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Bardapurkar R, Binayak G, Pandit S. Trophic microRNA: Post-transcriptional regulation of target genes and larval development impairment in Plutella xylostella upon precursor and mature microRNA ingestion. INSECT MOLECULAR BIOLOGY 2024. [PMID: 39049812 DOI: 10.1111/imb.12949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 07/13/2024] [Indexed: 07/27/2024]
Abstract
MicroRNAs (miRNAs) are post-transcriptional gene regulators. In the miRNA pathway's cytoplasmic part, the miRNA is processed from a hairpin-structured precursor to a double-stranded (ds) mature RNA and ultimately to a single-stranded mature miRNA. In insects, ingesting these two ds forms can regulate the target gene expression; this inspired the trophic miRNA's use as a functional genomics and pest management tool. However, systematic studies enabling comparisons of pre- and mature forms, dosages, administration times and instar-wise effects on target transcripts and phenotypes, which can help develop a miRNA administration method, are unavailable due to the different focuses of the previous investigations. We investigated the impact of trophically delivered Px-let-7 miRNA on the lepidopteran pest Plutella xylostella, to compare the efficacies of its pre- and ds-mature forms. Continuous feeding on the miRNA-supplemented diet suppressed expressions of FTZ-F1 and E74, the target ecdysone pathway genes. Both the pre-let-7 and mature let-7 miRNA forms similarly downregulated the target transcripts in all four larval instars. Pre-let-7 and let-7 ingestions decreased larval mass and instar duration and increased mortality in all instars, exhibiting adverse effects on larval growth and development. miRNA processing Dicer-1 and AGO-1's upregulations upon miRNA ingestion denoted the systemic miRNA spread in larval tissues. The scrambled sequence controls did not affect the target transcripts, suggesting the sequence-specific targeting by the mature miRNA and hairpin cassette's non-involvement in the target downregulation. This work provides a framework for miRNA and target gene function analyses and potentiates the trophic miRNA's utility in pest management.
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Affiliation(s)
- Rutwik Bardapurkar
- Agricultural Biotechnology and Chemical Ecology Research Laboratory, Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Gauri Binayak
- Agricultural Biotechnology and Chemical Ecology Research Laboratory, Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Sagar Pandit
- Agricultural Biotechnology and Chemical Ecology Research Laboratory, Department of Biology, Indian Institute of Science Education and Research, Pune, India
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2
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Zhang J, Zhan C, Fan J, Wu D, Zhang R, Wu D, Chen X, Lu Y, Li M, Lin M, Gong J, Jiang D. Structural insights into double-stranded RNA recognition and transport by SID-1. Nat Struct Mol Biol 2024; 31:1095-1104. [PMID: 38664565 DOI: 10.1038/s41594-024-01276-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 03/14/2024] [Indexed: 07/20/2024]
Abstract
RNA uptake by cells is critical for RNA-mediated gene interference (RNAi) and RNA-based therapeutics. In Caenorhabditis elegans, RNAi is systemic as a result of SID-1-mediated double-stranded RNA (dsRNA) across cells. Despite the functional importance, the underlying mechanisms of dsRNA internalization by SID-1 remain elusive. Here we describe cryogenic electron microscopy structures of SID-1, SID-1-dsRNA complex and human SID-1 homologs SIDT1 and SIDT2, elucidating the structural basis of dsRNA recognition and import by SID-1. The homodimeric SID-1 homologs share conserved architecture, but only SID-1 possesses the molecular determinants within its extracellular domains for distinguishing dsRNA from single-stranded RNA and DNA. We show that the removal of the long intracellular loop between transmembrane helix 1 and 2 attenuates dsRNA uptake and systemic RNAi in vivo, suggesting a possible endocytic mechanism of SID-1-mediated dsRNA internalization. Our study provides mechanistic insights into dsRNA internalization by SID-1, which may facilitate the development of dsRNA applications based on SID-1.
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Affiliation(s)
- Jiangtao Zhang
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of MOE, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Chunhua Zhan
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of MOE, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Junping Fan
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University Health Science Center, Beijing, China
| | - Dian Wu
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of MOE, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ruixue Zhang
- Key Laboratory of Agricultural Microbiome (MARA), Biotechnology Research Institute, Chinese Academy Agricultural Sciences, Beijing, China
| | - Di Wu
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xinyao Chen
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ying Lu
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ming Li
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Min Lin
- Food Laboratory of Zhongyuan, College of Agriculture, Henan University, Kaifeng, Henan, China
| | - Jianke Gong
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of MOE, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Daohua Jiang
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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3
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Wang R, Cong Y, Qian D, Yan C, Gong D. Structural basis for double-stranded RNA recognition by SID1. Nucleic Acids Res 2024; 52:6718-6727. [PMID: 38742627 PMCID: PMC11194109 DOI: 10.1093/nar/gkae395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/23/2024] [Accepted: 04/30/2024] [Indexed: 05/16/2024] Open
Abstract
The nucleic acid transport properties of the systemic RNAi-defective (SID) 1 family make them attractive targets for developing RNA-based therapeutics and drugs. However, the molecular basis for double-stranded (ds) RNA recognition by SID1 family remains elusive. Here, we report the cryo-EM structures of Caenorhabditis elegans (c) SID1 alone and in complex with dsRNA, both at a resolution of 2.2 Å. The dimeric cSID1 interacts with two dsRNA molecules simultaneously. The dsRNA is located at the interface between β-strand rich domain (BRD)1 and BRD2 and nearly parallel to the membrane plane. In addition to extensive ionic interactions between basic residues and phosphate backbone, several hydrogen bonds are formed between 2'-hydroxyl group of dsRNA and the contact residues. Additionally, the electrostatic potential surface shows three basic regions are fitted perfectly into three major grooves of dsRNA. These structural characteristics enable cSID1 to bind dsRNA in a sequence-independent manner and to distinguish between DNA and RNA. The cSID1 exhibits no conformational changes upon binding dsRNA, with the exception of a few binding surfaces. Structural mapping of dozens of loss-of-function mutations allows potential interpretation of their diverse functional mechanisms. Our study marks an important step toward mechanistic understanding of the SID1 family-mediated dsRNA uptake.
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Affiliation(s)
- Runhao Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, China
| | - Ye Cong
- School of Life Sciences, Tsinghua University, Beijing, 100084, China. Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China. Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China. State Key Laboratory of Membrane Biology, Tsinghua University, Beijing 100084, China
| | - Dandan Qian
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, China
| | - Chuangye Yan
- School of Life Sciences, Tsinghua University, Beijing, 100084, China. Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China. Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China. State Key Laboratory of Membrane Biology, Tsinghua University, Beijing 100084, China
| | - Deshun Gong
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, China
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4
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Hirano Y, Ohto U, Ichi I, Sato R, Miyake K, Shimizu T. Cryo-EM analysis reveals human SID-1 transmembrane family member 1 dynamics underlying lipid hydrolytic activity. Commun Biol 2024; 7:664. [PMID: 38811802 PMCID: PMC11137008 DOI: 10.1038/s42003-024-06346-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 05/17/2024] [Indexed: 05/31/2024] Open
Abstract
Two mammalian homologs of systemic RNA interference defective protein 1 (SID-1) (SIDT1/2) are suggested to function as double-stranded RNA (dsRNA) transporters for extracellular dsRNA uptake or for release of incorporated dsRNA from lysosome to cytoplasm. SIDT1/2 is also suggested to be involved in cholesterol transport and lipid metabolism. Here, we determine the cryo-electron microscopy structures of human SIDT1, homodimer in a side-by-side arrangement, with two distinct conformations, the cholesterol-bound form and the unbound form. Our structures reveal that the membrane-spanning region of SIDT1 harbors conserved histidine and aspartate residues coordinating to putative zinc ion, in a structurally similar manner to alkaline ceramidases or adiponectin receptors that require zinc for ceramidase activity. We identify that SIDT1 has a ceramidase activity that is attenuated by cholesterol binding. Observations from two structures suggest that cholesterol molecules serve as allosteric regulator that binds the transmembrane region of SIDT1 and induces the conformation change and the reorientation of the catalytic residues. This study represents a contribution to the elucidation of the cholesterol-mediated mechanisms of lipid hydrolytic activity and RNA transport in the SID-1 family proteins.
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Affiliation(s)
- Yoshinori Hirano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Umeharu Ohto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Ikuyo Ichi
- Natural Science Division, Ochanomizu University, Bunkyo-ku, Tokyo, 112-8610, Japan
- Institute for Human Life Innovation, Faculty of Core Research, Ochanomizu University, Bunkyo-ku, Tokyo, 112-8610, Japan
| | - Ryota Sato
- Division of Innate Immunity, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Kensuke Miyake
- Division of Innate Immunity, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Toshiyuki Shimizu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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5
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Camara H, Inan MD, Vergani-Junior CA, Pinto S, Knittel TL, Salgueiro WG, Tonon-da-Silva G, Ramirez J, de Moraes D, Braga DL, De-Souza EA, Mori MA. Tissue-specific overexpression of systemic RNA interference components limits lifespan in C. elegans. Gene 2024; 895:148014. [PMID: 37984536 DOI: 10.1016/j.gene.2023.148014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 11/22/2023]
Abstract
Intertissue RNA transport recently emerged as a novel signaling mechanism. In mammals, mounting evidence suggests that small RNA transfer between cells is widespread and used in various physiological contexts. In the nematode C. elegans, a similar mechanism is conferred by the systemic RNAi pathway. Members of the Systemic RNA Interference Defective (SID) family act at different steps of cellular RNA uptake and export. The limiting step in systemic RNA interference (RNAi) is the import of extracellular RNAs via the conserved double-stranded (dsRNA)-gated dsRNA channel SID-1. To better understand the role of RNAs as intertissue signaling molecules, we modified the function of SID-1 in specific tissues of C. elegans. We observed that sid-1 loss-of-function mutants are as healthy as wild-type worms. Conversely, overexpression of sid-1 in C. elegans intestine, muscle, or neurons rendered worms short-lived. The effects of intestinal sid-1 overexpression were attenuated by silencing the components of systemic RNAi sid-1, sid-2 and sid-5, implicating systemic RNA signaling in the lifespan reduction. Accordingly, tissue-specific overexpression of sid-2 and sid-5 also reduced worm lifespan. Additionally, an RNAi screen for components of several non-coding RNA pathways revealed that silencing the miRNA biogenesis proteins PASH-1 and DCR-1 rendered the lifespan of worms with intestinal sid-1 overexpression similar to controls. Collectively, our data support the notion that systemic RNA signaling must be tightly regulated, and unbalancing that process provokes a reduction in lifespan. We termed this phenomenon Intercellular/Extracellular Systemic RNA imbalance (InExS).
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Affiliation(s)
- Henrique Camara
- Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas, Brazil; Program in Genetics and Molecular Biology, Universidade Estadual de Campinas, Campinas, SP, Brazil; Program in Molecular Biology, Universidade Federal de São Paulo, Brazil
| | - Mehmet Dinçer Inan
- Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas, Brazil; Program in Genetics and Molecular Biology, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Carlos A Vergani-Junior
- Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas, Brazil; Program in Genetics and Molecular Biology, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Silas Pinto
- Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas, Brazil; Program in Genetics and Molecular Biology, Universidade Estadual de Campinas, Campinas, SP, Brazil; Program in Molecular Biology, Universidade Federal de São Paulo, Brazil
| | - Thiago L Knittel
- Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas, Brazil; Program in Genetics and Molecular Biology, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Willian G Salgueiro
- Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas, Brazil; Program in Genetics and Molecular Biology, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Guilherme Tonon-da-Silva
- Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas, Brazil; Program in Genetics and Molecular Biology, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Juliana Ramirez
- Program in Molecular Biology, Universidade Federal de São Paulo, Brazil
| | - Diogo de Moraes
- Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas, Brazil; Program in Genetics and Molecular Biology, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Deisi L Braga
- Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas, Brazil; Program in Genetics and Molecular Biology, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Evandro A De-Souza
- Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas, Brazil; Program in Molecular Biology, Universidade Federal de São Paulo, Brazil; Program in Molecular Biology and Biotechnology, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, RJ, Brazil
| | - Marcelo A Mori
- Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas, Brazil; Program in Genetics and Molecular Biology, Universidade Estadual de Campinas, Campinas, SP, Brazil; Program in Molecular Biology, Universidade Federal de São Paulo, Brazil; Obesity and Comorbidities Research Center (OCRC), Universidade Estadual de Campinas, Campinas, SP, Brazil; Experimental Medicine Research Cluster (EMRC), Universidade Estadual de Campinas, Campinas, SP, Brazil.
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6
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Yang T, Xiao H, Chen X, Zheng L, Guo H, Wang J, Jiang X, Zhang CY, Yang F, Ji X. Characterization of N-glycosylation and its functional role in SIDT1-Mediated RNA uptake. J Biol Chem 2024; 300:105654. [PMID: 38237680 PMCID: PMC10850970 DOI: 10.1016/j.jbc.2024.105654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 02/08/2024] Open
Abstract
The mammalian SID-1 transmembrane family members, SIDT1 and SIDT2, are multipass transmembrane proteins that mediate the cellular uptake and intracellular trafficking of nucleic acids, playing important roles in the immune response and tumorigenesis. Previous work has suggested that human SIDT1 and SIDT2 are N-glycosylated, but the precise site-specific N-glycosylation information and its functional contribution remain unclear. In this study, we use high-resolution liquid chromatography tandem mass spectrometry to comprehensively map the N-glycosites and quantify the N-glycosylation profiles of SIDT1 and SIDT2. Further molecular mechanistic probing elucidates the essential role of N-linked glycans in regulating cell surface expression, RNA binding, protein stability, and RNA uptake of SIDT1. Our results provide crucial information about the potential functional impact of N-glycosylation in the regulation of SIDT1-mediated RNA uptake and provide insights into the molecular mechanisms of this promising nucleic acid delivery system with potential implications for therapeutic applications.
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Affiliation(s)
- Tingting Yang
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Haonan Xiao
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Xiulan Chen
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Le Zheng
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Hangtian Guo
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Jiaqi Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Xiaohong Jiang
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Chen-Yu Zhang
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China; Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu, China.
| | - Fuquan Yang
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
| | - Xiaoyun Ji
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China; Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu, China; Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, Jiangsu, China; Engineering Research Center of Protein and Peptide Medicine, Ministry of Education, Nanjing, Jiangsu, China.
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7
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Ow MC, Hall SE. Inheritance of Stress Responses via Small Non-Coding RNAs in Invertebrates and Mammals. EPIGENOMES 2023; 8:1. [PMID: 38534792 DOI: 10.3390/epigenomes8010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/06/2023] [Accepted: 12/12/2023] [Indexed: 03/28/2024] Open
Abstract
While reports on the generational inheritance of a parental response to stress have been widely reported in animals, the molecular mechanisms behind this phenomenon have only recently emerged. The booming interest in epigenetic inheritance has been facilitated in part by the discovery that small non-coding RNAs are one of its principal conduits. Discovered 30 years ago in the Caenorhabditis elegans nematode, these small molecules have since cemented their critical roles in regulating virtually all aspects of eukaryotic development. Here, we provide an overview on the current understanding of epigenetic inheritance in animals, including mice and C. elegans, as it pertains to stresses such as temperature, nutritional, and pathogenic encounters. We focus on C. elegans to address the mechanistic complexity of how small RNAs target their cohort mRNAs to effect gene expression and how they govern the propagation or termination of generational perdurance in epigenetic inheritance. Presently, while a great amount has been learned regarding the heritability of gene expression states, many more questions remain unanswered and warrant further investigation.
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Affiliation(s)
- Maria C Ow
- Department of Biology, Syracuse University, Syracuse, NY 13210, USA
| | - Sarah E Hall
- Department of Biology and Program in Neuroscience, Syracuse University, Syracuse, NY 13210, USA
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8
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Chai P, Lebedenko CG, Flynn RA. RNA Crossing Membranes: Systems and Mechanisms Contextualizing Extracellular RNA and Cell Surface GlycoRNAs. Annu Rev Genomics Hum Genet 2023; 24:85-107. [PMID: 37068783 DOI: 10.1146/annurev-genom-101722-101224] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
The subcellular localization of a biopolymer often informs its function. RNA is traditionally confined to the cytosolic and nuclear spaces, where it plays critical and conserved roles across nearly all biochemical processes. Our recent observation of cell surface glycoRNAs may further explain the extracellular role of RNA. While cellular membranes are efficient gatekeepers of charged polymers such as RNAs, a large body of research has demonstrated the accumulation of specific RNA species outside of the cell, termed extracellular RNAs (exRNAs). Across various species and forms of life, protein pores have evolved to transport RNA across membranes, thus providing a mechanistic path for exRNAs to achieve their extracellular topology. Here, we review types of exRNAs and the pores capable of RNA transport to provide a logical and testable path toward understanding the biogenesis and regulation of cell surface glycoRNAs.
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Affiliation(s)
- Peiyuan Chai
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA;
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Charlotta G Lebedenko
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA;
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Ryan A Flynn
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA;
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, USA
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9
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Zhang H, Chen J, Gao J, Zhang Q, Liu X, Han Z. New insights into transmission pathways and possible off-target effects of insecticidal dsRNA released by treated plants. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2022; 188:105281. [PMID: 36464336 DOI: 10.1016/j.pestbp.2022.105281] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/29/2022] [Accepted: 11/02/2022] [Indexed: 06/17/2023]
Abstract
RNAi has shown great potential in controlling pests and pathogens, and dsRNA-based pesticides have been used in different ways. Due to off-target effects, the transmission pathways and possible impacts of dsRNA on non-target organisms after release should be researched. Here, we tested pathways of dsRNA transmission through the rice-hopper-spider food chain and their efficiency for triggering RNAi. The results revealed five new pathways by which plants transfer dsRNA into the environment through the food chain. We found that ingestion of the tissues or guttation droplets of treated plant could trigger both targeted and off-target RNAi both in consumers and predators. Ingestion of consumer hoppers could also result in localized RNAi in the midguts of the predator spiders. Trace amounts of dsRNA were detected in plant root excretions and in hopper honeydew. Cutting the root tips dramatically increased the levels of dsRNA in root excretions. Host shifting experiments proved that hoppers could transfer a trace amount of dsRNA via vomit. With specially designed dsRNAs, we showed that dsRNA sharing matching sequences of 29 bp or 32 bp in length with non-target genes could trigger off-target RNAi, but that dsRNA sharing 13 bp matching sequences could not. We conclude that field-released pesticidal dsRNA could be transmitted via the hydrophilic transport system in plants, and that this may pose a safety risk to non-target animal consumers that are closely related to target pests. Rational use of pesticidal dsRNAs should involve careful consideration of dsRNA design to manage the biosafety risk.
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Affiliation(s)
- Hainan Zhang
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiasheng Chen
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
| | - Jing Gao
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Qi Zhang
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaolong Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Zhaojun Han
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China.
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10
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A Tale of Two Lobsters—Transcriptomic Analysis Reveals a Potential Gap in the RNA Interference Pathway in the Tropical Rock Lobster Panulirus ornatus. Int J Mol Sci 2022; 23:ijms231911752. [PMID: 36233053 PMCID: PMC9569428 DOI: 10.3390/ijms231911752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/28/2022] [Accepted: 09/28/2022] [Indexed: 11/25/2022] Open
Abstract
RNA interference (RNAi) has been widely utilised in many invertebrate models since its discovery, and in a majority of instances presents as a highly efficient and potent gene silencing mechanism. This is emphasized in crustaceans with almost all taxa having the capacity to trigger effective silencing, with a notable exception in the spiny lobsters where repeated attempts at dsRNA induced RNAi have demonstrated extremely ineffective gene knockdown. A comparison of the core RNAi machinery in transcriptomic data from spiny lobsters (Panulirus ornatus) and the closely related slipper lobsters (Thenus australiensis, where silencing is highly effective) revealed that both lobsters possess all proteins involved in the small interfering and microRNA pathways, and that there was little difference at both the sequence and domain architecture level. Comparing the expression of these genes however demonstrated that T. australiensis had significantly higher expression in the transcripts encoding proteins which directly interact with dsRNA when compared to P. ornatus, validated via qPCR. These results suggest that low expression of the core RNAi genes may be hindering the silencing response in P. ornatus, and suggest that it may be critical to enhance the expression of these genes to induce efficient silencing in spiny lobsters.
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11
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Gaeta AL, Nourse JB, Willicott K, McKay LE, Keogh CM, Peter K, Russell SN, Hamamichi S, Berkowitz LA, Caldwell KA, Caldwell GA. Systemic RNA Interference Defective (SID) genes modulate dopaminergic neurodegeneration in C. elegans. PLoS Genet 2022; 18:e1010115. [PMID: 35984862 PMCID: PMC9432717 DOI: 10.1371/journal.pgen.1010115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 08/31/2022] [Accepted: 08/01/2022] [Indexed: 02/02/2023] Open
Abstract
The fine-tuning of gene expression is critical for all cellular processes; aberrations in this activity can lead to pathology, and conversely, resilience. As their role in coordinating organismal responses to both internal and external factors have increasingly come into focus, small non-coding RNAs have emerged as an essential component to disease etiology. Using Systemic RNA interference Defective (SID) mutants of the nematode Caenorhabditis elegans, deficient in gene silencing, we examined the potential consequences of dysfunctional epigenomic regulation in the context of Parkinson's disease (PD). Specifically, the loss of either the sid-1 or sid-3 genes, which encode a dsRNA transporter and an endocytic regulatory non-receptor tyrosine kinase, respectively, conferred neuroprotection to dopaminergic (DA) neurons in an established transgenic C. elegans strain wherein overexpression of human α-synuclein (α-syn) from a chromosomally integrated multicopy transgene causes neurodegeneration. We further show that knockout of a specific microRNA, mir-2, attenuates α-syn neurotoxicity; suggesting that the native targets of mir-2-dependent gene silencing represent putative neuroprotective modulators. In support of this, we demonstrated that RNAi knockdown of multiple mir-2 targets enhanced α-syn-induced DA neurodegeneration. Moreover, we demonstrate that mir-2 overexpression originating in the intestine can induce neurodegeneration of DA neurons, an effect that was reversed by pharmacological inhibition of SID-3 activity. Interestingly, sid-1 mutants retained mir-2-induced enhancement of neurodegeneration. Transcriptomic analysis of α-syn animals with and without a sid-1 mutation revealed 27 differentially expressed genes with human orthologs related to a variety of diseases, including PD. Among these was pgp-8, encoding a P-glycoprotein-related ABC transporter. Notably, sid-1; pgp-8 double mutants abolished the neurodegeneration resulting from intestinal mir-2 overexpression. This research positions known regulators of small RNA-dependent gene silencing within a framework that facilitates mechanistic evaluation of epigenetic responses to exogenous and endogenous factors influencing DA neurodegeneration, revealing a path toward new targets for therapeutic intervention of PD.
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Affiliation(s)
- Anthony L. Gaeta
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America
| | - J. Brucker Nourse
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Karolina Willicott
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Luke E. McKay
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Candice M. Keogh
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Kylie Peter
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Shannon N. Russell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Shusei Hamamichi
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Laura A. Berkowitz
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Kim A. Caldwell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America
- Center for Convergent Bioscience and Medicine, The University of Alabama, Tuscaloosa, Alabama, United States of America
- Alabama Research Institute on Aging, The University of Alabama, Tuscaloosa, Alabama, United States of America
- Departments of Neurology and Neurobiology, Center for Neurodegeneration and Experimental Therapeutics, Nathan Shock Center of Excellence for Basic Research in the Biology of Aging, University of Alabama at Birmingham, Heersink School of Medicine, Birmingham, Alabama, United States of America
| | - Guy A. Caldwell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America
- Center for Convergent Bioscience and Medicine, The University of Alabama, Tuscaloosa, Alabama, United States of America
- Departments of Neurology and Neurobiology, Center for Neurodegeneration and Experimental Therapeutics, Nathan Shock Center of Excellence for Basic Research in the Biology of Aging, University of Alabama at Birmingham, Heersink School of Medicine, Birmingham, Alabama, United States of America
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12
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RNAi as a Foliar Spray: Efficiency and Challenges to Field Applications. Int J Mol Sci 2022; 23:ijms23126639. [PMID: 35743077 PMCID: PMC9224206 DOI: 10.3390/ijms23126639] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 02/04/2023] Open
Abstract
RNA interference (RNAi) is a powerful tool that is being increasingly utilized for crop protection against viruses, fungal pathogens, and insect pests. The non-transgenic approach of spray-induced gene silencing (SIGS), which relies on spray application of double-stranded RNA (dsRNA) to induce RNAi, has come to prominence due to its safety and environmental benefits in addition to its wide host range and high target specificity. However, along with promising results in recent studies, several factors limiting SIGS RNAi efficiency have been recognized in insects and plants. While sprayed dsRNA on the plant surface can produce a robust RNAi response in some chewing insects, plant uptake and systemic movement of dsRNA is required for delivery to many other target organisms. For example, pests such as sucking insects require the presence of dsRNA in vascular tissues, while many fungal pathogens are predominately located in internal plant tissues. Investigating the mechanisms by which sprayed dsRNA enters and moves through plant tissues and understanding the barriers that may hinder this process are essential for developing efficient ways to deliver dsRNA into plant systems. In this review, we assess current knowledge of the plant foliar and cellular uptake of dsRNA molecules. We will also identify major barriers to uptake, including leaf morphological features as well as environmental factors, and address methods to overcome these barriers.
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Nitnavare RB, Bhattacharya J, Singh S, Kour A, Hawkesford MJ, Arora N. Next Generation dsRNA-Based Insect Control: Success So Far and Challenges. FRONTIERS IN PLANT SCIENCE 2021; 12:673576. [PMID: 34733295 PMCID: PMC8558349 DOI: 10.3389/fpls.2021.673576] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 09/22/2021] [Indexed: 06/02/2023]
Abstract
RNA interference (RNAi) is a method of gene silencing where dsRNA is digested into small interfering RNA (siRNA) in the presence of enzymes. These siRNAs then target homologous mRNA sequences aided by the RNA-induced silencing complex (RISC). The mechanism of dsRNA uptake has been well studied and established across many living organisms including insects. In insects, RNAi is a novel and potential tool to develop future pest management means targeting various classes of insects including dipterans, coleopterans, hemipterans, lepidopterans, hymenopterans and isopterans. However, the extent of RNAi in individual class varies due to underlying mechanisms. The present review focuses on three major insect classes viz hemipterans, lepidopterans and coleopterans and the rationale behind this lies in the fact that studies pertaining to RNAi has been extensively performed in these groups. Additionally, these classes harbour major agriculturally important pest species which require due attention. Interestingly, all the three classes exhibit varying levels of RNAi efficiencies with the coleopterans exhibiting maximum response, while hemipterans are relatively inefficient. Lepidopterans on the other hand, show minimum response to RNAi. This has been attributed to many facts and few important being endosomal escape, high activity dsRNA-specific nucleases, and highly alkaline gut environment which renders the dsRNA unstable. Various methods have been established to ensure safe delivery of dsRNA into the biological system of the insect. The most common method for dsRNA administration is supplementing the diet of insects via spraying onto leaves and other commonly eaten parts of the plant. This method is environment-friendly and superior to the hazardous effects of pesticides. Another method involves submergence of root systems in dsRNA solutions and subsequent uptake by the phloem. Additionally, more recent techniques are nanoparticle- and Agrobacterium-mediated delivery systems. However, due to the novelty of these biotechnological methods and recalcitrant nature of certain crops, further optimization is required. This review emphasizes on RNAi developments in agriculturally important insect species and the major hurdles for efficient RNAi in these groups. The review also discusses in detail the development of new techniques to enhance RNAi efficiency using liposomes and nanoparticles, transplastomics, microbial-mediated delivery and chemical methods.
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Affiliation(s)
- Rahul B. Nitnavare
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, United Kingdom
- Department of Plant Science, Rothamsted Research, Harpenden, United Kingdom
| | - Joorie Bhattacharya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | - Satnam Singh
- Punjab Agricultural University (PAU), Regional Research Station, Faridkot, India
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, United Kingdom
| | - Amardeep Kour
- Punjab Agricultural University (PAU), Regional Research Station, Bathinda, India
| | | | - Naveen Arora
- Department of Genetics and Plant Breeding, Punjab Agricultural University (PAU), Ludhiana, India
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Khodakova AS, Vilchis DV, Blackburn D, Amanor F, Samuel BS. Population scale nucleic acid delivery to Caenorhabditis elegans via electroporation. G3 (BETHESDA, MD.) 2021; 11:jkab123. [PMID: 33872353 PMCID: PMC8495937 DOI: 10.1093/g3journal/jkab123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 03/16/2021] [Indexed: 11/14/2022]
Abstract
The free-living nematode Caenorhabditis elegans remains one of the most robust and flexible genetic systems for interrogating the complexities of animal biology. Targeted genetic manipulations, such as RNA interference (RNAi), CRISPR/Cas9- or array-based transgenesis, all depend on initial delivery of nucleic acids. Delivery of dsRNA by feeding can be effective, but the expression in Escherichia coli is not conducive to experiments intended to remain sterile or with defined microbial communities. Soaking-based delivery requires prolonged exposure of animals to high-material concentrations without a food source and is of limited throughput. Last, microinjection of individual animals can precisely deliver materials to animals' germlines, but is limited by the need to target and inject each animal one-by-one. Thus, we sought to address some of these challenges in nucleic acid delivery by developing a population-scale delivery method. We demonstrate efficient electroporation-mediated delivery of dsRNA throughout the worm and effective RNAi-based silencing, including in the germline. Finally, we show that guide RNA delivered by electroporation can be utilized by transgenic Cas9 expressing worms for population-scale genetic targeting. Together, these methods expand the scale and scope of genetic methodologies that can be applied to the C. elegans system.
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Affiliation(s)
- Anastasia S Khodakova
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- SMART Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daniela Vidal Vilchis
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dana Blackburn
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ferdinand Amanor
- SMART Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Buck S Samuel
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- SMART Program, Baylor College of Medicine, Houston, TX 77030, USA
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15
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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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16
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Ito Y, Taniguchi K, Kuranaga Y, Eid N, Inomata Y, Lee SW, Uchiyama K. Uptake of MicroRNAs from Exosome-Like Nanovesicles of Edible Plant Juice by Rat Enterocytes. Int J Mol Sci 2021; 22:3749. [PMID: 33916868 PMCID: PMC8038500 DOI: 10.3390/ijms22073749] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are small RNAs present in extracellular vesicles (EVs) that, when transferred to a target cell, affect its biological functions. Plant miRNAs regulate the expression of certain mammalian genes. Here, we characterized EVs in fruit and vegetable juice, and their miRNA cargo, and investigated whether such miRNA-containing EVs could be taken up by mammalian enterocytes in vitro. Using filtration and ultra-centrifugation methods, EVs were purified from commercially available and manually squeezed plant juice. EV morphological features and subcellular localization were analyzed using the NanoSight tracking system and electron microscopy. Plant EV miRNA levels were evaluated using quantitative reverse transcription PCR. For the in vitro EV uptake experiments, rat intestinal epithelial cells (IEC6) were used. Plant EVs shared morphological features with mammalian EVs and contained miR156a-5p, miR166a-3p, and miR168a-5p. EVs were present in the cell sap-filled central vacuoles and were taken up by IEC6 cells. Edible plant cells produce EVs that contain various miRNAs and release them into the central vacuole. The exogenous plant EVs are taken up by mammalian enterocytes in vitro. These findings suggest the possibility that exogenous plant miRNAs carried by EVs can be absorbed via the gastrointestinal tract.
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Affiliation(s)
- Yuko Ito
- Department of General and Gastrological Surgery, Osaka Medical College, 2-7, Takatsuki, Osaka 569-8686, Japan; (K.T.); (Y.I.); (S.-W.L.); (K.U.)
| | - Kohei Taniguchi
- Department of General and Gastrological Surgery, Osaka Medical College, 2-7, Takatsuki, Osaka 569-8686, Japan; (K.T.); (Y.I.); (S.-W.L.); (K.U.)
- Translational Research Program, Osaka Medical College, 2-7, Daigaku-cho, Takatsuki, Osaka 569-8686, Japan
| | - Yuki Kuranaga
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1, Yanagito, Gifu 501-1193, Japan;
| | - Nabil Eid
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box 17666 Al Ain, United Arab Emirates;
| | - Yosuke Inomata
- Department of General and Gastrological Surgery, Osaka Medical College, 2-7, Takatsuki, Osaka 569-8686, Japan; (K.T.); (Y.I.); (S.-W.L.); (K.U.)
| | - Sang-Woong Lee
- Department of General and Gastrological Surgery, Osaka Medical College, 2-7, Takatsuki, Osaka 569-8686, Japan; (K.T.); (Y.I.); (S.-W.L.); (K.U.)
| | - Kazuhisa Uchiyama
- Department of General and Gastrological Surgery, Osaka Medical College, 2-7, Takatsuki, Osaka 569-8686, Japan; (K.T.); (Y.I.); (S.-W.L.); (K.U.)
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17
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Wytinck N, Manchur CL, Li VH, Whyard S, Belmonte MF. dsRNA Uptake in Plant Pests and Pathogens: Insights into RNAi-Based Insect and Fungal Control Technology. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1780. [PMID: 33339102 PMCID: PMC7765514 DOI: 10.3390/plants9121780] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/07/2020] [Accepted: 12/13/2020] [Indexed: 12/11/2022]
Abstract
Efforts to develop more environmentally friendly alternatives to traditional broad-spectrum pesticides in agriculture have recently turned to RNA interference (RNAi) technology. With the built-in, sequence-specific knockdown of gene targets following delivery of double-stranded RNA (dsRNA), RNAi offers the promise of controlling pests and pathogens without adversely affecting non-target species. Significant advances in the efficacy of this technology have been observed in a wide range of species, including many insect pests and fungal pathogens. Two different dsRNA application methods are being developed. First, host induced gene silencing (HIGS) harnesses dsRNA production through the thoughtful and precise engineering of transgenic plants and second, spray induced gene silencing (SIGS) that uses surface applications of a topically applied dsRNA molecule. Regardless of the dsRNA delivery method, one aspect that is critical to the success of RNAi is the ability of the target organism to internalize the dsRNA and take advantage of the host RNAi cellular machinery. The efficiency of dsRNA uptake mechanisms varies across species, and in some uptake is negligible, rendering them effectively resistant to this new generation of control technologies. If RNAi-based methods of control are to be used widely, it is critically important to understand the mechanisms underpinning dsRNA uptake. Understanding dsRNA uptake mechanisms will also provide insight into the design and formulation of dsRNAs for improved delivery and provide clues into the development of potential host resistance to these technologies.
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Affiliation(s)
| | | | | | | | - Mark F. Belmonte
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (N.W.); (C.L.M.); (V.H.L.); (S.W.)
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18
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Kim IH, Kim DJ, Gwak WS, Woo SD. Increased survival of the honey bee Apis mellifera infected with the microsporidian Nosema ceranae by effective gene silencing. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2020; 105:e21734. [PMID: 32901985 DOI: 10.1002/arch.21734] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/20/2020] [Accepted: 08/20/2020] [Indexed: 06/11/2023]
Abstract
This study examined the control of nosemosis caused by Nosema ceranae, one of the hard-to-control diseases of honey bees, using RNA interference (RNAi) technology. Double-stranded RNA (dsRNA) for RNAi application targeted the mitosome-related genes of N. ceranae. Among the various mitosome-related genes, NCER_100882, NCER_101456, NCER_100157, and NCER_100686 exhibited relatively low homologies with the orthologs of Apis mellifera. Four gene-specific dsRNAs were prepared against the target genes and applied to the infected A. mellifera to analyze Nosema proliferation and honey bee survival. Two dsRNAs specifics to NCER_101456 and NCER_100157 showed high inhibitory effects on spore production by exhibiting only 62% and 67%, respectively, compared with the control. In addition, these dsRNA treatments significantly rescued the honey bees from the fatal nosemosis. It was confirmed that the inhibition of Nosema spore proliferation and the increase in the survival rate of honey bees were resulted from a decrease in the expression level of each target gene by dsRNA treatment. However, dsRNA mixture treatment was no more effective than single treatments in the rescue from the nosemosis. It is expected that the four newly identified mitosome-related target genes in this study can be effectively used for nosemosis control using RNAi technology.
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Affiliation(s)
- In-Hui Kim
- Department of Agricultural Biology, College of Agriculture, Life & Environment Science, Chungbuk National University, Cheongju, Republic of Korea
- Research Policy Bureau, Rural Development Administration, Jeonju, Republic of Korea
| | - Dong-Jun Kim
- Department of Agricultural Biology, College of Agriculture, Life & Environment Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Won-Seok Gwak
- Department of Agricultural Biology, College of Agriculture, Life & Environment Science, Chungbuk National University, Cheongju, Republic of Korea
- Vaccine Commercialization Center, Gyeongbuk Institute for Bio-Industry, Andong, Republic of Korea
| | - Soo-Dong Woo
- Department of Agricultural Biology, College of Agriculture, Life & Environment Science, Chungbuk National University, Cheongju, Republic of Korea
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19
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SIDT1-dependent absorption in the stomach mediates host uptake of dietary and orally administered microRNAs. Cell Res 2020; 31:247-258. [PMID: 32801357 PMCID: PMC8026584 DOI: 10.1038/s41422-020-0389-3] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/14/2020] [Indexed: 12/14/2022] Open
Abstract
Dietary microRNAs have been shown to be absorbed by mammals and regulate host gene expression, but the absorption mechanism remains unknown. Here, we show that SIDT1 expressed on gastric pit cells in the stomach is required for the absorption of dietary microRNAs. SIDT1-deficient mice show reduced basal levels and impaired dynamic absorption of dietary microRNAs. Notably, we identified the stomach as the primary site for dietary microRNA absorption, which is dramatically attenuated in the stomachs of SIDT1-deficient mice. Mechanistic analyses revealed that the uptake of exogenous microRNAs by gastric pit cells is SIDT1 and low-pH dependent. Furthermore, oral administration of plant-derived miR2911 retards liver fibrosis, and this protective effect was abolished in SIDT1-deficient mice. Our findings reveal a major mechanism underlying the absorption of dietary microRNAs, uncover an unexpected role of the stomach and shed light on developing small RNA therapeutics by oral delivery.
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20
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Svoboda P. Key Mechanistic Principles and Considerations Concerning RNA Interference. FRONTIERS IN PLANT SCIENCE 2020; 11:1237. [PMID: 32903622 PMCID: PMC7438612 DOI: 10.3389/fpls.2020.01237] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 07/28/2020] [Indexed: 05/03/2023]
Abstract
Canonical RNAi, one of the so-called RNA-silencing mechanisms, is defined as sequence-specific RNA degradation induced by long double-stranded RNA (dsRNA). RNAi occurs in four basic steps: (i) processing of long dsRNA by RNase III Dicer into small interfering RNA (siRNA) duplexes, (ii) loading of one of the siRNA strands on an Argonaute protein possessing endonucleolytic activity, (iii) target recognition through siRNA basepairing, and (iv) cleavage of the target by the Argonaute's endonucleolytic activity. This basic pathway diversified and blended with other RNA silencing pathways employing small RNAs. In some organisms, RNAi is extended by an amplification loop employing an RNA-dependent RNA polymerase, which generates secondary siRNAs from targets of primary siRNAs. Given the high specificity of RNAi and its presence in invertebrates, it offers an opportunity for highly selective pest control. The aim of this text is to provide an introductory overview of key mechanistic aspects of RNA interference for understanding its potential and constraints for its use in pest control.
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21
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Rosa MT, Loreto ELS. The Catenulida flatworm can express genes from its microbiome or from the DNA it ingests. Sci Rep 2019; 9:19045. [PMID: 31836792 PMCID: PMC6910973 DOI: 10.1038/s41598-019-55659-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/28/2019] [Indexed: 12/14/2022] Open
Abstract
Stenostomum are tiny planarians of the phylum Platyhelminthes that reproduce asexually. We transfected these worms using plasmids containing a gfp reporter gene. Here we show that they can express genes present in plasmids carried by bacteria and those that are encoded by naked DNA, such as plasmids or PCR fragments, transfected by electroporation; they can also express genes taken up during feeding. The microbiome associated with worm maintenance was evaluated, and the results indicated that when a plasmid is maintained in the microbiome, gfp gene expression is stable. When genes originate from naked DNA or bacteria not maintained in the microbiome, GFP expression is transient. Therefore, changes in the microbiome can modify the ability of worms to express foreign genes. In stable GFP-expressing worms, NSG showed that the gfp gene was maintained in the plasmid and was not integrated into the chromosome. These results suggest that, at least for some organisms such as flatworms, the expression of genes provided by the microbiome or the environment can be considered among the potential sources of phenotypic plasticity, which can have implications for evolvability.
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Affiliation(s)
| | - Elgion L S Loreto
- Department of Biochemistry and Molecular Biology, CCNE, Univ. Fed. de Santa Maria, Av. Roraima 1000, 97105-900, Santa Maria, RS, Brazil.
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22
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Nguyen TA, Smith BRC, Elgass KD, Creed SJ, Cheung S, Tate MD, Belz GT, Wicks IP, Masters SL, Pang KC. SIDT1 Localizes to Endolysosomes and Mediates Double-Stranded RNA Transport into the Cytoplasm. THE JOURNAL OF IMMUNOLOGY 2019; 202:3483-3492. [PMID: 31061008 DOI: 10.4049/jimmunol.1801369] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 04/14/2019] [Indexed: 12/15/2022]
Abstract
dsRNA is a common by-product of viral replication and acts as a potent trigger of antiviral immunity. SIDT1 and SIDT2 are closely related members of the SID-1 transmembrane family. SIDT2 functions as a dsRNA transporter and is required to traffic internalized dsRNA from endocytic compartments into the cytosol for innate immune activation, but the role of SIDT1 in dsRNA transport and in the innate immune response to viral infection is unclear. In this study, we show that Sidt1 expression is upregulated in response to dsRNA and type I IFN exposure and that SIDT1 interacts with SIDT2. Moreover, similar to SIDT2, SIDT1 localizes to the endolysosomal compartment, interacts with the long dsRNA analog poly(I:C), and, when overexpressed, enhances endosomal escape of poly(I:C) in vitro. To elucidate the role of SIDT1 in vivo, we generated SIDT1-deficient mice. Similar to Sidt2-/- mice, SIDT1-deficient mice produced significantly less type I IFN following infection with HSV type 1. In contrast to Sidt2-/- mice, however, SIDT1-deficient animals showed no impairment in survival postinfection with either HSV type 1 or encephalomyocarditis virus. Consistent with this, we observed that, unlike SIDT2, tissue expression of SIDT1 was relatively restricted, suggesting that, whereas SIDT1 can transport extracellular dsRNA into the cytoplasm following endocytosis in vitro, the transport activity of SIDT2 is likely to be functionally dominant in vivo.
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Affiliation(s)
- Tan A Nguyen
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Blake R C Smith
- Murdoch Children's Research Institute, Parkville, Victoria 3052, Australia
| | - Kirstin D Elgass
- Monash Micro Imaging, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia
| | - Sarah J Creed
- Monash Micro Imaging, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia
| | - Shane Cheung
- Monash Micro Imaging, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia
| | - Michelle D Tate
- Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, Victoria 3168, Australia; and
| | - Gabrielle T Belz
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Ian P Wicks
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Seth L Masters
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Ken C Pang
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; .,Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia.,Murdoch Children's Research Institute, Parkville, Victoria 3052, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria 3052, Australia
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23
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Veremeyko T, Kuznetsova IS, Dukhinova M, W Y Yung A, Kopeikina E, Barteneva NS, Ponomarev ED. Neuronal extracellular microRNAs miR-124 and miR-9 mediate cell-cell communication between neurons and microglia. J Neurosci Res 2018; 97:162-184. [PMID: 30367726 PMCID: PMC6587827 DOI: 10.1002/jnr.24344] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/27/2018] [Accepted: 09/28/2018] [Indexed: 12/21/2022]
Abstract
In contrast to peripheral macrophages, microglia in the central nervous system (CNS) exhibit a specific deactivated phenotype; however, it is not clear how this phenotype is maintained. Two alternative hypotheses were postulated recently: (a) microglia differ from peripheral macrophages being derived from the yolk sac (YS), whereas peripheral macrophages originate from bone marrow (BM); (b) microglia acquire a specific phenotype under the influence of the CNS microenvironment. We have previously shown that microglia express miR-124, which was also induced in BM-derived macrophages co-cultured with a neurons. We here investigated the possibility of horizontal transfer of the neuron-specific microRNAs miR-124 and miR-9 from primary neurons to microglia/macrophages. We found that after incubation with neuronal conditioned media (NCM), macrophages downregulated activation markers MHC class II and CD45. Neither cultured adult microglia nor YS- and BM-derived macrophages demonstrated intrinsic levels of miR-124 expression. However, after incubation with NCM, miR-124 was induced in both YS- and BM-derived macrophages. Biochemical analysis demonstrated that the NCM contained miR-124 and miR-9 in complex with small proteins, large high-density lipoproteins (HDLs), and exosomes. MiR-124 and miR-9 were promptly released from neurons, and this process was inhibited by tetrodotoxin, indicating an important role of neuronal electric activity in secretion of these microRNAs. Incubation of macrophages with exogenous miR-124 resulted in efficient translocation of miR-124 into the cytoplasm. This study demonstrates an important role of neuronal miRNAs in communication of neurons with microglia, which favors the hypothesis that microglia acquire a specific phenotype under the influence of the CNS microenvironment.
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Affiliation(s)
- Tatyana Veremeyko
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Inna S Kuznetsova
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Marina Dukhinova
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Amanda W Y Yung
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ekaterina Kopeikina
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Natasha S Barteneva
- Program in Cellular and Molecular Medicine, Children's Hospital Boston and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts.,School of Science and Technology, Nazarbayev University, Astana, Kazakhstan
| | - Eugene D Ponomarev
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong.,Kunming Institute of Zoology, Chinese University of Hong Kong Joint Laboratory of Bioresources and Molecular Research of Common Diseases, Kunmin, China
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24
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Abstract
In the nematode Caenorhabditis elegans, RNA interference (RNAi) triggered by double-stranded RNA (dsRNA) spreads systemically to cause gene silencing throughout the organism and its progeny. We confirm that Caenorhabditis nematode SID-1 orthologs have dsRNA transport activity and demonstrate that the SID-1 paralog CHUP-1 does not transport dsRNA. Sequence comparison of these similar proteins, in conjunction with analysis of loss-of-function missense alleles, identifies several conserved 2–7 amino acid microdomains within the extracellular domain (ECD) that are important for dsRNA transport. Among these missense alleles, we identify and characterize a sid-1 allele, qt95, which causes tissue-specific silencing defects most easily explained as a systemic RNAi export defect. However, we conclude from genetic and biochemical analyses that sid-1(qt95) disrupts only import, and speculate that the apparent export defect is caused by the cumulative effect of sequentially impaired dsRNA import steps. Thus, consistent with previous studies, we fail to detect a requirement for sid-1 in dsRNA export, but demonstrate for the first time that SID-1 functions in the intestine to support environmental RNAi (eRNAi).
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25
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Evangelista CCS, Guidelli GV, Borges G, Araujo TF, Souza TAJD, Neves UPDC, Tunnacliffe A, Pereira TC. Multiple genes contribute to anhydrobiosis (tolerance to extreme desiccation) in the nematode Panagrolaimus superbus. Genet Mol Biol 2017; 40:790-802. [PMID: 29111563 PMCID: PMC5738622 DOI: 10.1590/1678-4685-gmb-2017-0030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 07/20/2017] [Indexed: 11/21/2022] Open
Abstract
The molecular basis of anhydrobiosis, the state of suspended animation entered by some species during extreme desiccation, is still poorly understood despite a number of transcriptome and proteome studies. We therefore conducted functional screening by RNA interference (RNAi) for genes involved in anhydrobiosis in the holo-anhydrobiotic nematode Panagrolaimus superbus. A new method of survival analysis, based on staining, and proof-of-principle RNAi experiments confirmed a role for genes involved in oxidative stress tolerance, while a novel medium-scale RNAi workflow identified a further 40 anhydrobiosis-associated genes, including several involved in proteostasis, DNA repair and signal transduction pathways. This suggests that multiple genes contribute to anhydrobiosis in P. superbus.
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Affiliation(s)
- Cláudia Carolina Silva Evangelista
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, SP, Brazil.,Programa de Pós-Graduação em Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Giovanna Vieira Guidelli
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Gustavo Borges
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Thais Fenz Araujo
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Tiago Alves Jorge de Souza
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, SP, Brazil.,Programa de Pós-Graduação em Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Ubiraci Pereira da Costa Neves
- Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Alan Tunnacliffe
- Deptartment of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Tiago Campos Pereira
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, SP, Brazil.,Programa de Pós-Graduação em Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, SP, Brazil
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26
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Shpak N, Manor R, Abilevich LK, Mantal O, Shavit K, Aflalo ED, Toiber D, Sagi A. Short versus long double-stranded RNA activation of a post-transcriptional gene knockdown pathway. RNA Biol 2017; 14:1766-1775. [PMID: 28816598 DOI: 10.1080/15476286.2017.1356567] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
RNA interference (RNAi) utilizes a conserved cellular autoimmune defense mechanism involving the internalization of dsRNA into cells and the activation of a set of RNAi related genes. Using RNAi, complete sex reversal is achievable in males of the prawn Macrobrachium rosenbergii by knocking down the transcript level of an insulin-like androgenic gland hormone (Mr-IAG) through injections of dsRNA of the entire Mr-IAG ORF sequence (dsMr-IAG - 518bp). Interestingly, in-vivo knockdown success and dsMr-IAG lengths seemed to correlate, with long dsRNA being the most effective and short dsRNA fragments showing no effect. However, little is known about the RNAi machinery in M. rosenbergii. We discovered the Mr-Dicer and Mr-Argonaute gene families, associated with the major knockdown pathways, in our M. rosenbergii transcriptomic library. In response to dsMr-IAG administration, only post-transcriptional pathway-related gene transcript levels were upregulated. In addition, a passive dsRNA channel (a SID1 gene ortholog) that allows external dsRNA to enter cells was found. Its function was validated by observing Mr-SID1 specific upregulation dependent on dsRNA lengths, while attempted loss-of-function experiments were lethal. Our results, which suggest differential systemic responses to dsRNA lengths, provide evidence that the above RNAi-based manipulation occurs via the post-transcriptional pathway. The temporal nature of the latter pathway supports the safety of using such RNAi-based biotechnologies in aquaculture and environmental applications. Unlike reports of RNAi driven by the administration of small dsRNA fragments in-vitro, the case presented here demonstrates length dependency in-vivo, suggesting further complexity in the context of the entire organism.
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Affiliation(s)
- Nir Shpak
- a Department of Life Sciences , Ben-Gurion University of the Negev , Beer-Sheva , Israel
| | - Rivka Manor
- a Department of Life Sciences , Ben-Gurion University of the Negev , Beer-Sheva , Israel
| | - Lihie Katzir Abilevich
- a Department of Life Sciences , Ben-Gurion University of the Negev , Beer-Sheva , Israel
| | - Ortal Mantal
- a Department of Life Sciences , Ben-Gurion University of the Negev , Beer-Sheva , Israel
| | - Keshet Shavit
- a Department of Life Sciences , Ben-Gurion University of the Negev , Beer-Sheva , Israel
| | - Eliahu D Aflalo
- a Department of Life Sciences , Ben-Gurion University of the Negev , Beer-Sheva , Israel
| | - Debra Toiber
- a Department of Life Sciences , Ben-Gurion University of the Negev , Beer-Sheva , Israel
| | - Amir Sagi
- a Department of Life Sciences , Ben-Gurion University of the Negev , Beer-Sheva , Israel.,b National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev , Beer-Sheva , Israel
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27
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Genome-Wide RNAi Screens for RNA Processing Events in Drosophila melanogaster S2 Cells. Methods Mol Biol 2017. [PMID: 28766301 DOI: 10.1007/978-1-4939-7204-3_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Over the past 10 years, the design and application of genome-wide screening (GWS) has improved to the point that it can now be done at level of the individual laboratory. The advantages of GWSs compared to classical genetic screens include: immediate identification of a positive scoring gene, relatively short period of time necessary to conduct the screen (as little as 1 week), cell lines do not present developmental needs for gene expression that an organism normally would, and validation/confirmation of results is straightforward. Here, we describe a general protocol for GWS to be conducted in Drosophila melanogaster S2 cells. We provide specific details on what type of experiments must be done before initiating a screen, the materials that are required to conduct a screen, and make suggestions on methods to carry out secondary screening and counter-screening once the initial GWS is complete. Multiple considerations are also raised that focus on how to anticipate false positives/negatives and how to minimize their occurrence through intelligent design. Finally, we provide specific examples of data that our group has gathered from published genome-wide screens in order to exemplify how "hits" are scored and confirmed.
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28
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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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29
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Chan SY, Snow JW. Uptake and impact of natural diet-derived small RNA in invertebrates: Implications for ecology and agriculture. RNA Biol 2017; 14:402-414. [PMID: 27763816 PMCID: PMC5411125 DOI: 10.1080/15476286.2016.1248329] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/05/2016] [Accepted: 10/10/2016] [Indexed: 02/08/2023] Open
Abstract
The putative transfer and gene regulatory activities of diet-derived small RNAs (sRNAs) in ingesting animals are still debated. The existence of natural uptake of diet-derived sRNA by invertebrate species could have significant implication for our understanding of ecological relationships and could synergize with efforts to use RNA interference (RNAi) technology in agriculture. Here, we synthesize information gathered from studies in invertebrates using natural or artificial dietary delivery of sRNA and from studies of sRNA in vertebrate animals and plants to review our current understanding of uptake and impact of natural diet-derived sRNA on invertebrates. Our understanding has been influenced and sometimes confounded by the diversity of invertebrates and ingested plants studied, our limited insights into how gene expression may be modulated by dietary sRNAs at the mechanistic level, and the paucity of studies focusing directly on natural uptake of sRNA. As such, we suggest 2 strategies to investigate this phenomenon more comprehensively and thus facilitate the realization of its potentially broad impact on ecology and agriculture in the future.
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Affiliation(s)
- Stephen Y. Chan
- Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
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30
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Lukasik A, Zielenkiewicz P. Plant MicroRNAs-Novel Players in Natural Medicine? Int J Mol Sci 2016; 18:ijms18010009. [PMID: 28025496 PMCID: PMC5297644 DOI: 10.3390/ijms18010009] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 12/14/2016] [Accepted: 12/16/2016] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) represent a class of small non-coding RNAs that act as efficient gene expression regulators and thus play many important roles in living organisms. Due to their involvement in several known human pathological and pathogenic states, miRNA molecules have become an important issue in medicine and gained the attention of scientists from the pharmaceutical industry. In recent few years, a growing number of studies have provided evidence that miRNAs may be transferred from one species to another and regulate gene expression in the recipients’ cells. The most intriguing results revealed that stable miRNAs derived from food plants may enter the mammals’ circulatory system and, after reaching the target, inhibit the production of specific mammalian protein. Part of the scientific community has perceived this as an attractive hypothesis that may provide a foundation for novel therapeutic approaches. In turn, others are convinced about the “false positive” effect of performed experiments from which the mentioned results were achieved. In this article, we review the recent literature that provides evidence (from both fronts) of dietary, plant miRNA uptake and functionality in various consumers. Additionally, we discuss possible miRNA transport mechanisms from plant food sources to human cells.
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Affiliation(s)
- Anna Lukasik
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Piotr Zielenkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
- Department of Plant Molecular Biology, Institute of Experimental Plant Biology and Biotechnology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
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31
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Itsathitphaisarn O, Thitamadee S, Weerachatyanukul W, Sritunyalucksana K. Potential of RNAi applications to control viral diseases of farmed shrimp. J Invertebr Pathol 2016; 147:76-85. [PMID: 27867019 DOI: 10.1016/j.jip.2016.11.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 11/02/2016] [Accepted: 11/07/2016] [Indexed: 01/08/2023]
Abstract
Viral pathogens pose a primary threat to global shrimp aquaculture. Despite the urgent industry need for them, practical anti-viral control methods are unavailable due, in part, to lack of an adaptive immune response in crustaceans that renders conventional vaccination methods ineffective. One currently studied method of high interest for protecting shrimp against viral infection relies on the post-transcriptional gene silencing mechanism called RNA interference (RNAi) that is induced by gene-specific constructs of double stranded RNA (dsRNA). Although this approach was first described for successful protection of shrimp against white spot disease (WSD) by injecting dsRNA specific to genes of white spot syndrome virus (WSSV) into shrimp in the laboratory in 2005 no practical method for use of dsRNA in shrimp farms has been developed to date. The apparent bottleneck for farm-scale applications of RNAi-mediated viral control in shrimp aquaculture is the lack of simple and cost-effective delivery methods. This review summarizes recent studies on use and delivery of dsRNA to shrimp via injection and oral routes in hatcheries and on farms and it discusses the research directions that might lead to development of practical methods for applications with farmed shrimp. Oral delivery methods tested so far include use of dsRNA-expressing bacteria as a component of dry feed pellets or use of living brine shrimp (Artemia) pre-fed with dsRNA before they are fed to shrimp. Also tested have been dsRNA enclosed in nanocontainers including chitosan, liposomes and viral-like particles (VLP) before direct injection or use as components of feed pellets for hatchery or pond-reared shrimp.
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Affiliation(s)
- Ornchuma Itsathitphaisarn
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Siripong Thitamadee
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Bangkok 10400, Thailand; Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Wattana Weerachatyanukul
- Department of Anatomy and Structural Biology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Kallaya Sritunyalucksana
- Shrimp-Pathogen Interaction (SPI) Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Yothi Office, Rama VI Rd., Bangkok 10400, Thailand.
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32
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Fishilevich E, Vélez AM, Storer NP, Li H, Bowling AJ, Rangasamy M, Worden SE, Narva KE, Siegfried BD. RNAi as a management tool for the western corn rootworm, Diabrotica virgifera virgifera. PEST MANAGEMENT SCIENCE 2016; 72:1652-1663. [PMID: 27218412 DOI: 10.1002/ps.4324] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Revised: 04/27/2016] [Accepted: 05/13/2016] [Indexed: 06/05/2023]
Abstract
The western corn rootworm (WCR), Diabrotica virgifera virgifera, is the most important pest of corn in the US Corn Belt. Economic estimates indicate that costs of control and yield loss associated with WCR damage exceed $US 1 billion annually. Historically, corn rootworm management has been extremely difficult because of its ability to evolve resistance to both chemical insecticides and cultural control practices. Since 2003, the only novel commercialized developments in rootworm management have been transgenic plants expressing Bt insecticidal proteins. Four transgenic insecticidal proteins are currently registered for rootworm management, and field resistance to proteins from the Cry3 family highlights the importance of developing traits with new modes of action. One of the newest approaches for controlling rootworm pests involves RNA interference (RNAi). This review describes the current understanding of the RNAi mechanisms in WCR and the use of this technology for WCR management. Further, the review addresses ecological risk assessment of RNAi and insect resistance management of RNAi for corn rootworm. © 2016 Society of Chemical Industry.
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Affiliation(s)
| | - Ana M Vélez
- Department of Entomology, University of Nebraska, Lincoln, NE, USA
| | | | | | | | | | | | | | - Blair D Siegfried
- Entomology and Nematology Department, University of Florida, Gainesville, FL, USA
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33
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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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34
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Li W, Koutmou KS, Leahy DJ, Li M. Systemic RNA Interference Deficiency-1 (SID-1) Extracellular Domain Selectively Binds Long Double-stranded RNA and Is Required for RNA Transport by SID-1. J Biol Chem 2015; 290:18904-13. [PMID: 26067272 DOI: 10.1074/jbc.m115.658864] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Indexed: 12/26/2022] Open
Abstract
During systemic RNA interference (RNAi) in Caenorhabditis elegans, RNA spreads across different cells and tissues in a process that requires the systemic RNA interference deficient-1 (sid-1) gene, which encodes an integral membrane protein. SID-1 acts cell-autonomously and is required for cellular import of interfering RNAs. Heterologous expression of SID-1 in Drosophila Schneider 2 cells enables passive uptake of dsRNA and subsequent soaking RNAi. Previous studies have suggested that SID-1 may serve as an RNA channel, but its precise molecular role remains unclear. To test the hypothesis that SID-1 mediates a direct biochemical recognition of RNA molecule and subsequent permeation, we expressed the extracellular domain (ECD) of SID-1 and purified it to near homogeneity. Recombinant purified SID-1 ECD selectively binds dsRNA but not dsDNA in a length-dependent and sequence-independent manner. Genetic missense mutations in SID-1 ECD causal for deficient systemic RNAi resulted in significant reduction in its affinity for dsRNA. Furthermore, full-length proteins with these mutations decrease SID-1-mediated RNA transport efficiency, providing evidence that dsRNA binding to SID-1 ECD is related to RNA transport. To examine the functional similarity of mammalian homologs of SID-1 (SIDT1 and SIDT2), we expressed and purified mouse SIDT1 and SIDT2 ECDs. We show that they bind long dsRNA in vitro, supportive of dsRNA recognition. In summary, our study illustrates the functional importance of SID-1 ECD as a dsRNA binding domain that contributes to RNA transport.
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Affiliation(s)
- Weiqiang Li
- From the Solomon H. Snyder Department of Neuroscience, the Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 and
| | | | - Daniel J Leahy
- the Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 and
| | - Min Li
- From the Solomon H. Snyder Department of Neuroscience, GlaxoSmithKline, King of Prussia, Pennsylvania 19406
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35
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Sela M, Kloog Y, Rechavi O. Non-coding RNAs as the bridge between epigenetic mechanisms, lineages and domains of life. J Physiol 2015; 592:2369-73. [PMID: 24882818 DOI: 10.1113/jphysiol.2014.273045] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Many cases of heritable environmental responses have been documented but the underlying mechanisms are largely unknown. Recently, inherited RNA interference has been shown to act as a multigenerational genome surveillance apparatus. We suggest that inheritance of regulatory RNAs is at the root of many other epigenetic phenomena, the trigger that induces other epigenetic mechanisms, such as the depositing of histone modifications and DNA methylation. In addition, we explore the possibility that interacting organisms influence each other's transcriptomes by exchanging heterologous non-coding RNAs.
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Affiliation(s)
- Mor Sela
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 64332, Israel
| | - Yoel Kloog
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 64332, Israel
| | - Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 64332, Israel
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36
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The Tribolium castaneum cell line TcA: a new tool kit for cell biology. Sci Rep 2014; 4:6840. [PMID: 25354547 PMCID: PMC4213800 DOI: 10.1038/srep06840] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 10/13/2014] [Indexed: 11/08/2022] Open
Abstract
The red flour beetle, Tribolium castaneum, is an agriculturally important insect pest that has been widely used as a model organism. Recently, an adherent cell line (BCIRL-TcA-CLG1 or TcA) was developed from late pupae of the red flour beetle. Next generation transcriptome sequencing of TcA cells demonstrated expression of a wide variety of genes associated with specialized functions in chitin metabolism, immune responses and cellular and systemic RNAi pathways. Accordingly, we evaluated the sensitivity of TcA cells to dsRNA to initiate an RNAi response. TcA cells were highly sensitive to minute amounts of dsRNA, with a minimum effective dose of 100 pg/mL resulting in significant suppression of gene expression. We have also developed a plasmid containing two TcA-specific promoters, the promoter from the 40S ribosomal protein subunit (TC006550) and a bi-directional heat shock promoter (TcHS70) from the intergenic space between heat shock proteins 68a and b. These promoters have been employed to provide high levels of either constitutive (TC006550) or inducible (TcHS70) gene expression of the reporter proteins. Our results show that the TcA cell line, with its sensitivity to RNAi and functional TcA-specific promoters, is an invaluable resource for studying basic molecular and physiological questions.
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Xu J, Yoshimura K, Mon H, Li Z, Zhu L, Iiyama K, Kusakabe T, Lee JM. Establishment of Caenorhabditis elegans SID-1-dependent DNA delivery system in cultured silkworm cells. Mol Biotechnol 2014; 56:193-8. [PMID: 23979877 DOI: 10.1007/s12033-013-9694-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The systemic RNA interference defective-1 (SID-1) can transport double-stranded RNA (dsRNA) into cytosol across the cytoplasmic membrane. We report here that ectopic expression of Caenorhabditis elegans SID-1 allows BmN4 cells to import extracellular plasmid dsDNA into cells via the direct soaking method. Interestingly, BmN4-SID1 cells incorporate dsRNA and plasmid DNA simultaneously. Furthermore, the ectopic SID-1 allows us to establish a stably transformed cell line by the simple soaking method. Our results provide an alternative method for silkworm gene function analysis with low cost and low cell toxicity.
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Affiliation(s)
- Jian Xu
- Laboratory of Silkworm Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, 6-10-1 Hakozaki Higashi-ku, Fukuoka, 812-8581, Japan
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38
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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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Establishment of a soaking RNA interference and Bombyx mori nucleopolyhedrovirus (BmNPV)-hypersensitive cell line using Bme21 cell. Appl Microbiol Biotechnol 2013; 97:10435-44. [DOI: 10.1007/s00253-013-5279-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 09/12/2013] [Accepted: 09/17/2013] [Indexed: 10/26/2022]
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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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Abstract
Systemic RNAi, the intercellular spreading of RNAi silencing, requires SID-1 and SID-3 to import silencing signals in Caenorhabditis elegans. How are these signals exported? SID-5, an endosome-associated protein, is a candidate for the job.
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Affiliation(s)
- Christian E Rocheleau
- Division of Endocrinology and Metabolism, Department of Medicine, McGill University and the Research Institute of the McGill University Health Centre, Montreal, Quebec H3A 0C7, Canada.
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42
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Xu J, Nagata Y, Mon H, Li Z, Zhu L, Iiyama K, Kusakabe T, Lee JM. Soaking RNAi-mediated modification of Sf9 cells for baculovirus expression system by ectopic expression of Caenorhabditis elegans SID-1. Appl Microbiol Biotechnol 2013; 97:5921-31. [PMID: 23467826 DOI: 10.1007/s00253-013-4785-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 02/13/2013] [Accepted: 02/15/2013] [Indexed: 12/17/2022]
Abstract
RNA interference (RNAi) is a biological phenomenon that silences the expression of genes of interest. Passive double-stranded RNA (dsRNA) uptake has been uniquely observed in Caenorhabditis elegans due to the expression of systemic RNAi defective-1 (SID-1). We report that ectopic expression of CeSID-1 endows the Sf9 cells with a capacity for soaking RNAi. Soaking the Sf9-SID1 with dsRNA corresponding to either exogenous or endogenous target genes induced a significant decrease in the amount of mRNA or protein. These results enabled us to modify the target proteins of baculovirus expression vector system in both quantities and posttranslational modifications. The current low-cost and high-efficiency RNAi system is useful for high-throughput gene function analysis and mass production of recombinant protein.
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Affiliation(s)
- Jian Xu
- Laboratory of Silkworm Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, 6-10-1 Hakozaki Higashi-ku, Fukuoka 812-8581, Japan
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43
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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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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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McEwan DL, Weisman AS, Hunter CP. Uptake of extracellular double-stranded RNA by SID-2. Mol Cell 2012; 47:746-54. [PMID: 22902558 DOI: 10.1016/j.molcel.2012.07.014] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Revised: 05/10/2012] [Accepted: 07/10/2012] [Indexed: 01/25/2023]
Abstract
Ingested dsRNAs trigger RNA interference (RNAi) in many invertebrates, including the nematode Caenorhabditis elegans. Here we show that the C. elegans apical intestinal membrane protein SID-2 is required in C. elegans for the import of ingested dsRNA and that, when expressed in Drosophila S2 cells, SID-2 enables the uptake of dsRNAs. SID-2-dependent dsRNA transport requires an acidic extracellular environment and is selective for dsRNAs with at least 50 base pairs. Through structure-function analysis, we identify several SID-2 regions required for this activity, including three extracellular, positively charged histidines. Finally, we find that SID-2-dependent transport is inhibited by drugs that interfere with vesicle transport. Therefore, we propose that environmental dsRNAs are imported from the acidic intestinal lumen by SID-2 via endocytosis and are released from internalized vesicles in a secondary step mediated by the dsRNA channel SID-1. Similar multistep mechanisms may underlie the widespread observations of environmental RNAi.
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Affiliation(s)
- Deborah L McEwan
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
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Abstract
In the nematode Caenorhabditis elegans (C. elegans), gene inactivation by RNA interference can achieve remarkable potency due to the amplification of initial silencing triggers by RNA-dependent RNA polymerases (RdRPs). RdRPs catalyze the biogenesis of an abundant species of secondary small interfering RNAs (siRNAs) using the target mRNA as template. The interaction between primary siRNAs derived from the exogenous double-stranded RNA (dsRNA) trigger and the target mRNA is required for the recruitment of RdRPs. Other genetic requirements for RdRP activities have not been characterized. Recent studies have identified the RDE-10/RDE-11 complex which interacts with the primary siRNA bound target mRNA and acts upstream of the RdRPs. rde-10 and rde-11 mutants show an RNAi defective phenotype because the biogenesis of secondary siRNAs is completely abolished. In addition, the RDE-10/RDE-11 complex plays a similar role in the endogenous RNAi pathway for the biogenesis of a subset of siRNAs targeting recently acquired, duplicated genes.
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Affiliation(s)
- Chi Zhang
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
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Pratt AJ, Rambo RP, Lau PW, MacRae IJ. Preparation and characterization of the extracellular domain of human Sid-1. PLoS One 2012; 7:e33607. [PMID: 22509261 PMCID: PMC3324469 DOI: 10.1371/journal.pone.0033607] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 02/13/2012] [Indexed: 11/18/2022] Open
Abstract
In C. elegans, the cell surface protein Sid-1 imports extracellular dsRNA into the cytosol of most non-neuronal cells, enabling systemic spread of RNA interference (RNAi) throughout the worm. Sid-1 homologs are found in many other animals, although for most a function for the protein has not yet been established. Sid-1 proteins are composed of an N-terminal extracellular domain (ECD) followed by 9-12 predicted transmembrane regions. We developed a baculovirus system to express and purify the ECD of the human Sid-1 protein SidT1. Recombinant SidT1 ECD is glycosylated and spontaneously assembles into a stable and discrete tetrameric structure. Electron microscopy (EM) and small angle x-ray scattering (SAXS) studies reveal that the SidT1 ECD tetramer is a compact, puck-shaped globular particle, which we hypothesize may control access of dsRNA to the transmembrane pore. These characterizations provide inroads towards understanding the mechanism of this unique RNA transport system from structural prospective.
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Affiliation(s)
- Ashley J. Pratt
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Robert P. Rambo
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Pick-Wei Lau
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Ian J. MacRae
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
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Abstract
Mammalian cells resist the uptake of nucleic acids. The lipid bilayer of the plasma membrane presents one barrier. Here, we report on a second physicochemical barrier for uptake. To create a sensitive probe for nucleic acid-cell interactions, we synthesized fluorescent conjugates in which lipids are linked to DNA oligonucleotides. We found that these conjugates incorporate readily into the plasma membrane but are not retained there. Expulsion of lipid-oligonucleotide conjugates from the plasma membrane increases with oligonucleotide length. Conversely, the incorporation of conjugates increases markedly in cells that lack the major anionic components of the glycocalyx, sialic acid and glycosaminoglycans, and in cells that had incorporated highly cationic lipids into their plasma membrane. We conclude that anionic oligosaccharides provide a formidable barrier to the uptake of nucleic acids by mammalian cells. This conclusion has implications for genomic stability, as well as the delivery of genes and siRNAs into mammalian cells.
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Affiliation(s)
- Michael J Palte
- Medical Scientist Training Program, Molecular & Cellular Pharmacology Graduate Training Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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Kobayashi I, Tsukioka H, Kômoto N, Uchino K, Sezutsu H, Tamura T, Kusakabe T, Tomita S. SID-1 protein of Caenorhabditis elegans mediates uptake of dsRNA into Bombyx cells. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2012; 42:148-154. [PMID: 22178129 DOI: 10.1016/j.ibmb.2011.11.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Revised: 11/28/2011] [Accepted: 11/29/2011] [Indexed: 05/28/2023]
Abstract
RNA interference is one of the most revolutionary tools in the study of gene function, particularly in non-model systems. However, in Bombyx mori, as with many lepidopteran species, attempts at systemic RNAi have had mixed success. Gene identification and phylogenetic analyses suggest that Bombyx has the core RNAi machinery, which is necessary to undergo RNAi as a cellular response. We introduced sid genes from Caenorhabditis elegans into Bombyx BmN4 cells to enhance the uptake of dsRNA and revealed that the SID-1 protein, but not SID-2, has the ability to endow the RNAi effect with the addition of dsRNA to the medium. Observed RNAi effect was dependent on both the levels of sid-1 expression and the concentration of the dsRNA. These results suggest that SID-1 promotes the uptake of dsRNA from the medium into Bombyx cells. We generated transgenic animals that express sid-1 but have not detected significant enhancements of in vivo phenotype in response to the injection of the dsRNA into hemocoel.
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Affiliation(s)
- Isao Kobayashi
- Transgenic Silkworm Research Unit, National Institute of Agrobiological Sciences, 1-2 Ohwashi, Tsukuba, Ibaraki 305-8634, Japan
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Abstract
SUMMARYAlmost a decade has passed since the first report of RNA interference (RNAi) in a parasitic helminth. Whilst much progress has been made with RNAi informing gene function studies in disparate nematode and flatworm parasites, substantial and seemingly prohibitive difficulties have been encountered in some species, hindering progress. An appraisal of current practices, trends and ideals of RNAi experimental design in parasitic helminths is both timely and necessary for a number of reasons: firstly, the increasing availability of parasitic helminth genome/transcriptome resources means there is a growing need for gene function tools such as RNAi; secondly, fundamental differences and unique challenges exist for parasite species which do not apply to model organisms; thirdly, the inherent variation in experimental design, and reported difficulties with reproducibility undermine confidence. Ideally, RNAi studies of gene function should adopt standardised experimental design to aid reproducibility, interpretation and comparative analyses. Although the huge variations in parasite biology and experimental endpoints make RNAi experimental design standardization difficult or impractical, we must strive to validate RNAi experimentation in helminth parasites. To aid this process we identify multiple approaches to RNAi experimental validation and highlight those which we deem to be critical for gene function studies in helminth parasites.
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