed TE expression from five Drosophila wild-type strains. Our data show for the first time that the activity of TEs is strictly linked to the activity of the genes implicated in the piwi-interacting RNA biogenesis and therefore fits an arms race scenario between TE sequences and host control genes.
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Affiliation(s)
- Emmanuelle Lerat
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Université de Lyon, Villeurbanne 69622, France
| | - Marie Fablet
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Université de Lyon, Villeurbanne 69622, France
| | - Laurent Modolo
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Université de Lyon, Villeurbanne 69622, France
| | - Hélène Lopez-Maestre
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Université de Lyon, Villeurbanne 69622, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Université de Lyon, Villeurbanne 69622, France
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Mugat B, Akkouche A, Serrano V, Armenise C, Li B, Brun C, Fulga TA, Van Vactor D, Pélisson A, Chambeyron S. MicroRNA-Dependent Transcriptional Silencing of Transposable Elements in Drosophila Follicle Cells. PLoS Genet 2015; 11:e1005194. [PMID: 25993106 PMCID: PMC4451950 DOI: 10.1371/journal.pgen.1005194] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 04/02/2015] [Indexed: 12/21/2022] Open
Abstract
RNA interference-related silencing mechanisms concern very diverse and distinct biological processes, from gene regulation (via the microRNA pathway) to defense against molecular parasites (through the small interfering RNA and the Piwi-interacting RNA pathways). Small non-coding RNAs serve as specificity factors that guide effector proteins to ribonucleic acid targets via base-pairing interactions, to achieve transcriptional or post-transcriptional regulation. Because of the small sequence complementarity required for microRNA-dependent post-transcriptional regulation, thousands of microRNA (miRNA) putative targets have been annotated in Drosophila. In Drosophila somatic ovarian cells, genomic parasites, such as transposable elements (TEs), are transcriptionally repressed by chromatin changes induced by Piwi-interacting RNAs (piRNAs) that prevent them from invading the germinal genome. Here we show, for the first time, that a functional miRNA pathway is required for the piRNA-mediated transcriptional silencing of TEs in this tissue. Global miRNA depletion, caused by tissue- and stage-specific knock down of drosha (involved in miRNA biogenesis), AGO1 or gawky (both responsible for miRNA activity), resulted in loss of TE-derived piRNAs and chromatin-mediated transcriptional de-silencing of TEs. This specific TE de-repression was also observed upon individual titration (by expression of the complementary miRNA sponge) of two miRNAs (miR-14 and miR-34) as well as in a miR-14 loss-of-function mutant background. Interestingly, the miRNA defects differentially affected TE- and 3' UTR-derived piRNAs. To our knowledge, this is the first indication of possible differences in the biogenesis or stability of TE- and 3' UTR-derived piRNAs. This work is one of the examples of detectable phenotypes caused by loss of individual miRNAs in Drosophila and the first genetic evidence that miRNAs have a role in the maintenance of genome stability via piRNA-mediated TE repression.
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Affiliation(s)
- Bruno Mugat
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, Montpellier, France
| | - Abdou Akkouche
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, Montpellier, France
| | - Vincent Serrano
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, Montpellier, France
| | - Claudia Armenise
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, Montpellier, France
| | - Blaise Li
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, Montpellier, France
| | - Christine Brun
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, Montpellier, France
| | - Tudor A. Fulga
- Department of Cell Biology and Program in Neuroscience, Harvard Medical School, Boston, Massachusetts, United States of America
| | - David Van Vactor
- Department of Cell Biology and Program in Neuroscience, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Alain Pélisson
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, Montpellier, France
| | - Séverine Chambeyron
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, Montpellier, France
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