1
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Lalit F, Jose AM. Selecting genes for analysis using historically contingent progress: from RNA changes to protein-protein interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.592119. [PMID: 38746289 PMCID: PMC11092662 DOI: 10.1101/2024.05.01.592119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Progress in biology has generated numerous lists of genes that share some property. But, advancing from these lists of genes to understanding their roles is slow and unsystematic. Here we use RNA silencing in C. elegans to illustrate an approach for prioritizing genes for detailed study given limited resources. The partially subjective relationships between genes forged by both deduced functional relatedness and biased progress in the field was captured as mutual information and used to cluster genes that were frequently identified yet remain understudied. Studied genes in these clusters suggest regulatory links connecting RNA silencing with other processes like the cell cycle. Many proteins encoded by the understudied genes are predicted to physically interact with known regulators of RNA silencing. These predicted influencers of RNA-regulated expression could be used for feedback regulation, which is essential for the homeostasis observed in all living systems. Thus, among the gene products altered when a process is perturbed are regulators of that process, providing a way to use RNA sequencing to identify candidate protein-protein interactions. Together, the analysis of perturbed transcripts and potential interactions of the proteins they encode could help prioritize candidate regulators of any process.
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2
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Qi W, Xu F, Heimbucher T, Baumeister R. Protection of germline immortality by the soma via a secreted endoribonuclease. Bioessays 2021; 43:e2100195. [PMID: 34655094 DOI: 10.1002/bies.202100195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/24/2021] [Accepted: 09/28/2021] [Indexed: 11/08/2022]
Abstract
In sexually reproducing organisms maintenance of germ stem cell immortality is fundamental for transmitting genetic material to future generations. While previous research has mainly considered intrinsic regulatory mechanisms in the germline, our recent study has found a direct contribution of somatic cells in preserving germline immortality via the somatically expressed endoribonuclease ENDU-2 in Caenorhabditis elegans. We have identified ENDU-2 as a secreted protein that can be taken up by the germline. Here, we discuss how ENDU-2 might uncouple its RNA-binding and RNA-cleavage activities to control gene expression via either an endoribonuclease dependent or an independent way. We also speculate on a possible functional conservation of its mammalian homologs in mediating cell-cell communication as well as its potential significance in understanding human pathogenesis such as cancer development.
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Affiliation(s)
- Wenjing Qi
- Bioinformatics and Molecular Genetics (Faculty of Biology), Albert-Ludwigs-University Freiburg, Germany
| | - Fan Xu
- Bioinformatics and Molecular Genetics (Faculty of Biology), Albert-Ludwigs-University Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), Albert-Ludwigs-University Freiburg, Germany
| | - Thomas Heimbucher
- Bioinformatics and Molecular Genetics (Faculty of Biology), Albert-Ludwigs-University Freiburg, Germany
| | - Ralf Baumeister
- Bioinformatics and Molecular Genetics (Faculty of Biology), Albert-Ludwigs-University Freiburg, Germany.,Center for Biochemistry and Molecular Cell Research (Faculty of Medicine), Albert-Ludwigs-University Freiburg, Germany.,Signalling Research Centers BIOSS and CIBSS, Albert-Ludwigs-University Freiburg, Germany
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3
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Braukmann F, Jordan D, Jenkins B, Koulman A, Miska EA. SID-2 negatively regulates development likely independent of nutritional dsRNA uptake. RNA Biol 2021; 18:888-899. [PMID: 33044912 PMCID: PMC8081039 DOI: 10.1080/15476286.2020.1827619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 01/05/2023] Open
Abstract
RNA interference (RNAi) is a gene regulatory mechanism based on RNA-RNA interaction conserved through eukaryotes. Surprisingly, many animals can take-up human-made double stranded RNA (dsRNA) from the environment to initiate RNAi suggesting a mechanism for dsRNA-based information exchange between organisms and their environment. However, no naturally occurring example has been identified since the discovery of the phenomenon 22 years ago. Therefore it remains enigmatic why animals are able to take up dsRNA. Here, we explore other possible functions by performing phenotypic studies of dsRNA uptake deficient sid-2 mutants in Caenorhabditis elegans. We find that SID-2 does not have a nutritional role in feeding experiments using genetic sensitized mutants. Furthermore, we use robot assisted imaging to show that sid-2 mutants accelerate growth rate and, by maternal contribution, body length at hatching. Finally, we perform transcriptome and lipidome analysis showing that sid-2 has no effect on energy storage lipids, but affects signalling lipids and the embryo transcriptome. Overall, these results suggest that sid-2 has mild effects on development and is unlikely functioning in the nutritional uptake of dsRNA. These findings broaden our understanding of the biological role of SID-2 and motivate studies identifying the role of environmental dsRNA uptake.
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Affiliation(s)
- Fabian Braukmann
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - David Jordan
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Benjamin Jenkins
- Core Metabolomics and Lipidomics Laboratory, Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Albert Koulman
- Core Metabolomics and Lipidomics Laboratory, Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Eric Alexander Miska
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
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4
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Chen LT, Lin CT, Lin LY, Hsu JM, Wu YC, Pan CL. Neuronal mitochondrial dynamics coordinate systemic mitochondrial morphology and stress response to confer pathogen resistance in C. elegans. Dev Cell 2021; 56:1770-1785.e12. [PMID: 33984269 DOI: 10.1016/j.devcel.2021.04.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 12/09/2020] [Accepted: 04/21/2021] [Indexed: 01/02/2023]
Abstract
Mitochondrial functions across different tissues are regulated in a coordinated fashion to optimize the fitness of an organism. Mitochondrial unfolded protein response (UPRmt) can be nonautonomously elicited by mitochondrial perturbation in neurons, but neuronal signals that propagate such response and its physiological significance remain incompletely understood. Here, we show that in C. elegans, loss of neuronal fzo-1/mitofusin induces nonautonomous UPRmt through multiple neurotransmitters and neurohormones, including acetylcholine, serotonin, glutamate, tyramine, and insulin-like peptides. Neuronal fzo-1 depletion also triggers nonautonomous mitochondrial fragmentation, which requires autophagy and mitophagy genes. Systemic activation of UPRmt and mitochondrial fragmentation in C. elegans via perturbing neuronal mitochondrial dynamics improves resistance to pathogenic Pseudomonas infection, which is supported by transcriptomic signatures of immunity and stress-response genes. We propose that C. elegans surveils neuronal mitochondrial dynamics to coordinate systemic UPRmt and mitochondrial connectivity for pathogen defense and optimized survival under bacterial infection.
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Affiliation(s)
- Li-Tzu Chen
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, No.7 Chung-Shan South Road, Taipei 10002, Taiwan; Center of Precision Medicine, College of Medicine, National Taiwan University, No.7 Chung-Shan South Road, Taipei 10002, Taiwan
| | - Chih-Ta Lin
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, No.7 Chung-Shan South Road, Taipei 10002, Taiwan
| | - Liang-Yi Lin
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, No.7 Chung-Shan South Road, Taipei 10002, Taiwan
| | - Jiun-Min Hsu
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, No.7 Chung-Shan South Road, Taipei 10002, Taiwan
| | - Yu-Chun Wu
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, No.7 Chung-Shan South Road, Taipei 10002, Taiwan; Center of Precision Medicine, College of Medicine, National Taiwan University, No.7 Chung-Shan South Road, Taipei 10002, Taiwan
| | - Chun-Liang Pan
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, No.7 Chung-Shan South Road, Taipei 10002, Taiwan; Center of Precision Medicine, College of Medicine, National Taiwan University, No.7 Chung-Shan South Road, Taipei 10002, Taiwan.
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5
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Frolows N, Ashe A. Small RNAs and chromatin in the multigenerational epigenetic landscape of Caenorhabditis elegans. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200112. [PMID: 33866817 DOI: 10.1098/rstb.2020.0112] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
For decades, it was thought that the only heritable information transmitted from one individual to another was that encoded in the DNA sequence. However, it has become increasingly clear that this is not the case and that the transmission of molecules from within the cytoplasm of the gamete also plays a significant role in heritability. The roundworm, Caenorhabditis elegans, has emerged as one of the leading model organisms in which to study the mechanisms of transgenerational epigenetic inheritance (TEI). Collaborative efforts over the past few years have revealed that RNA molecules play a critical role in transmitting transgenerational responses, but precisely how they do so is as yet uncertain. In addition, the role of histone modifications in epigenetic inheritance is increasingly apparent, and RNA and histones interact in a way that we do not yet fully understand. Furthermore, both exogenous and endogenous RNA molecules, as well as other environmental triggers, are able to induce heritable epigenetic changes that affect transcription across the genome. In most cases, these epigenetic changes last only for a handful of generations, but occasionally can be maintained much longer: perhaps indefinitely. In this review, we discuss the current understanding of the role of RNA and histones in TEI, as well as making clear the gaps in our knowledge. We also speculate on the evolutionary implications of epigenetic inheritance, particularly in the context of a short-lived, clonally propagating species. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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Affiliation(s)
- Natalya Frolows
- School of Life and Environmental Sciences, University of Sydney, New South Wales, 2006, Australia.,CSIRO Health and Biosecurity, Sydney, New South Wales, 2113, Australia
| | - Alyson Ashe
- School of Life and Environmental Sciences, University of Sydney, New South Wales, 2006, Australia
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6
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Hagen J, Sarkies P, Selkirk ME. Lentiviral transduction facilitates RNA interference in the nematode parasite Nippostrongylus brasiliensis. PLoS Pathog 2021; 17:e1009286. [PMID: 33497411 PMCID: PMC7864396 DOI: 10.1371/journal.ppat.1009286] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 02/05/2021] [Accepted: 01/06/2021] [Indexed: 12/16/2022] Open
Abstract
Animal-parasitic nematodes have thus far been largely refractory to genetic manipulation, and methods employed to effect RNA interference (RNAi) have been ineffective or inconsistent in most cases. We describe here a new approach for genetic manipulation of Nippostrongylus brasiliensis, a widely used laboratory model of gastrointestinal nematode infection. N. brasiliensis was successfully transduced with Vesicular Stomatitis Virus glycoprotein G (VSV-G)-pseudotyped lentivirus. The virus was taken up via the nematode intestine, RNA reverse transcribed into proviral DNA, and transgene transcripts produced stably in infective larvae, which resulted in expression of the reporter protein mCherry. Improved transgene expression was achieved by incorporating the C. elegans hlh11 promoter and the tbb2 3´-UTR into viral constructs. MicroRNA-adapted short hairpin RNAs delivered in this manner were processed correctly and resulted in partial knockdown of β-tubulin isotype-1 (tbb-iso-1) and secreted acetylcholinesterase B (ache-B). The system was further refined by lentiviral delivery of double stranded RNAs, which acted as a trigger for RNAi following processing and generation of 22G-RNAs. Virus-encoded sequences were detectable in F1 eggs and third stage larvae, demonstrating that proviral DNA entered the germline and was heritable. Lentiviral transduction thus provides a new means for genetic manipulation of parasitic nematodes, including gene silencing and expression of exogenous genes. The complex life cycle of parasitic nematodes makes them very difficult to manipulate genetically, and methods to delete or silence genes which are routinely used in other organisms are ineffective in most species of nematodes which infect animals. This has hindered attempts to understand the function of defined genes and proteins, and their roles in development and interaction of nematode parasites with their host. We show here that foreign genetic material can be introduced into a widely used laboratory model of intestinal nematode infection by using a viral vector. The vector was modified to improve transgene expression, and a reporter protein expressed by transduced nematode larvae in vitro. We subsequently utilised the viral vector to deliver double stranded RNA molecules to the larvae. These molecules were processed along known pathways, resulting in partial knockdown of two test genes. This system represents a new means of genetically manipulating nematode parasites, and will aid in understanding their complex biology, in addition to defining new targets for control of infection.
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Affiliation(s)
- Jana Hagen
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Peter Sarkies
- MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom
| | - Murray E. Selkirk
- Department of Life Sciences, Imperial College London, London, United Kingdom
- * E-mail:
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7
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poly(UG)-tailed RNAs in genome protection and epigenetic inheritance. Nature 2020; 582:283-288. [PMID: 32499657 PMCID: PMC8396162 DOI: 10.1038/s41586-020-2323-8] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 04/16/2020] [Indexed: 12/17/2022]
Abstract
Mobile genetic elements threaten genome integrity in all organisms. MUT-2/RDE-3 is a ribonucleotidyltransferase required for transposon silencing and RNA interference (RNAi) in C. elegans1–4. When tethered to RNAs in heterologous expression systems, RDE-3 can add long stretches of alternating non-templated uridine (U) and guanosine (G) ribonucleotides to the 3’ termini of these RNAs (poly(UG) or pUG tails)5. Here we show that, in its natural context in C. elegans, RDE-3 adds pUG tails to targets of RNAi, as well as to transposon RNAs. pUG tails with more than 16 perfectly alternating 3’ U and G nucleotides convert RNA fragments into agents of gene silencing. pUG tails promote gene silencing by recruiting RNA-dependent RNA polymerases (RdRPs), which use pUG-tailed RNAs (pUG RNAs) as templates to synthesize small interfering RNAs (siRNAs). Our results show that cycles of pUG RNA–templated siRNA synthesis and siRNA-directed mRNA pUGylation underlie dsRNA-directed transgenerational epigenetic inheritance in the C. elegans germline. We speculate that this pUG RNA/siRNA silencing loop allows parents to inoculate progeny against the expression of unwanted or parasitic genetic elements
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8
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Ravikumar S, Devanapally S, Jose AM. Gene silencing by double-stranded RNA from C. elegans neurons reveals functional mosaicism of RNA interference. Nucleic Acids Res 2019; 47:10059-10071. [PMID: 31501873 PMCID: PMC6821342 DOI: 10.1093/nar/gkz748] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/12/2019] [Accepted: 08/20/2019] [Indexed: 12/12/2022] Open
Abstract
Delivery of double-stranded RNA (dsRNA) into animals can silence genes of matching sequence in diverse cell types through mechanisms that have been collectively called RNA interference. In the nematode Caenorhabditis elegans, dsRNA from multiple sources can trigger the amplification of silencing signals. Amplification occurs through the production of small RNAs by two RNA-dependent RNA polymerases (RdRPs) that are thought to be tissue-specific - EGO-1 in the germline and RRF-1 in somatic cells. Here we demonstrate that EGO-1 can compensate for the lack of RRF-1 when dsRNA from neurons is used to silence genes in intestinal cells. However, the lineal origins of cells that can use EGO-1 varies. This variability could be because random sets of cells can either receive different amounts of dsRNA from the same source or use different RdRPs to perform the same function. Variability is masked in wild-type animals, which show extensive silencing by neuronal dsRNA. As a result, cells appear similarly functional despite underlying differences that vary from animal to animal. This functional mosaicism cautions against inferring uniformity of mechanism based on uniformity of outcome. We speculate that functional mosaicism could contribute to escape from targeted therapies and could allow developmental systems to drift over evolutionary time.
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Affiliation(s)
- Snusha Ravikumar
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Sindhuja Devanapally
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Antony M Jose
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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9
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Posner R, Toker IA, Antonova O, Star E, Anava S, Azmon E, Hendricks M, Bracha S, Gingold H, Rechavi O. Neuronal Small RNAs Control Behavior Transgenerationally. Cell 2019; 177:1814-1826.e15. [PMID: 31178120 PMCID: PMC6579485 DOI: 10.1016/j.cell.2019.04.029] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/18/2019] [Accepted: 04/13/2019] [Indexed: 12/21/2022]
Abstract
It is unknown whether the activity of the nervous system can be inherited. In Caenorhabditis elegans nematodes, parental responses can transmit heritable small RNAs that regulate gene expression transgenerationally. In this study, we show that a neuronal process can impact the next generations. Neurons-specific synthesis of RDE-4-dependent small RNAs regulates germline amplified endogenous small interfering RNAs (siRNAs) and germline gene expression for multiple generations. Further, the production of small RNAs in neurons controls the chemotaxis behavior of the progeny for at least three generations via the germline Argonaute HRDE-1. Among the targets of these small RNAs, we identified the conserved gene saeg-2, which is transgenerationally downregulated in the germline. Silencing of saeg-2 following neuronal small RNA biogenesis is required for chemotaxis under stress. Thus, we propose a small-RNA-based mechanism for communication of neuronal processes transgenerationally. C. elegans neuronal small RNAs are characterized by RNA sequencing RDE-4-dependent neuronal endogenous small RNAs communicate with the germline Germline HRDE-1 mediates transgenerational regulation by neuronal small RNAs Neuronal small RNAs regulate germline genes to control behavior transgenerationally
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Affiliation(s)
- Rachel Posner
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Itai Antoine Toker
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Olga Antonova
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Ekaterina Star
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sarit Anava
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Eran Azmon
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Michael Hendricks
- Department of Biology, McGill University, Montreal, QC H3A 1B1, Canada
| | - Shahar Bracha
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Hila Gingold
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel.
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10
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Preston MA, Porter DF, Chen F, Buter N, Lapointe CP, Keles S, Kimble J, Wickens M. Unbiased screen of RNA tailing activities reveals a poly(UG) polymerase. Nat Methods 2019; 16:437-445. [PMID: 30988468 PMCID: PMC6613791 DOI: 10.1038/s41592-019-0370-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 02/24/2019] [Accepted: 03/05/2019] [Indexed: 12/22/2022]
Abstract
Ribonucleotidyl transferases (rNTases) add untemplated ribonucleotides to diverse RNAs. We have developed TRAID-seq, a screening strategy in Saccharomyces cerevisiae to identify sequences added to a reporter RNA at single-nucleotide resolution by overexpressed candidate enzymes from different organisms. The rNTase activities of 22 previously unexplored enzymes were determined. In addition to poly(A)- and poly(U)-adding enzymes, we identified a cytidine-adding enzyme that is likely to be part of a two-enzyme system that adds CCA to tRNAs in a eukaryote; a nucleotidyl transferase that adds nucleotides to RNA without apparent nucleotide preference; and a poly(UG) polymerase, Caenorhabditis elegans MUT-2, that adds alternating uridine and guanosine nucleotides to form poly(UG) tails. MUT-2 is known to be required for certain forms of RNA silencing, and mutants of the enzyme that result in defective silencing did not add poly(UG) tails in our assay. We propose that MUT-2 poly(UG) polymerase activity is required to promote genome integrity and RNA silencing.
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Affiliation(s)
- Melanie A Preston
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Promega Corporation, Madison, WI, USA
| | - Douglas F Porter
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Program in Epithelial Biology, Stanford University Medical School, Stanford, CA, USA
| | - Fan Chen
- Department of Statistics, University of Wisconsin-Madison, Madison, WI, USA
| | - Natascha Buter
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Promega Corporation, Madison, WI, USA
| | - Christopher P Lapointe
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
| | - Sunduz Keles
- Department of Statistics, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
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11
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Bezler A, Braukmann F, West SM, Duplan A, Conconi R, Schütz F, Gönczy P, Piano F, Gunsalus K, Miska EA, Keller L. Tissue- and sex-specific small RNAomes reveal sex differences in response to the environment. PLoS Genet 2019; 15:e1007905. [PMID: 30735500 PMCID: PMC6383947 DOI: 10.1371/journal.pgen.1007905] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 02/21/2019] [Accepted: 12/17/2018] [Indexed: 11/19/2022] Open
Abstract
RNA interference (RNAi) related pathways are essential for germline development and fertility in metazoa and can contribute to inter- and trans-generational inheritance. In the nematode Caenorhabditis elegans, environmental double-stranded RNA provided by feeding can lead to heritable changes in phenotype and gene expression. Notably, transmission efficiency differs between the male and female germline, yet the underlying mechanisms remain elusive. Here we use high-throughput sequencing of dissected gonads to quantify sex-specific endogenous piRNAs, miRNAs and siRNAs in the C. elegans germline and the somatic gonad. We identify genes with exceptionally high levels of secondary 22G RNAs that are associated with low mRNA expression, a signature compatible with silencing. We further demonstrate that contrary to the hermaphrodite germline, the male germline, but not male soma, is resistant to environmental RNAi triggers provided by feeding, in line with previous work. This sex-difference in silencing efficacy is associated with lower levels of gonadal RNAi amplification products. Moreover, this tissue- and sex-specific RNAi resistance is regulated by the germline, since mutant males with a feminized germline are RNAi sensitive. This study provides important sex- and tissue-specific expression data of miRNA, piRNA and siRNA as well as mechanistic insights into sex-differences of gene regulation in response to environmental cues.
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Affiliation(s)
- Alexandra Bezler
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Fabian Braukmann
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Sean M. West
- Center for Genomics & Systems Biology, New York University, New York, New York, United States of America
| | - Arthur Duplan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Raffaella Conconi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Frédéric Schütz
- Bioinformatics Core Facility; SIB Swiss Institute of Bioinformatics and Centre for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Pierre Gönczy
- Swiss Institute for Experimental Cancer Research (ISREC), Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Fabio Piano
- Center for Genomics & Systems Biology, New York University, New York, New York, United States of America
- Center for Genomics & Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Kristin Gunsalus
- Center for Genomics & Systems Biology, New York University, New York, New York, United States of America
- Center for Genomics & Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Eric A. Miska
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Laurent Keller
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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12
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Hu J, Xia Y. Increased virulence in the locust-specific fungal pathogen Metarhizium acridum expressing dsRNAs targeting the host F 1 F 0 -ATPase subunit genes. PEST MANAGEMENT SCIENCE 2019; 75:180-186. [PMID: 29797423 DOI: 10.1002/ps.5085] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 05/17/2018] [Accepted: 05/18/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Metarhizium acridum is a host-specific fungal pathogen with great potential for locust control. However, the slow killing action of M. acridum has impeded its widespread application. To enhance fungal virulence, we constructed transgenic M. acridum strains that express double-stranded (ds)RNAs targeting the genes of the F1 F0 -ATP synthase α and β subunits in Locusta migratoria. RESULTS The two host genes were transcriptionally suppressed in L. migratoria nymphs (instar V) infected by RNA interference (RNAi) strains targeting one or two subunit genes of the host ATP synthase, followed by reduced ATPase activity and ATP synthesis. Consequently, the RNAi strain targeting both subunit genes displayed high virulence that was 3.7-fold that in the wild-type strain. CONCLUSION Our results demonstrate that dsRNA expression in M. acridum can cause host RNA silencing during infection and greatly enhances the fungal virulence through interference with critical host genes, highlighting a new strategy for augmentation of fungal virulence against insect pests. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Jun Hu
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, China
- Chongqing Engineering Research Center for Fungal Insecticide, Chongqing, China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission, Chongqing, China
| | - Yuxian Xia
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, China
- Chongqing Engineering Research Center for Fungal Insecticide, Chongqing, China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission, Chongqing, China
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13
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Zhang X, Lai T, Zhang P, Zhang X, Yuan C, Jin Z, Li H, Yu Z, Qin C, Tör M, Ma P, Cheng Q, Hong Y. Mini review: Revisiting mobile RNA silencing in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 278:113-117. [PMID: 30471724 PMCID: PMC6556431 DOI: 10.1016/j.plantsci.2018.10.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 10/28/2018] [Accepted: 10/30/2018] [Indexed: 05/19/2023]
Abstract
Non-cell autonomous RNA silencing can spread from cell to cell and over long-distances in animals and plants. This process is genetically determined and requires mobile RNA signals. Genetic requirement and molecular nature of the mobile signals for non-cell-autonomous RNA silencing were intensively investigated in past few decades. No consensus dogma for mobile silencing can be reached in plants, yet published data are sometimes inconsistent and controversial. Thus, the genetic requirements and molecular signals involved in plant mobile silencing are still poorly understood. This article revisits our present understanding of intercellular and systemic non-cell autonomous RNA silencing, and summarises current debates on RNA signals for mobile silencing. In particular, we discuss new evidence on siRNA mobility, a DCL2-dependent genetic network for mobile silencing and its potential biological relevance as well as 22 nt siRNA being a mobile signal for non-cell-autonomous silencing in both Arabidopsis and Nicotiana benthamiana. This sets up a new trend in unravelling genetic components and small RNA signal molecules for mobile silencing in (across) plants and other organisms of different kingdoms. Finally we raise several outstanding questions that need to be addressed in future plant silencing research.
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Affiliation(s)
- Xian Zhang
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Tongfei Lai
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Pengcheng Zhang
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Xinlian Zhang
- Department of Statistics, University of Georgia, Athens, GA 30602, USA
| | - Chen Yuan
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Zhenhui Jin
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Hongmei Li
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Zhiming Yu
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Cheng Qin
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Mahmut Tör
- Worcester-Hangzhou Joint Molecular Plant Health Laboratory, Institute of Science and the Environment, University of Worcester, WR2 6AJ, UK
| | - Ping Ma
- Department of Statistics, University of Georgia, Athens, GA 30602, USA
| | - Qi Cheng
- Nitrogen Fixation Laboratory, Qi Institute, Jiaxing 314000, Zhejiang, China
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China; Worcester-Hangzhou Joint Molecular Plant Health Laboratory, Institute of Science and the Environment, University of Worcester, WR2 6AJ, UK; Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick CV4 7AL, UK.
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14
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Chen W, Zhang X, Fan Y, Li B, Ryabov E, Shi N, Zhao M, Yu Z, Qin C, Zheng Q, Zhang P, Wang H, Jackson S, Cheng Q, Liu Y, Gallusci P, Hong Y. A Genetic Network for Systemic RNA Silencing in Plants. PLANT PHYSIOLOGY 2018; 176:2700-2719. [PMID: 29439213 PMCID: PMC5884585 DOI: 10.1104/pp.17.01828] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 01/25/2018] [Indexed: 05/20/2023]
Abstract
Non-cell autonomous RNA silencing can spread from cell to cell and over long distances in animals and plants. However, the genetic requirements and signals involved in plant mobile gene silencing are poorly understood. Here, we identified a DICER-LIKE2 (DCL2)-dependent mechanism for systemic spread of posttranscriptional RNA silencing, also known as posttranscriptional gene silencing (PTGS), in Nicotiana benthamiana Using a suite of transgenic DCL RNAi lines coupled with a GFP reporter, we demonstrated that N. benthamiana DCL1, DCL2, DCL3, and DCL4 are required to produce microRNAs and 22, 24, and 21nt small interfering RNAs (siRNAs), respectively. All investigated siRNAs produced in local incipient cells were present at low levels in distal tissues. Inhibition of DCL2 expression reduced the spread of gene silencing, while suppression of DCL3 or DCL4 expression enhanced systemic PTGS. In contrast to DCL4 RNAi lines, DCL2-DCL4 double-RNAi lines developed systemic PTGS similar to that observed in DCL2 RNAi. We further showed that the 21 or 24 nt local siRNAs produced by DCL4 or DCL3 were not involved in long-distance gene silencing. Grafting experiments demonstrated that DCL2 was required in the scion to respond to the signal, but not in the rootstock to produce/send the signal. These results suggest a coordinated DCL genetic pathway in which DCL2 plays an essential role in systemic PTGS in N. benthamiana, while both DCL4 and DCL3 attenuate systemic PTGS. We discuss the potential role of 21, 22, and 24 nt siRNAs in systemic PTGS.
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Affiliation(s)
- Weiwei Chen
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Xian Zhang
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Yaya Fan
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Bin Li
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Eugene Ryabov
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom
| | - Nongnong Shi
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Mei Zhao
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Zhiming Yu
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Cheng Qin
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Qianqian Zheng
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Pengcheng Zhang
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Huizhong Wang
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Stephen Jackson
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom
| | - Qi Cheng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yule Liu
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Philippe Gallusci
- UMR EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, 210 Chemin de Leysotte, CS 50008, 33882 Villenave d'Ornon, France
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom
- Worcester-Hangzhou Joint Molecular Plant Health Laboratory, Institute of Science and the Environment, University of Worcester, WR2 6AJ, United Kingdom
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15
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Raman P, Zaghab SM, Traver EC, Jose AM. The double-stranded RNA binding protein RDE-4 can act cell autonomously during feeding RNAi in C. elegans. Nucleic Acids Res 2017; 45:8463-8473. [PMID: 28541563 PMCID: PMC5737277 DOI: 10.1093/nar/gkx484] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 05/17/2017] [Indexed: 02/07/2023] Open
Abstract
Long double-stranded RNA (dsRNA) can silence genes of matching sequence upon ingestion in many invertebrates and is therefore being developed as a pesticide. Such feeding RNA interference (RNAi) is best understood in the worm Caenorhabditis elegans, where the dsRNA-binding protein RDE-4 initiates silencing by recruiting an endonuclease to process long dsRNA into short dsRNA. These short dsRNAs are thought to move between cells because muscle-specific rescue of rde-4 using repetitive transgenes enables silencing in other tissues. Here, we extend this observation using additional promoters, report an inhibitory effect of repetitive transgenes, and discover conditions for cell-autonomous silencing in animals with tissue-specific rescue of rde-4. While expression of rde-4(+) in intestine, hypodermis, or neurons using a repetitive transgene can enable silencing also in unrescued tissues, silencing can be inhibited wihin tissues that express a repetitive transgene. Single-copy transgenes that express rde-4(+) in body-wall muscles or hypodermis, however, enable silencing selectively in the rescued tissue but not in other tissues. These results suggest that silencing by the movement of short dsRNA between cells is not an obligatory feature of feeding RNAi in C. elegans. We speculate that similar control of dsRNA movement could modulate tissue-specific silencing by feeding RNAi in other invertebrates.
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Affiliation(s)
- Pravrutha Raman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Soriayah M Zaghab
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Edward C Traver
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Antony M Jose
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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16
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Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
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17
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Braukmann F, Jordan D, Miska E. Artificial and natural RNA interactions between bacteria and C. elegans. RNA Biol 2017; 14:415-420. [PMID: 28332918 DOI: 10.1080/15476286.2017.1297912] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Nineteen years after Lisa Timmons and Andy Fire first described RNA transfer from bacteria to C. elegans in an experimental setting 48 the biologic role of this trans-kingdom RNA-based communication remains unknown. Here we summarize our current understanding on the mechanism and potential role of such social RNA.
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Affiliation(s)
- Fabian Braukmann
- a Gurdon Institute, University of Cambridge , Cambridge , UK.,b Department of Genetics , University of Cambridge , Cambridge , UK
| | - David Jordan
- a Gurdon Institute, University of Cambridge , Cambridge , UK.,b Department of Genetics , University of Cambridge , Cambridge , UK
| | - Eric Miska
- a Gurdon Institute, University of Cambridge , Cambridge , UK.,b Department of Genetics , University of Cambridge , Cambridge , UK.,c Wellcome Trust Sanger Institute , Wellcome Trust Genome Campus, Cambridge , UK
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18
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Fritz JV, Heintz-Buschart A, Ghosal A, Wampach L, Etheridge A, Galas D, Wilmes P. Sources and Functions of Extracellular Small RNAs in Human Circulation. Annu Rev Nutr 2016; 36:301-36. [PMID: 27215587 PMCID: PMC5479634 DOI: 10.1146/annurev-nutr-071715-050711] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Various biotypes of endogenous small RNAs (sRNAs) have been detected in human circulation, including microRNAs, transfer RNAs, ribosomal RNA, and yRNA fragments. These extracellular sRNAs (ex-sRNAs) are packaged and secreted by many different cell types. Ex-sRNAs exhibit differences in abundance in several disease states and have, therefore, been proposed for use as effective biomarkers. Furthermore, exosome-borne ex-sRNAs have been reported to elicit physiological responses in acceptor cells. Exogenous ex-sRNAs derived from diet (most prominently from plants) and microorganisms have also been reported in human blood. Essential issues that remain to be conclusively addressed concern the (a) presence and sources of exogenous ex-sRNAs in human bodily fluids, (b) detection and measurement of ex-sRNAs in human circulation, (c) selectivity of ex-sRNA export and import, (d) sensitivity and specificity of ex-sRNA delivery to cellular targets, and (e) cell-, tissue-, organ-, and organism-wide impacts of ex-sRNA-mediated cell-to-cell communication. We survey the present state of knowledge of most of these issues in this review.
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MESH Headings
- Animals
- Biological Transport
- Biomarkers/blood
- Cell Communication
- Diet
- Gastrointestinal Microbiome/immunology
- Gene Expression Regulation
- Host-Parasite Interactions
- Host-Pathogen Interactions
- Humans
- Immunity, Innate
- MicroRNAs/blood
- MicroRNAs/metabolism
- Models, Biological
- RNA, Bacterial/blood
- RNA, Bacterial/metabolism
- RNA, Plant/blood
- RNA, Plant/metabolism
- RNA, Ribosomal/blood
- RNA, Ribosomal/metabolism
- RNA, Small Interfering/blood
- RNA, Small Interfering/metabolism
- RNA, Small Untranslated/blood
- RNA, Small Untranslated/metabolism
- RNA, Transfer/blood
- RNA, Transfer/metabolism
- RNA, Viral/blood
- RNA, Viral/metabolism
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Affiliation(s)
- Joëlle V Fritz
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, L-4367 Belvaux, Luxembourg; ,
| | - Anna Heintz-Buschart
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, L-4367 Belvaux, Luxembourg; ,
| | - Anubrata Ghosal
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Linda Wampach
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, L-4367 Belvaux, Luxembourg; ,
| | - Alton Etheridge
- Pacific Northwest Diabetes Research Institute, Seattle, Washington 98122
| | - David Galas
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, L-4367 Belvaux, Luxembourg; ,
- Pacific Northwest Diabetes Research Institute, Seattle, Washington 98122
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, L-4367 Belvaux, Luxembourg; ,
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19
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Lin Z, Rodriguez NE, Zhao J, Ramey AN, Hyzy SL, Boyan BD, Schwartz Z. Selective enrichment of microRNAs in extracellular matrix vesicles produced by growth plate chondrocytes. Bone 2016; 88:47-55. [PMID: 27080510 PMCID: PMC4899086 DOI: 10.1016/j.bone.2016.03.018] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 03/28/2016] [Accepted: 03/31/2016] [Indexed: 01/09/2023]
Abstract
Matrix vesicles (MVs) are membrane organelles found in the extracellular matrix of calcifying cells, which contain matrix processing enzymes and regulate the extracellular environment via action of these enzymes. It is unknown whether MVs are also exosomic mediators of cell-cell communication via transfer of RNA material, and specifically, microRNA (miRNA). We investigated the presence of RNA in MVs isolated from cultures of costochondral growth zone chondrocytes. Our results showed that the average yield of MV RNA was 1.93±0.78ng RNA/10(4) cells, which was approximately 0.1% of the parent cell's total RNA. MV RNA was well-protected from RNase by the lipid membrane and was highly enriched in small RNA molecules compared to cells. Moreover, coding and non-coding small RNAs in MVs were in proportions that differed from parent cells. Enrichment of specific miRNAs was consistently observed in all three miRNA detection platforms that we used, suggesting that miRNAs are selectively packaged into MVs. MV-enriched miRNAs were related to different signaling pathways associated with bone formation. This study suggests a significant role for MVs as "matrisomes" in cell-cell communication in cartilage and bone development via transfer of specific miRNAs.
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Affiliation(s)
- Zhao Lin
- Department of Periodontics, Virginia Commonwealth University, Richmond, VA, United States; Department of Biomedical Engineering, School of Engineering, Virginia Commonwealth University, Richmond, VA, United States
| | - Nicholas E Rodriguez
- School of Biology, Virginia Commonwealth University, Richmond, VA, United States
| | - Junjun Zhao
- Department of Periodontics, Virginia Commonwealth University, Richmond, VA, United States; Department of Biomedical Engineering, School of Engineering, Virginia Commonwealth University, Richmond, VA, United States; General Dentistry, 9th People's Hospital, College of Stomatology, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Allison N Ramey
- Department of Biomedical Engineering, School of Engineering, Virginia Commonwealth University, Richmond, VA, United States
| | - Sharon L Hyzy
- Department of Biomedical Engineering, School of Engineering, Virginia Commonwealth University, Richmond, VA, United States
| | - Barbara D Boyan
- Department of Biomedical Engineering, School of Engineering, Virginia Commonwealth University, Richmond, VA, United States; Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, United States.
| | - Zvi Schwartz
- Department of Biomedical Engineering, School of Engineering, Virginia Commonwealth University, Richmond, VA, United States; Department of Periodontics, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
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20
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Imae R, Dejima K, Kage-Nakadai E, Arai H, Mitani S. Endomembrane-associated RSD-3 is important for RNAi induced by extracellular silencing RNA in both somatic and germ cells of Caenorhabditis elegans. Sci Rep 2016; 6:28198. [PMID: 27306325 PMCID: PMC4910058 DOI: 10.1038/srep28198] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 06/01/2016] [Indexed: 12/25/2022] Open
Abstract
RNA silencing signals in C. elegans spread among cells, leading to RNAi
throughout the body. During systemic spread of RNAi, membrane trafficking is thought
to play important roles. Here, we show that RNAi Spreading Defective-3
(rsd-3), which encodes a homolog of epsinR, a conserved ENTH (epsin
N-terminal homology) domain protein, generally participates in cellular uptake of
silencing RNA. RSD-3 is previously thought to be involved in systemic RNAi only in
germ cells, but we isolated several deletion alleles of rsd-3, and found that
these mutants are defective in the spread of silencing RNA not only into germ cells
but also into somatic cells. RSD-3 is ubiquitously expressed, and intracellularly
localized to the trans-Golgi network (TGN) and endosomes. Tissue-specific
rescue experiments indicate that RSD-3 is required for importing silencing RNA into
cells rather than exporting from cells. Structure/function analysis showed that the
ENTH domain alone is sufficient, and membrane association of the ENTH domain is
required, for RSD-3 function in systemic RNAi. Our results suggest that endomembrane
trafficking through the TGN and endosomes generally plays an important role in
cellular uptake of silencing RNA.
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Affiliation(s)
- Rieko Imae
- Department of Physiology, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
| | - Katsufumi Dejima
- Department of Physiology, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
| | - Eriko Kage-Nakadai
- Department of Physiology, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
| | - Hiroyuki Arai
- Graduate School of Pharmaceutical Science, University of Tokyo, Tokyo, Japan
| | - Shohei Mitani
- Department of Physiology, Tokyo Women's Medical University School of Medicine, Tokyo, Japan.,Tokyo Women's Medical University Institute for Integrated Medical Sciences, Tokyo, Japan
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21
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Mermigka G, Verret F, Kalantidis K. RNA silencing movement in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2016; 58:328-42. [PMID: 26297506 DOI: 10.1111/jipb.12423] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 08/20/2015] [Indexed: 05/21/2023]
Abstract
Multicellular organisms, like higher plants, need to coordinate their growth and development and to cope with environmental cues. To achieve this, various signal molecules are transported between neighboring cells and distant organs to control the fate of the recipient cells and organs. RNA silencing produces cell non-autonomous signal molecules that can move over short or long distances leading to the sequence specific silencing of a target gene in a well defined area of cells or throughout the entire plant, respectively. The nature of these signal molecules, the route of silencing spread, and the genes involved in their production, movement and reception are discussed in this review. Additionally, a short section on features of silencing spread in animal models is presented at the end of this review.
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Affiliation(s)
- Glykeria Mermigka
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Frédéric Verret
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Crete, Greece
| | - Kriton Kalantidis
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Crete, Greece
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22
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Antiviral RNA Interference against Orsay Virus Is neither Systemic nor Transgenerational in Caenorhabditis elegans. J Virol 2015; 89:12035-46. [PMID: 26401037 PMCID: PMC4645334 DOI: 10.1128/jvi.03664-14] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 08/28/2015] [Indexed: 02/06/2023] Open
Abstract
Antiviral RNA-mediated silencing (RNA interference [RNAi]) acts as a powerful innate immunity defense in plants, invertebrates, and mammals. In Caenorhabditis elegans, RNAi is systemic; i.e., RNAi silencing signals can move between cells and tissues. Furthermore, RNAi effects can be inherited transgenerationally and may last for many generations. Neither the biological relevance of systemic RNAi nor transgenerational RNAi is currently understood. Here we examined the role of both pathways in the protection of C. elegans from viral infection. We studied the Orsay virus, a positive-strand RNA virus related to Nodaviridae and the first and only virus known to infect C. elegans. Immunity to Orsay virus infection requires the RNAi pathway. Surprisingly, we found that genes required for systemic or transgenerational RNAi did not have a role in antiviral defense. Furthermore, we found that Orsay virus infection did not elicit a systemic RNAi response even when a target for RNAi was provided by using transgenes. Finally, we show that viral siRNAs, the effectors of RNAi, are not inherited to a level that provides any significant resistance to viral infection in the next generation. We conclude that systemic or transgenerational RNAi does not play a role in the defense against natural Orsay virus infection. Furthermore, our data suggest that there is a qualitative difference between experimental RNAi and antiviral RNAi. Our data are consistent with a model of systemic and transgenerational RNAi that requires a nuclear or germ line component that is lacking in almost all RNA virus infections. IMPORTANCE Since its discovery in Caenorhabditis elegans, RNAi has proven a valuable scientific tool in many organisms. In C. elegans, exogenous RNAi spreads throughout the organism and can be passed between generations; however, there has been controversy as to the endogenous role(s) that the RNAi pathway plays. One endogenous role for which spreading both within the infected organism and between generations would be advantageous is a role in viral defense. In plants, antiviral RNAi is systemic and the spread of RNAi between cells provides protection against subsequent viral infection. Here we investigated this by using the only naturally occurring virus known to infect C. elegans, Orsay virus, and surprisingly found that, in contrast to the exogenous RNAi pathway, the antiviral RNAi response targeted against this virus does not spread systemically throughout the organism and cannot be passed between generations. These results suggest that there are differences between the two pathways that remain to be discovered.
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23
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Jose AM. Movement of regulatory RNA between animal cells. Genesis 2015; 53:395-416. [PMID: 26138457 PMCID: PMC4915348 DOI: 10.1002/dvg.22871] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 06/28/2015] [Accepted: 06/29/2015] [Indexed: 12/12/2022]
Abstract
Recent studies suggest that RNA can move from one cell to another and regulate genes through specific base-pairing. Mechanisms that modify or select RNA for secretion from a cell are unclear. Secreted RNA can be stable enough to be detected in the extracellular environment and can enter the cytosol of distant cells to regulate genes. Mechanisms that import RNA into the cytosol of an animal cell can enable uptake of RNA from many sources including other organisms. This role of RNA is akin to that of steroid hormones, which cross cell membranes to regulate genes. The potential diagnostic use of RNA in human extracellular fluids has ignited interest in understanding mechanisms that enable the movement of RNA between animal cells. Genetic model systems will be essential to gain more confidence in proposed mechanisms of RNA transport and to connect an extracellular RNA with a specific biological function. Studies in the worm C. elegans and in other animals have begun to reveal parts of this novel mechanism of cell-to-cell communication. Here, I summarize the current state of this nascent field, highlight the many unknowns, and suggest future directions.
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Affiliation(s)
- Antony M Jose
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland
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24
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Weiberg A, Bellinger M, Jin H. Conversations between kingdoms: small RNAs. Curr Opin Biotechnol 2015. [PMID: 25622136 DOI: 10.1016/j.copbio.2014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Humans, animals, and plants are constantly under attack from pathogens and pests, resulting in severe consequences on global human health and crop production. Small RNA (sRNA)-mediated RNA interference (RNAi) is a conserved regulatory mechanism that is involved in almost all eukaryotic cellular processes, including host immunity and pathogen virulence. Recent evidence supports the significant contribution of sRNAs and RNAi to the communication between hosts and some eukaryotic pathogens, pests, parasites, or symbiotic microorganisms. Mobile silencing signals—most likely sRNAs—are capable of translocating from the host to its interacting organism, and vice versa. In this review, we will provide an overview of sRNA communications between different kingdoms, with a primary focus on the advances in plant-pathogen interaction systems.
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Affiliation(s)
- Arne Weiberg
- Department of Plant Pathology and Microbiology, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Marschal Bellinger
- Department of Plant Pathology and Microbiology, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Hailing Jin
- Department of Plant Pathology and Microbiology, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA.
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25
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Double-stranded RNA made in C. elegans neurons can enter the germline and cause transgenerational gene silencing. Proc Natl Acad Sci U S A 2015; 112:2133-8. [PMID: 25646479 DOI: 10.1073/pnas.1423333112] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
An animal that can transfer gene-regulatory information from somatic cells to germ cells may be able to communicate changes in the soma from one generation to the next. In the worm Caenorhabditis elegans, expression of double-stranded RNA (dsRNA) in neurons can result in the export of dsRNA-derived mobile RNAs to other distant cells. Here, we show that neuronal mobile RNAs can cause transgenerational silencing of a gene of matching sequence in germ cells. Consistent with neuronal mobile RNAs being forms of dsRNA, silencing of target genes that are expressed either in somatic cells or in the germline requires the dsRNA-selective importer SID-1. In contrast to silencing in somatic cells, which requires dsRNA expression in each generation, silencing in the germline is heritable after a single generation of exposure to neuronal mobile RNAs. Although initiation of inherited silencing within the germline requires SID-1, a primary Argonaute RDE-1, a secondary Argonaute HRDE-1, and an RNase D homolog MUT-7, maintenance of inherited silencing is independent of SID-1 and RDE-1, but requires HRDE-1 and MUT-7. Inherited silencing can persist for >25 generations in the absence of the ancestral source of neuronal dsRNA. Therefore, our results suggest that sequence-specific regulatory information in the form of dsRNA can be transferred from neurons to the germline to cause transgenerational silencing.
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Weiberg A, Bellinger M, Jin H. Conversations between kingdoms: small RNAs. Curr Opin Biotechnol 2015; 32:207-215. [PMID: 25622136 DOI: 10.1016/j.copbio.2014.12.025] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 12/22/2014] [Accepted: 12/30/2014] [Indexed: 12/30/2022]
Abstract
Humans, animals, and plants are constantly under attack from pathogens and pests, resulting in severe consequences on global human health and crop production. Small RNA (sRNA)-mediated RNA interference (RNAi) is a conserved regulatory mechanism that is involved in almost all eukaryotic cellular processes, including host immunity and pathogen virulence. Recent evidence supports the significant contribution of sRNAs and RNAi to the communication between hosts and some eukaryotic pathogens, pests, parasites, or symbiotic microorganisms. Mobile silencing signals—most likely sRNAs—are capable of translocating from the host to its interacting organism, and vice versa. In this review, we will provide an overview of sRNA communications between different kingdoms, with a primary focus on the advances in plant-pathogen interaction systems.
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Affiliation(s)
- Arne Weiberg
- Department of Plant Pathology and Microbiology, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Marschal Bellinger
- Department of Plant Pathology and Microbiology, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Hailing Jin
- Department of Plant Pathology and Microbiology, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA.
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Nagy AI, Vázquez-Manrique RP, Lopez M, Christov CP, Sequedo MD, Herzog M, Herlihy AE, Bodak M, Gatsi R, Baylis HA. IP3 signalling regulates exogenous RNAi in Caenorhabditis elegans. EMBO Rep 2015; 16:341-50. [PMID: 25608529 DOI: 10.15252/embr.201439585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
RNA interference (RNAi) is a widespread and widely exploited phenomenon. Here, we show that changing inositol 1,4,5-trisphosphate (IP3) signalling alters RNAi sensitivity in Caenorhabditis elegans. Reducing IP3 signalling enhances sensitivity to RNAi in a broad range of genes and tissues. Conversely up-regulating IP3 signalling decreases sensitivity. Tissue-specific rescue experiments suggest IP3 functions in the intestine. We also exploit IP3 signalling mutants to further enhance the sensitivity of RNAi hypersensitive strains. These results demonstrate that conserved cell signalling pathways can modify RNAi responses, implying that RNAi responses may be influenced by an animal's physiology or environment.
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Affiliation(s)
- Anikó I Nagy
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Rafael P Vázquez-Manrique
- Research Group in Molecular, Cellular and Genomic Biomedicine, Health Research Institute-La Fe, Valencia, Spain Centre for Biomedical Network Research on Rare Diseases (CIBERER), Valencia, Spain
| | - Marie Lopez
- Department of Zoology, University of Cambridge, Cambridge, UK
| | | | - María Dolores Sequedo
- Research Group in Molecular, Cellular and Genomic Biomedicine, Health Research Institute-La Fe, Valencia, Spain Centre for Biomedical Network Research on Rare Diseases (CIBERER), Valencia, Spain
| | - Mareike Herzog
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Anna E Herlihy
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Maxime Bodak
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Roxani Gatsi
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Howard A Baylis
- Department of Zoology, University of Cambridge, Cambridge, UK
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Carradec Q, Götz U, Arnaiz O, Pouch J, Simon M, Meyer E, Marker S. Primary and secondary siRNA synthesis triggered by RNAs from food bacteria in the ciliate Paramecium tetraurelia. Nucleic Acids Res 2015; 43:1818-33. [PMID: 25593325 PMCID: PMC4330347 DOI: 10.1093/nar/gku1331] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In various organisms, an efficient RNAi response can be triggered by feeding cells with bacteria producing double-stranded RNA (dsRNA) against an endogenous gene. However, the detailed mechanisms and natural functions of this pathway are not well understood in most cases. Here, we studied siRNA biogenesis from exogenous RNA and its genetic overlap with endogenous RNAi in the ciliate Paramecium tetraurelia by high-throughput sequencing. Using wild-type and mutant strains deficient for dsRNA feeding we found that high levels of primary siRNAs of both strands are processed from the ingested dsRNA trigger by the Dicer Dcr1, the RNA-dependent RNA polymerases Rdr1 and Rdr2 and other factors. We further show that this induces the synthesis of secondary siRNAs spreading along the entire endogenous mRNA, demonstrating the occurrence of both 3′-to-5′ and 5′-to-3′ transitivity for the first time in the SAR clade of eukaryotes (Stramenopiles, Alveolates, Rhizaria). Secondary siRNAs depend on Rdr2 and show a strong antisense bias; they are produced at much lower levels than primary siRNAs and hardly contribute to RNAi efficiency. We further provide evidence that the Paramecium RNAi machinery also processes single-stranded RNAs from its bacterial food, broadening the possible natural functions of exogenously induced RNAi in this organism.
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Affiliation(s)
- Quentin Carradec
- Institut de Biologie de l'ENS, IBENS, Ecole Normale Supérieure, Inserm, U1024, CNRS, UMR 8197, 75005 Paris, France UPMC, IFD, Sorbonne Universités, 4 place Jussieu, 75252 Paris cedex 05, France
| | - Ulrike Götz
- Zentrum für Human- und Molekularbiologie, Molekulare Zelldynamik, Universität des Saarlandes, Campus A2 4, 66123 Saarbrücken, Germany
| | - Olivier Arnaiz
- Centre de Génétique Moléculaire, CNRS UPR3404, 91198 Gif-sur-Yvette cedex, France
| | - Juliette Pouch
- Institut de Biologie de l'ENS, IBENS, Ecole Normale Supérieure, Inserm, U1024, CNRS, UMR 8197, 75005 Paris, France
| | - Martin Simon
- Zentrum für Human- und Molekularbiologie, Molekulare Zelldynamik, Universität des Saarlandes, Campus A2 4, 66123 Saarbrücken, Germany
| | - Eric Meyer
- Institut de Biologie de l'ENS, IBENS, Ecole Normale Supérieure, Inserm, U1024, CNRS, UMR 8197, 75005 Paris, France
| | - Simone Marker
- Institut de Biologie de l'ENS, IBENS, Ecole Normale Supérieure, Inserm, U1024, CNRS, UMR 8197, 75005 Paris, France Zentrum für Human- und Molekularbiologie, Molekulare Zelldynamik, Universität des Saarlandes, Campus A2 4, 66123 Saarbrücken, Germany
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29
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Sarkies P, Miska EA. Small RNAs break out: the molecular cell biology of mobile small RNAs. Nat Rev Mol Cell Biol 2014; 15:525-35. [DOI: 10.1038/nrm3840] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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30
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Karlikow M, Goic B, Saleh MC. RNAi and antiviral defense in Drosophila: setting up a systemic immune response. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2014; 42:85-92. [PMID: 23684730 DOI: 10.1016/j.dci.2013.05.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 05/03/2013] [Accepted: 05/06/2013] [Indexed: 06/02/2023]
Abstract
RNA interference (RNAi) controls gene expression in eukaryotic cells and thus, cellular homeostasis. In addition, in plants, nematodes and arthropods it is a central antiviral effector mechanism. Antiviral RNAi has been well described as a cell autonomous response, which is triggered by double-stranded RNA (dsRNA) molecules. This dsRNA is the precursor for the silencing of viral RNA in a sequence-specific manner. In plants, systemic antiviral immunity has been demonstrated, however much less is known in animals. Recently, some evidence for a systemic antiviral response in arthropods has come to light. Cell autonomous RNAi may not be sufficient to reach an efficient antiviral response, and the organism might rely on the spread and uptake of an RNAi signal of unknown origin. In this review, we offer a perspective on how RNAi-mediated antiviral immunity could confer systemic protection in insects and we propose directions for future research to understand the mechanism of RNAi-immune signal sorting, spreading and amplification.
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Affiliation(s)
- Margot Karlikow
- Institut Pasteur, Viruses and RNA Interference, Centre National de la Recherche Scientifique UMR3569, Paris, France
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31
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Affiliation(s)
- Peter Sarkies
- Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
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32
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Antiviral RNA silencing initiated in the absence of RDE-4, a double-stranded RNA binding protein, in Caenorhabditis elegans. J Virol 2013; 87:10721-9. [PMID: 23885080 DOI: 10.1128/jvi.01305-13] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Small interfering RNAs (siRNAs) processed from double-stranded RNA (dsRNA) of virus origins mediate potent antiviral defense through a process referred to as RNA interference (RNAi) or RNA silencing in diverse organisms. In the simple invertebrate Caenorhabditis elegans, the RNAi process is initiated by a single Dicer, which partners with the dsRNA binding protein RDE-4 to process dsRNA into viral siRNAs (viRNAs). Notably, in C. elegans this RNA-directed viral immunity (RDVI) also requires a number of worm-specific genes for its full antiviral potential. One such gene is rsd-2 (RNAi spreading defective 2), which was implicated in RDVI in our previous studies. In the current study, we first established an antiviral role by showing that rsd-2 null mutants permitted higher levels of viral RNA accumulation, and that this enhanced viral susceptibility was reversed by ectopic expression of RSD-2. We then examined the relationship of rsd-2 with other known components of RNAi pathways and established that rsd-2 functions in a novel pathway that is independent of rde-4 but likely requires the RNA-dependent RNA polymerase RRF-1, suggesting a critical role for RSD-2 in secondary viRNA biogenesis, likely through coordinated action with RRF-1. Together, these results suggest that RDVI in the single-Dicer organism C. elegans depends on the collective actions of both RDE-4-dependent and RDE-4-independent mechanisms to produce RNAi-inducing viRNAs. Our study reveals, for the first time, a novel siRNA-producing mechanism in C. elegans that bypasses the need for a dsRNA-binding protein.
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33
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RNAi pathways in the recognition of foreign RNA: antiviral responses and host–parasite interactions in nematodes. Biochem Soc Trans 2013; 41:876-80. [DOI: 10.1042/bst20130021] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The nematode Caenorhabditis elegans was the first animal for which RNAi (RNA interference) in response to exogenous triggers was shown experimentally and subsequently the molecular components of the RNAi pathway have been characterized in some detail. However, the function of RNAi in the life cycle of nematodes in the wild is still unclear. In the present article, we argue that RNAi could be used in nematodes as a mechanism to sense and respond to foreign RNA that the animal might be exposed to either through viral infection or through ingestion of food sources. This could be of potential importance to the life cycle of parasitic nematodes as they ingest RNA from different hosts at different points during their life cycle. We postulate that RNA ingested from the host could be used by the parasite to regulate its own genes, through the amplification mechanism intrinsic to the nematode RNAi pathway.
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34
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Billeter AT, Barnett RE, Druen D, Polk HC, van Berkel VH. MicroRNA as a new factor in lung and esophageal cancer. Semin Thorac Cardiovasc Surg 2013. [PMID: 23200070 DOI: 10.1053/j.semtcvs.2012.06.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Lung cancer is the most lethal cancer due to late detection in advanced stages; early diagnosis of lung cancer allows surgical treatment and improves the outcome. The prevalence of gastroesophageal reflux-related adenocarcinomas of the esophagus is increasing; repetitive surveillance endoscopies are necessary to detect development of cancer. A blood-based biomarker would simplify the diagnosis and treatment of both diseases. MicroRNAs (miRNAs) are short RNA strands that interfere with protein production. miRNAs play pivotal roles in cell homeostasis, and dysregulation of miRNAs can lead to the development of cancer. miRNAs can be found in all body fluids and have been proposed to serve as messengers between closely localized cells but also distant organs. Cancer cells actively secrete miRNAs, and these miRNA profiles can be found in blood. We outline, here, how these miRNAs may aid in diagnosis and treatment of lung and esophageal cancers, as well as their apparent limitations.
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Affiliation(s)
- Adrian T Billeter
- Department of Surgery, Price Institute of Surgical Research, University of Louisville School of Medicine, Louisville, Kentucky 40202, USA.
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35
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A novel strategy for cell-autonomous gene knockdown in Caenorhabditis elegans defines a cell-specific function for the G-protein subunit GOA-1. Genetics 2013; 194:363-73. [PMID: 23525334 DOI: 10.1534/genetics.113.149724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We developed a novel knockdown strategy to examine cell-specific gene function in Caenorhabditis elegans. In this strategy a null mutation in any gene is replaced with a genetically stable transgene that contains a wild-type copy of the gene fused to a 3' tag that targets the mRNA transcript for degradation by the host nonsense-mediated decay (NMD) machinery. In NMD-defective animals, tagged transgene mRNA is expressed at levels similar to the endogenous gene it replaced and is translated into wild-type protein that fully rescues gene function. Cell-specific activation of NMD cell autonomously knocks down transgene expression in specific cell types without affecting its expression or function in other cells of the organism. To demonstrate the utility of this system, we replaced the goa-1 gene, encoding the pan-neuronally expressed G-protein subunit GOA-1, with a degradation-tagged transgene. We then knocked down expression of the transgene from only two neurons, the hermaphrodite-specific neurons (HSNs), and showed that GOA-1 acts cell autonomously in the HSNs to inhibit egg-laying behavior.
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36
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Control of cell-fate plasticity and maintenance of multipotency by DAF-16/FoxO in quiescent Caenorhabditis elegans. Proc Natl Acad Sci U S A 2013; 110:2181-6. [PMID: 23341633 DOI: 10.1073/pnas.1222377110] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The Caenorhabditis elegans vulval precursor cells (VPCs) offer a paradigm for investigating how multipotency of progenitor cells is maintained during periods of quiescence. The VPCs are born in the first larval stage. When hermaphrodites are grown under favorable conditions, the EGF-mediated "inductive" signal and the LIN-12/Notch-mediated "lateral" signal confer a precise spatial pattern of distinct vulval cell fates in the third larval stage, a day after hatching. Under adverse conditions, hermaphrodites undergo a prolonged quiescent period as dauer larvae, which can endure for several months with progenitor cells such as VPCs in developmental arrest. If favorable conditions ensue, larvae recover and resume development as postdauer third stage larvae, with the same VPC spatial-patterning events as in continuously developing third stage larvae. Here, we identify several consequences of dauer life history for VPC specification. In wild-type dauers, VPCs undergo a phenomenon reminiscent of natural direct reprogramming to maintain or reestablish multipotency; they acquire an active block to signal transduction by EGF receptor and LIN-12/Notch and have a different mechanism for regulating transcription of the lateral signal. Furthermore, DAF-16/FoxO, a target of insulin/insulin-like growth factor signaling, is required to promote VPC fate plasticity during dauer and for normal vulval patterning after passage through dauer, suggesting that DAF-16/FoxO coordinates environment and life history with plasticity of cell fate.
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Abstract
The significance of noncoding RNAs in animal biology is being increasingly recognized. The nematode Caenorhabditis elegans has an extensive system of short RNAs that includes microRNAs, piRNAs, and endogenous siRNAs, which regulate development, control life span, provide resistance to viruses and transposons, and monitor gene duplications. Progress in our understanding of short RNAs was stimulated by the discovery of RNA interference, a phenomenon of sequence-specific gene silencing induced by exogenous double-stranded RNA, at the turn of the twenty-first century. This chapter provides a broad overview of the exogenous and endogenous RNAi processes in C. elegans and describes recent advances in genetic, genomic, and molecular analyses of nematode's short RNAs and proteins involved in the RNAi-related pathways.
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Affiliation(s)
- Alla Grishok
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA.
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38
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Sharma A. Transgenerational epigenetic inheritance: focus on soma to germline information transfer. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2012; 113:439-46. [PMID: 23257323 DOI: 10.1016/j.pbiomolbio.2012.12.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 11/30/2012] [Accepted: 12/06/2012] [Indexed: 01/29/2023]
Abstract
In trangenerational epigenetic inheritance, phenotypic information not encoded in DNA sequence is transmitted across generations. In germline-dependent mode, memory of environmental exposure in parental generation is transmitted through gametes, leading to appearance of phenotypes in the unexposed future generations. The memory is considered to be encoded in epigenetic factors like DNA methylation, histone modifications and regulatory RNAs. Environmental exposure may cause epigenetic modifications in the germline either directly or indirectly through primarily affecting the soma. The latter possibility is most intriguing because it contradicts the established dogma that hereditary information flows only from germline to soma, not in reverse. As such, identification of the factor(s) mediating soma to germline information transfer in transgenerational epigenetic inheritance would be pathbreaking. Regulatory RNAs and hormone have previously been implicated or proposed to play a role in soma to germline communication in epigenetic inheritance. This review examines the recent examples of gametogenic transgenerational inheritance in plants and animals in order to assess if evidence of regulatory RNAs and hormones as mediators of information transfer is supported. Overall, direct evidence for both mobile regulatory RNAs and hormones is found to exist in plants. In animals, although involvement of mobile RNAs seems imminent, direct evidence of RNA-mediated soma to germline information transfer in transgenerational epigenetic inheritance is yet to be obtained. Direct evidence is also lacking for hormones in animals. However, detailed examination of recently reported examples of transgenerational inheritance reveals circumstantial evidence supporting a role of hormones in information transmission.
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Affiliation(s)
- Abhay Sharma
- CSIR-Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Delhi University Campus, Mall Road, Delhi 110007, India.
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Hinas A, Wright AJ, Hunter CP. SID-5 is an endosome-associated protein required for efficient systemic RNAi in C. elegans. Curr Biol 2012; 22:1938-43. [PMID: 22981770 PMCID: PMC10518204 DOI: 10.1016/j.cub.2012.08.020] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 07/04/2012] [Accepted: 08/09/2012] [Indexed: 12/28/2022]
Abstract
In the nematode C. elegans, RNAi silencing signals are efficiently taken up from the environment and transported between cells and tissues. Previous studies implicating endosomal proteins in systemic RNAi lack conclusive evidence. Here, we report the identification and characterization of SID-5, a C. elegans endosome-associated protein that is required for efficient systemic RNAi in response to both ingested and expressed double-stranded RNA (dsRNA). SID-5 is detected in cytoplasmic foci that partially colocalize with GFP fusions of late endosomal proteins RAB-7 and LMP-1. Furthermore, knockdown of various endosomal proteins similarly relocalizes both SID-5 and LMP-1::GFP. Consistent with a non-cell-autonomous function, intestine-specific SID-5 expression restored body wall muscle (bwm) target gene silencing in response to ingested dsRNA. Finally, we show that sid-5 is required for the previously described sid-1-independent transport of ingested RNAi triggers across the intestine. Together, these data demonstrate that an endosome-associated protein, SID-5, promotes the transport of RNAi silencing signals between cells. Furthermore, SID-5 acts differently than the previously described SID-1, SID-2, and SID-3 proteins, thus expanding the systemic RNAi pathway.
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Affiliation(s)
- Andrea Hinas
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
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40
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Conserved tyrosine kinase promotes the import of silencing RNA into Caenorhabditis elegans cells. Proc Natl Acad Sci U S A 2012; 109:14520-5. [PMID: 22912399 DOI: 10.1073/pnas.1201153109] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
RNA silencing in Caenorhabditis elegans is transmitted between cells by the transport of double-stranded RNA (dsRNA). The efficiency of such transmission, however, depends on both the cell type and the environment. Here, we identify systemic RNAi defective-3 (SID-3) as a conserved tyrosine kinase required for the efficient import of dsRNA. Without SID-3, cells perform RNA silencing well but import dsRNA poorly. Upon overexpression of SID-3, cells import dsRNA more efficiently than do wild-type cells and such efficient import of dsRNA requires an intact SID-3 kinase domain. The mammalian homolog of SID-3, activated cdc-42-associated kinase (ACK), acts in many signaling pathways that respond to environmental changes and is known to directly associate with endocytic vesicles, which have been implicated in dsRNA transport. Therefore, our results suggest that the SID-3/ACK tyrosine kinase acts as a regulator of RNA import into animal cells.
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41
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Silencing of host genes directed by virus-derived short interfering RNAs in Caenorhabditis elegans. J Virol 2012; 86:11645-53. [PMID: 22896621 DOI: 10.1128/jvi.01501-12] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Small interfering RNAs (siRNAs) processed from viral replication intermediates by RNase III-like enzyme Dicer guide sequence-specific antiviral silencing in fungi, plants, and invertebrates. In plants, virus-derived siRNAs (viRNAs) can target and silence cellular transcripts and, in some cases, are responsible for the induction of plant diseases. Currently it remains unclear whether viRNAs are also capable of modulating the expression of cellular genes in the animal kingdom, although animal virus-encoded microRNAs (miRNAs) are known to guide efficient silencing of host genes, thereby facilitating virus replication. In this report, we showed that viRNAs derived from a modified nodavirus triggered potent silencing of homologous cellular transcripts produced by the endogenous gene or transgene in the nematode worm Caenorhabditis elegans. Like that found in plants, virus-induced gene silencing (VIGS) in C. elegans also involves RRF-1, a worm RNA-dependent RNA polymerase (RdRP) that is known to produce single-stranded secondary siRNAs in a Dicer-independent manner. We further demonstrated that VIGS in C. elegans is inheritable, suggesting that VIGS has the potential to generate profound epigenetic consequences in future generations. Altogether, these findings, for the first time, confirmed that viRNAs have the potential to modulate host gene expression in the animal kingdom. Most importantly, the success in uncoupling the trigger and the target of the antiviral silencing would allow for the exploration of novel features of virus-host interactions mediated by viRNAs in the animal kingdom.
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Morozov SY, Solovyev AG. Did silencing suppression counter-defensive strategy contribute to origin and evolution of the triple gene block coding for plant virus movement proteins? FRONTIERS IN PLANT SCIENCE 2012; 3:136. [PMID: 22783263 PMCID: PMC3390553 DOI: 10.3389/fpls.2012.00136] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 06/05/2012] [Indexed: 05/25/2023]
Affiliation(s)
- Sergey Y. Morozov
- Belozersky Institute of Physico-Chemical Biology, Moscow State UniversityMoscow, Russia
| | - Andrey G. Solovyev
- Belozersky Institute of Physico-Chemical Biology, Moscow State UniversityMoscow, Russia
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43
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Ashe A, Sapetschnig A, Weick EM, Mitchell J, Bagijn MP, Cording AC, Doebley AL, Goldstein LD, Lehrbach NJ, Le Pen J, Pintacuda G, Sakaguchi A, Sarkies P, Ahmed S, Miska EA. piRNAs can trigger a multigenerational epigenetic memory in the germline of C. elegans. Cell 2012; 150:88-99. [PMID: 22738725 PMCID: PMC3464430 DOI: 10.1016/j.cell.2012.06.018] [Citation(s) in RCA: 505] [Impact Index Per Article: 42.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 06/18/2012] [Accepted: 06/18/2012] [Indexed: 11/23/2022]
Abstract
Transgenerational effects have wide-ranging implications for human health, biological adaptation, and evolution; however, their mechanisms and biology remain poorly understood. Here, we demonstrate that a germline nuclear small RNA/chromatin pathway can maintain stable inheritance for many generations when triggered by a piRNA-dependent foreign RNA response in C. elegans. Using forward genetic screens and candidate approaches, we find that a core set of nuclear RNAi and chromatin factors is required for multigenerational inheritance of environmental RNAi and piRNA silencing. These include a germline-specific nuclear Argonaute HRDE1/WAGO-9, a HP1 ortholog HPL-2, and two putative histone methyltransferases, SET-25 and SET-32. piRNAs can trigger highly stable long-term silencing lasting at least 20 generations. Once established, this long-term memory becomes independent of the piRNA trigger but remains dependent on the nuclear RNAi/chromatin pathway. Our data present a multigenerational epigenetic inheritance mechanism induced by piRNAs.
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Affiliation(s)
- Alyson Ashe
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
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44
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Intercellular communication: diverse structures for exchange of genetic information. Nat Rev Mol Cell Biol 2012; 13:328-35. [PMID: 22510790 DOI: 10.1038/nrm3335] [Citation(s) in RCA: 493] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
An emerging concept is that cellular communication in mammals can be mediated by the exchange of genetic information, mainly in the form of microRNAs. This can occur when extracellular vesicles, such as exosomes, secreted by a donor cell are taken up by an acceptor cell. Transfer of genetic material can also occur through intimate membrane contacts between donor and acceptor cells. Specialized cell-cell contacts, such as synapses, have the potential to combine these modes of genetic transfer.
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