1
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Zhao Y, Chen J, Wang R, Pu X, Wang D. A review of transgenerational and multigenerational toxicology in the in vivo model animal Caenorhabditis elegans. J Appl Toxicol 2023; 43:122-145. [PMID: 35754092 DOI: 10.1002/jat.4360] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/09/2022] [Accepted: 06/24/2022] [Indexed: 11/09/2022]
Abstract
A large number of pollutants existing in the environment can last for a long time, and their potential toxic effects can transfer from parents to their offspring. Thus, it is necessary to investigate the toxicity of environmental pollutants across multigenerations and the underlying mechanisms in organisms. Due to its short life cycle and sensitivity to environmental exposures, Caenorhabditis elegans is an important animal model for toxicity assessment of environmental pollutants across multigenerations. In this review, we introduced the transgenerational and multigenerational toxicity caused by various environmental pollutants in C. elegans. Moreover, we discussed the underlying mechanisms for the observed transgenerational and multigenerational toxicity of environmental contaminants in C. elegans.
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Affiliation(s)
- Yunli Zhao
- Medical School, Southeast University, Nanjing, China.,School of Public Health, Bengbu Medical College, Bengbu, China
| | - Jingya Chen
- School of Public Health, Bengbu Medical College, Bengbu, China
| | - Rui Wang
- School of Public Health, Bengbu Medical College, Bengbu, China
| | - Xiaoxiao Pu
- School of Public Health, Bengbu Medical College, Bengbu, China
| | - Dayong Wang
- Medical School, Southeast University, Nanjing, China
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2
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Priyadarshini M, AlHarbi S, Frøkjær-Jensen C. Acute and inherited piRNA-mediated silencing in a rde-3 ribonucleotidyltransferase mutant. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000638. [PMID: 36188099 PMCID: PMC9520340 DOI: 10.17912/micropub.biology.000638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/04/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022]
Abstract
We recently developed a piRNA-based silencing assay (piRNAi) to study small-RNA mediated epigenetic silencing: acute gene silencing is induced by synthetic piRNAs expressed from extra-chromosomal array and transgenerational inheritance can be quantified after array loss. The assay allows inheritance assays by injecting piRNAs directly into mutant animals and targeting endogenous genes ( e.g. , him-5 and him-8 ) with obvious phenotypes (increased male frequency). Here we demonstrate the piRNAi assay by quantifying acute and inherited silencing in the ribonucleotidyltransferase rde-3 (ne3370) mutant. In the absence of rde-3, acute silencing was reduced but still detectable, whereas inherited silencing was abolished.
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Affiliation(s)
- Monika Priyadarshini
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division (BESE), KAUST Environmental Epigenetics Program (KEEP), Thuwal, 23955-6900, Saudi Arabia
,
Current address: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sarah AlHarbi
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division (BESE), KAUST Environmental Epigenetics Program (KEEP), Thuwal, 23955-6900, Saudi Arabia
| | - Christian Frøkjær-Jensen
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division (BESE), KAUST Environmental Epigenetics Program (KEEP), Thuwal, 23955-6900, Saudi Arabia
,
Correspondence to: Christian Frøkjær-Jensen (
)
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3
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Guo X, Yuan J, Song X, Wang X, Sun Q, Tian J, Li X, Ding M, Liu Y. Bacteria metabolites from Peganum harmala L. polysaccharides inhibits polyQ aggregation through proteasome-mediated protein degradation in C. elegans. Int J Biol Macromol 2020; 161:681-691. [PMID: 32544588 DOI: 10.1016/j.ijbiomac.2020.06.091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/30/2020] [Accepted: 06/10/2020] [Indexed: 12/31/2022]
Abstract
Huntington's disease (HD) is a relentlessly progressive neurodegenerative disease featured by the over-expanded polyglutamine (polyQ)-induced protein aggregation. Using Caenorhabditis elegans (C. elegans) as a model system, we show that water soluble polysaccharide extracted from the herb Peganum harmala L. (PS1) not only reduces polyQ aggregation but also alleviates the associated neurotoxicity. Genetic and pharmacologic analysis suggested that PS1 treatment acts though proteasome-mediated protein degradation pathway to inhibit polyQ aggregation. Notably, the efficacy of PS1 is aroused specifically by co-incubation with live Escherichia coli OP50, which is the sole food source for worms. Further UPLC-Q-TOF/MS analysis determined the bioactivity of polyQ inhibition, which is composed of several oligosaccharides, including stachyoses, verbascoses, trisaccharides and tetrasaccharides composed of galacturonic acids. Together, our study revealed a potential drug target for further HD treatment and pinpointed the possibility that the secreted metabolites produced from bacteria treated with various compounds may provide direct beneficial effect to human bodies.
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Affiliation(s)
- Xiaoyu Guo
- Beijing University of Chinese Medicine, Beijing 102488, China
| | - Jiang Yuan
- Beijing University of Chinese Medicine, Beijing 102488, China
| | - Xingzhuo Song
- Beijing University of Chinese Medicine, Beijing 102488, China
| | - Xirui Wang
- Beijing University of Chinese Medicine, Beijing 102488, China
| | - Qianqian Sun
- Beijing University of Chinese Medicine, Beijing 102488, China
| | - Jingyun Tian
- Beijing University of Chinese Medicine, Beijing 102488, China
| | - Xia Li
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Mei Ding
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yonggang Liu
- Beijing University of Chinese Medicine, Beijing 102488, China.
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4
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Construction and analysis of artificial chromosomes with de novo holocentromeres in Caenorhabditis elegans. Essays Biochem 2020; 64:233-249. [PMID: 32756873 DOI: 10.1042/ebc20190067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/16/2020] [Accepted: 07/20/2020] [Indexed: 02/07/2023]
Abstract
Artificial chromosomes (ACs), generated in yeast (YACs) and human cells (HACs), have facilitated our understanding of the trans-acting proteins, cis-acting elements, such as the centromere, and epigenetic environments that are necessary to maintain chromosome stability. The centromere is the unique chromosomal region that assembles the kinetochore and connects to microtubules to orchestrate chromosome movement during cell division. While monocentromeres are the most commonly characterized centromere organization found in studied organisms, diffused holocentromeres along the chromosome length are observed in some plants, insects and nematodes. Based on the well-established DNA microinjection method in holocentric Caenorhabditis elegans, concatemerization of foreign DNA can efficiently generate megabase-sized extrachromosomal arrays (Exs), or worm ACs (WACs), for analyzing the mechanisms of WAC formation, de novo centromere formation, and segregation through mitosis and meiosis. This review summarizes the structural, size and stability characteristics of WACs. Incorporating LacO repeats in WACs and expressing LacI::GFP allows real-time tracking of newly formed WACs in vivo, whereas expressing LacI::GFP-chromatin modifier fusions can specifically adjust the chromatin environment of WACs. The WACs mature from passive transmission to autonomous segregation by establishing a holocentromere efficiently in a few cell cycles. Importantly, WAC formation does not require any C. elegans genomic DNA sequence. Thus, DNA substrates injected can be changed to evaluate the effects of DNA sequence and structure in WAC segregation. By injecting a complex mixture of DNA, a less repetitive WAC can be generated and propagated in successive generations for DNA sequencing and analysis of the established holocentromere on the WAC.
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5
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Billmyre KK, Doebley AL, Spichal M, Heestand B, Belicard T, Sato-Carlton A, Flibotte S, Simon M, Gnazzo M, Skop A, Moerman D, Carlton PM, Sarkies P, Ahmed S. The meiotic phosphatase GSP-2/PP1 promotes germline immortality and small RNA-mediated genome silencing. PLoS Genet 2019; 15:e1008004. [PMID: 30921322 PMCID: PMC6456222 DOI: 10.1371/journal.pgen.1008004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/09/2019] [Accepted: 02/05/2019] [Indexed: 12/21/2022] Open
Abstract
Germ cell immortality, or transgenerational maintenance of the germ line, could be promoted by mechanisms that could occur in either mitotic or meiotic germ cells. Here we report for the first time that the GSP-2 PP1/Glc7 phosphatase promotes germ cell immortality. Small RNA-induced genome silencing is known to promote germ cell immortality, and we identified a separation-of-function allele of C. elegans gsp-2 that is compromised for germ cell immortality and is also defective for small RNA-induced genome silencing and meiotic but not mitotic chromosome segregation. Previous work has shown that GSP-2 is recruited to meiotic chromosomes by LAB-1, which also promoted germ cell immortality. At the generation of sterility, gsp-2 and lab-1 mutant adults displayed germline degeneration, univalents, histone methylation and histone phosphorylation defects in oocytes, phenotypes that mirror those observed in sterile small RNA-mediated genome silencing mutants. Our data suggest that a meiosis-specific function of GSP-2 ties small RNA-mediated silencing of the epigenome to germ cell immortality. We also show that transgenerational epigenomic silencing at hemizygous genetic elements requires the GSP-2 phosphatase, suggesting a functional link to small RNAs. Given that LAB-1 localizes to the interface between homologous chromosomes during pachytene, we hypothesize that small localized discontinuities at this interface could promote genomic silencing in a manner that depends on small RNAs and the GSP-2 phosphatase.
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Affiliation(s)
- Katherine Kretovich Billmyre
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Anna-Lisa Doebley
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Maya Spichal
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Bree Heestand
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Tony Belicard
- Medical Research Council London Institute of Medical Sciences, London, United Kingdom
- Institute for Clinical Sciences, Imperial College London, London, United Kingdom
| | | | - Stephane Flibotte
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matt Simon
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Megan Gnazzo
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ahna Skop
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Donald Moerman
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Peter Sarkies
- Medical Research Council London Institute of Medical Sciences, London, United Kingdom
- Institute for Clinical Sciences, Imperial College London, London, United Kingdom
| | - Shawn Ahmed
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
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6
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Kalinava N, Ni JZ, Gajic Z, Kim M, Ushakov H, Gu SG. C. elegans Heterochromatin Factor SET-32 Plays an Essential Role in Transgenerational Establishment of Nuclear RNAi-Mediated Epigenetic Silencing. Cell Rep 2018; 25:2273-2284.e3. [PMID: 30463021 PMCID: PMC6317888 DOI: 10.1016/j.celrep.2018.10.086] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 09/24/2018] [Accepted: 10/24/2018] [Indexed: 12/14/2022] Open
Abstract
The dynamic process by which nuclear RNAi engages a transcriptionally active target, before the repressive state is stably established, remains largely a mystery. Here, we found that the onset of exogenous dsRNA-induced nuclear RNAi in C. elegans is a transgenerational process, and it requires a putative histone methyltransferase (HMT), SET-32. By developing a CRISPR-based genetic approach, we found that silencing establishment at the endogenous targets of germline nuclear RNAi also requires SET-32. Although SET-32 and two H3K9 HMTs, MET-2 and SET-25, are dispensable for the maintenance of silencing, they do contribute to transcriptional repression in mutants that lack the germline nuclear Argonaute protein HRDE-1, suggesting a conditional role of heterochromatin in the maintenance phase. Our study indicates that (1) establishment and maintenance of siRNA-guided transcriptional repression are two distinct processes with different genetic requirements and (2) the rate-limiting step of the establishment phase is a transgenerational, chromatin-based process.
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Affiliation(s)
- Natallia Kalinava
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
| | - Julie Zhouli Ni
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
| | - Zoran Gajic
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
| | - Matthew Kim
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
| | - Helen Ushakov
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
| | - Sam Guoping Gu
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
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7
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Ugolini I, Halic M. Fidelity in RNA-based recognition of transposable elements. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2018.0168. [PMID: 30397104 PMCID: PMC6232588 DOI: 10.1098/rstb.2018.0168] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2018] [Indexed: 12/28/2022] Open
Abstract
Genomes are under constant threat of invasion by transposable elements and other genomic parasites. How can host genomes recognize these elements and target them for degradation? This requires a system that is highly adaptable, and at the same time highly specific. Current data suggest that perturbation of transcription patterns by transposon insertions could be detected by the RNAi surveillance pathway. Multiple transposon insertions might generate sufficient amounts of primal small RNAs to initiate generation of secondary small RNAs and silencing. At the same time primal small RNAs need to be constantly degraded to reduce the level of noise small RNAs below the threshold required for initiation of silencing. Failure in RNA degradation results in loss of fidelity of small RNA pathways and silencing of ectopic targets. This article is part of the theme issue ‘5′ and 3′ modifications controlling RNA degradation’.
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Affiliation(s)
- Ilaria Ugolini
- Department of Biochemistry and Gene Center, LMU Munich, 81377 Munich, Germany
| | - Mario Halic
- Department of Biochemistry and Gene Center, LMU Munich, 81377 Munich, Germany
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8
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Liang J, De Castro A, Flores L. Detecting Protein Subcellular Localization by Green Fluorescence Protein Tagging and 4',6-Diamidino-2-phenylindole Staining in Caenorhabditis elegans. J Vis Exp 2018. [PMID: 30102267 DOI: 10.3791/57914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
In this protocol, a green fluorescence protein (GFP) fusion protein and 4',6-diamidino-2-phenylindole (DAPI) staining are used to track protein subcellular localization changes; in particular, a nuclear translocation under a heat stress condition. Proteins react correspondingly to external and internal signals. A common mechanism is to change its subcellular localization. This article describes a protocol to track protein localization that does not require an antibody, radioactive labeling, or a confocal microscope. In this article, GFP is used to tag the target protein EXL-1 in C. elegans, a member of the chloride intracellular channel proteins (CLICs) family, including mammalian CLIC4. An integrated translational exl-1::gfp transgenic line (with a promoter and a full gene sequence) was created by transformation and γ-radiation, and stably expresses the gene and gfp. Recent research showed that upon heat stress, not oxidative stress, EXL-1::GFP accumulates in the nucleus. Overlapping the GFP signal with both the nuclei structure and the DAPI signals confirms the EXL-1 subcellular localization changes under stress. This protocol presents two different fixation methods for DAPI staining: ethanol fixation and acetone fixation. The DAPI staining protocol presented in this article is fast and efficient and preserves both the GFP signal and the protein subcellular localization changes. This method only requires a fluorescence microscope with Nomarski, a FITC filter, and a DAPI filter. It is suitable for a small laboratory setting, undergraduate student research, high school student research, and biotechnology classrooms.
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Affiliation(s)
- Jun Liang
- Department of Science, Borough of Manhattan Community College/CUNY;
| | - Aijo De Castro
- Department of Science, Borough of Manhattan Community College/CUNY
| | - Lizette Flores
- Department of Science, Borough of Manhattan Community College/CUNY
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9
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Jose AM. Replicating and Cycling Stores of Information Perpetuate Life. Bioessays 2018; 40:e1700161. [PMID: 29493806 PMCID: PMC7303024 DOI: 10.1002/bies.201700161] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 01/06/2018] [Indexed: 12/12/2022]
Abstract
Life is perpetuated through a single-cell bottleneck between generations in many organisms. Here, I highlight that this cell holds information in two distinct stores: in the linear DNA sequence that is replicated during cell divisions, and in the three-dimensional arrangement of molecules that can change during development but is recreated at the start of each generation. These two interdependent stores of information - one replicating with each cell division and the other cycling with a period of one generation - coevolve while perpetuating an organism. Unlike the genome sequence, the arrangement of molecules, including DNA, RNAs, proteins, sugars, lipids, etc., is not well understood. Because this arrangement and the genome sequence are transmitted together from one generation to the next, analysis of both is necessary to understand evolution and origins of inherited diseases. Recent developments suggest that tools are in place to examine how all the information to build an organism is encoded within a single cell, and how this cell code is reproduced in every generation. See also the video abstract here: https://youtu.be/IdWEL-T6TPU.
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Affiliation(s)
- Antony M. Jose
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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10
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Kalinava N, Ni JZ, Peterman K, Chen E, Gu SG. Decoupling the downstream effects of germline nuclear RNAi reveals that H3K9me3 is dispensable for heritable RNAi and the maintenance of endogenous siRNA-mediated transcriptional silencing in Caenorhabditis elegans. Epigenetics Chromatin 2017; 10:6. [PMID: 28228846 PMCID: PMC5311726 DOI: 10.1186/s13072-017-0114-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 02/08/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Germline nuclear RNAi in C. elegans is a transgenerational gene-silencing pathway that leads to H3K9 trimethylation (H3K9me3) and transcriptional silencing at the target genes. H3K9me3 induced by either exogenous double-stranded RNA (dsRNA) or endogenous siRNA (endo-siRNA) is highly specific to the target loci and transgenerationally heritable. Despite these features, the role of H3K9me3 in siRNA-mediated transcriptional silencing and inheritance of the silencing state at native target genes is unclear. In this study, we took combined genetic and whole-genome approaches to address this question. RESULTS Here we demonstrate that siRNA-mediated H3K9me3 requires combined activities of three H3K9 histone methyltransferases: MET-2, SET-25, and SET-32. set-32 single, met-2 set-25 double, and met-2 set-25;set-32 triple mutant adult animals all exhibit prominent reductions in H3K9me3 throughout the genome, with met-2 set-25;set-32 mutant worms losing all detectable H3K9me3 signals. Surprisingly, loss of high-magnitude H3K9me3 at the native nuclear RNAi targets has no effect on the transcriptional silencing state. In addition, the exogenous dsRNA-induced transcriptional silencing and heritable RNAi at oma-1, a well-established nuclear RNAi reporter gene, are completely resistant to the loss of H3K9me3. CONCLUSIONS Nuclear RNAi-mediated H3K9me3 in C. elegans requires multiple histone methyltransferases, including MET-2, SET-25, and SET-32. H3K9me3 is not essential for dsRNA-induced heritable RNAi or the maintenance of endo-siRNA-mediated transcriptional silencing in C. elegans. We propose that siRNA-mediated transcriptional silencing in C. elegans can be maintained by an H3K9me3-independent mechanism.
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Affiliation(s)
- Natallia Kalinava
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA
| | - Julie Zhouli Ni
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA
| | - Kimberly Peterman
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA
| | - Esteban Chen
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA
| | - Sam Guoping Gu
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA.,Nelson Labs A125, 604 Allison Road, Piscataway, NJ 08854 USA
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11
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Frøkjær-Jensen C, Jain N, Hansen L, Davis MW, Li Y, Zhao D, Rebora K, Millet JRM, Liu X, Kim SK, Dupuy D, Jorgensen EM, Fire AZ. An Abundant Class of Non-coding DNA Can Prevent Stochastic Gene Silencing in the C. elegans Germline. Cell 2016; 166:343-357. [PMID: 27374334 PMCID: PMC4947018 DOI: 10.1016/j.cell.2016.05.072] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 03/31/2016] [Accepted: 05/18/2016] [Indexed: 11/30/2022]
Abstract
Cells benefit from silencing foreign genetic elements but must simultaneously avoid inactivating endogenous genes. Although chromatin modifications and RNAs contribute to maintenance of silenced states, the establishment of silenced regions will inevitably reflect underlying DNA sequence and/or structure. Here we demonstrate that a pervasive non-coding DNA feature in Caenorhabditis elegans, characterized by 10-basepair periodic An/Tn-clusters (PATCs), can license transgenes for germline expression within repressive chromatin domains. Transgenes containing natural or synthetic PATCs are resistant to position effect variegation and stochastic silencing in the germline. Among endogenous genes, intron length and PATC-character undergo dramatic changes as orthologs move from active to repressive chromatin over evolutionary time, indicating a dynamic character to the An/Tn periodicity. We propose that PATCs form the basis of a cellular immune system, identifying certain endogenous genes in heterochromatic contexts as privileged while foreign DNA can be suppressed with no requirement for a cellular memory of prior exposure.
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Affiliation(s)
- Christian Frøkjær-Jensen
- Department of Biology, Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT 84112, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA; Department of Biomedical Sciences and Danish National Research Foundation Centre for Cardiac Arrhythmia, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Nimit Jain
- Department of Bioengineering, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Loren Hansen
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - M Wayne Davis
- Department of Biology, Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Yongbin Li
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Di Zhao
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Karine Rebora
- IECB, University of Bordeaux, Laboratoire ARNA-INSERM, U869, 33600 Pessac, France
| | - Jonathan R M Millet
- IECB, University of Bordeaux, Laboratoire ARNA-INSERM, U869, 33600 Pessac, France
| | - Xiao Liu
- Department of Developmental Biology, Stanford University Medical Center, Stanford, CA 94305, USA; School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Stuart K Kim
- Department of Developmental Biology, Stanford University Medical Center, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Denis Dupuy
- IECB, University of Bordeaux, Laboratoire ARNA-INSERM, U869, 33600 Pessac, France
| | - Erik M Jorgensen
- Department of Biology, Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT 84112, USA.
| | - Andrew Z Fire
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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12
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The Fifth Letter. Evol Bioinform Online 2016. [DOI: 10.1007/978-3-319-28755-3_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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13
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Streamlined Genome Engineering with a Self-Excising Drug Selection Cassette. Genetics 2015; 200:1035-49. [PMID: 26044593 DOI: 10.1534/genetics.115.178335] [Citation(s) in RCA: 403] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 06/01/2015] [Indexed: 01/20/2023] Open
Abstract
A central goal in the development of genome engineering technology is to reduce the time and labor required to produce custom genome modifications. Here we describe a new selection strategy for producing fluorescent protein (FP) knock-ins using CRISPR/Cas9-triggered homologous recombination. We have tested our approach in Caenorhabditis elegans. This approach has been designed to minimize hands-on labor at each step of the procedure. Central to our strategy is a newly developed self-excising cassette (SEC) for drug selection. SEC consists of three parts: a drug-resistance gene, a visible phenotypic marker, and an inducible Cre recombinase. SEC is flanked by LoxP sites and placed within a synthetic intron of a fluorescent protein tag, resulting in an FP-SEC module that can be inserted into any C. elegans gene. Upon heat shock, SEC excises itself from the genome, leaving no exogenous sequences outside the fluorescent protein tag. With our approach, one can generate knock-in alleles in any genetic background, with no PCR screening required and without the need for a second injection step to remove the selectable marker. Moreover, this strategy makes it possible to produce a fluorescent protein fusion, a transcriptional reporter and a strong loss-of-function allele for any gene of interest in a single injection step.
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