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Otis JP, Mowry KL. Hitting the mark: Localization of mRNA and biomolecular condensates in health and disease. Wiley Interdiscip Rev RNA 2023; 14:e1807. [PMID: 37393916 PMCID: PMC10758526 DOI: 10.1002/wrna.1807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/29/2023] [Accepted: 06/06/2023] [Indexed: 07/04/2023]
Abstract
Subcellular mRNA localization is critical to a multitude of biological processes such as development of cellular polarity, embryogenesis, tissue differentiation, protein complex formation, cell migration, and rapid responses to environmental stimuli and synaptic depolarization. Our understanding of the mechanisms of mRNA localization must now be revised to include formation and trafficking of biomolecular condensates, as several biomolecular condensates that transport and localize mRNA have recently been discovered. Disruptions in mRNA localization can have catastrophic effects on developmental processes and biomolecular condensate biology and have been shown to contribute to diverse diseases. A fundamental understanding of mRNA localization is essential to understanding how aberrations in this biology contribute the etiology of numerous cancers though support of cancer cell migration and biomolecular condensate dysregulation, as well as many neurodegenerative diseases, through misregulation of mRNA localization and biomolecular condensate biology. This article is categorized under: RNA Export and Localization > RNA Localization RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Jessica P. Otis
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, United States, 02912
| | - Kimberly L. Mowry
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, United States, 02912
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2
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Moon KB, Park SJ, Park JS, Lee HJ, Shin SY, Lee SM, Choi GJ, Kim SG, Cho HS, Jeon JH, Kim YS, Park YI, Kim HS. Corrigendum: Editing of StSR4 by Cas9- RNPs confers resistance to Phytophthora infestans in potato. Front Plant Sci 2023; 13:1063362. [PMID: 37293182 PMCID: PMC10245271 DOI: 10.3389/fpls.2022.1063362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 10/11/2022] [Indexed: 06/10/2023]
Abstract
[This corrects the article DOI: 10.3389/fpls.2022.997888.].
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Affiliation(s)
- Ki-Beom Moon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Su-Jin Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Ji-Sun Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Hyo-Jun Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, Daejeon, Republic of Korea
| | - Seung Young Shin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, Daejeon, Republic of Korea
| | - Soo Min Lee
- Center for Eco-Friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Gyung Ja Choi
- Center for Eco-Friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Sang-Gyu Kim
- Department of Biological Sciences, Korea Advanced Institute for Science and Technology, Daejeon, Republic of Korea
| | - Hye Sun Cho
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Jae-Heung Jeon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Yong-Sam Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- GenKOre, Daejeon, Republic of Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
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Salvagnin U, Unkel K, Sprink T, Bundock P, Sevenier R, Bogdanović M, Todorović S, Cankar K, Hakkert JC, Schijlen E, Nieuwenhuis R, Hingsamer M, Kulmer V, Kernitzkyi M, Bosch D, Martens S, Malnoy M. A comparison of three different delivery methods for achieving CRISPR/Cas9 mediated genome editing in Cichorium intybus L. Front Plant Sci 2023; 14:1111110. [PMID: 37123849 PMCID: PMC10131283 DOI: 10.3389/fpls.2023.1111110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 03/22/2023] [Indexed: 05/03/2023]
Abstract
Root chicory (Cichorium intybus L. var. sativum) is used to extract inulin, a fructose polymer used as a natural sweetener and prebiotic. However, bitter tasting sesquiterpene lactones, giving chicory its known flavour, need to be removed during inulin extraction. To avoid this extraction and associated costs, recently chicory variants with a lower sesquiterpene lactone content were created by inactivating the four copies of the germacrene A synthase gene (CiGAS-S1, -S2, -S3, -L) which encode the enzyme initiating bitter sesquiterpene lactone biosynthesis in chicory. In this study, different delivery methods for CRISPR/Cas9 reagents have been compared regarding their efficiency to induce mutations in the CiGAS genes, the frequency of off-target mutations as well as their environmental and economic impacts. CRISPR/Cas9 reagents were delivered by Agrobacterium-mediated stable transformation or transient delivery by plasmid or preassembled ribonucleic complexes (RNPs) using the same sgRNA. All methods used lead to a high number of INDEL mutations within the CiGAS-S1 and CiGAS-S2 genes, which match the used sgRNA perfectly; additionally, the CiGAS-S3 and CiGAS-L genes, which have a single mismatch with the sgRNA, were mutated but with a lower mutation efficiency. While using both RNPs and plasmids delivery resulted in biallelic, heterozygous or homozygous mutations, plasmid delivery resulted in 30% of unwanted integration of plasmid fragments in the genome. Plants transformed via Agrobacteria often showed chimerism and a mixture of CiGAS genotypes. This genetic mosaic becomes more diverse when plants were grown over a prolonged period. While the genotype of the on-targets varied between the transient and stable delivery methods, no off-target activity in six identified potential off-targets with two to four mismatches was found. The environmental impacts (greenhouse gas (GHG) emissions and primary energy demand) of the methods are highly dependent on their individual electricity demand. From an economic view - like for most research and development activities - employment and value-added multiplier effects are high; particularly when compared to industrial or manufacturing processes. Considering all aspects, we conclude that using RNPs is the most suitable method for genome editing in chicory since it led to a high efficiency of editing, no off-target mutations, non-transgenic plants with no risk of unwanted integration of plasmid DNA and without needed segregation of transgenes.
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Affiliation(s)
- Umberto Salvagnin
- Fondazione Edmund Mach (FEM), Centro Ricerca e Innovazione, San Michele all’Adige, TN, Italy
- *Correspondence: Umberto Salvagnin, ; Mickael Malnoy,
| | - Katharina Unkel
- Julius Kuehn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Quedlinburg, Germany
| | - Thorben Sprink
- Julius Kuehn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Quedlinburg, Germany
| | - Paul Bundock
- Keygene N.V., Agro Business Park 90, Wageningen, Netherlands
| | - Robert Sevenier
- Keygene N.V., Agro Business Park 90, Wageningen, Netherlands
| | - Milica Bogdanović
- Department for Plant Physiology, Institute for Biological Research “Siniša Stanković”-National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Slađana Todorović
- Department for Plant Physiology, Institute for Biological Research “Siniša Stanković”-National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Katarina Cankar
- Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands
| | | | - Elio Schijlen
- Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands
| | - Ronald Nieuwenhuis
- Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands
| | | | | | | | - Dirk Bosch
- Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands
| | - Stefan Martens
- Fondazione Edmund Mach (FEM), Centro Ricerca e Innovazione, San Michele all’Adige, TN, Italy
| | - Mickael Malnoy
- Fondazione Edmund Mach (FEM), Centro Ricerca e Innovazione, San Michele all’Adige, TN, Italy
- *Correspondence: Umberto Salvagnin, ; Mickael Malnoy,
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4
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Moon KB, Park SJ, Park JS, Lee HJ, Shin SY, Lee SM, Choi GJ, Kim SG, Cho HS, Jeon JH, Kim YS, Park YI, Kim HS. Editing of StSR4 by Cas9- RNPs confers resistance to Phytophthora infestans in potato. Front Plant Sci 2022; 13:997888. [PMID: 36212382 PMCID: PMC9539116 DOI: 10.3389/fpls.2022.997888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/06/2022] [Indexed: 06/10/2023]
Abstract
Potato (Solanum tuberosum L.) cultivation is threatened by various environmental stresses, especially disease. Genome editing technologies are effective tools for generating pathogen-resistant potatoes. Here, we established an efficient RNP-mediated CRISPR/Cas9 genome editing protocol in potato to develop Phytophthora infestans resistant mutants by targeting the susceptibility gene, Signal Responsive 4 (SR4), in protoplasts. Mutations in StSR4 were efficiently introduced into the regenerated potato plants, with a maximum efficiency of 34%. High co-expression of StEDS1 and StPAD4 in stsr4 mutants induced the accumulation of salicylic acid (SA), and enhanced the expression of the pathogen resistance marker StPR1. In addition, increased SA content in the stsr4 mutant enhanced its resistance to P. infestans more than that in wild type. However, the growth of stsr4_3-19 and stsr4_3-698 mutants with significantly high SA was strongly inhibited, and a dwarf phenotype was induced. Therefore, it is important to adequate SA accumulation in order to overcome StSR4 editing-triggered growth inhibition and take full advantages of the improved pathogen resistance of stsr4 mutants. This RNP-mediated CRISPR/Cas9-based potato genome editing protocol will accelerate the development of pathogen-resistant Solanaceae crops via molecular breeding.
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Affiliation(s)
- Ki-Beom Moon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Su-Jin Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Ji-Sun Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Hyo-Jun Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, Daejeon, Republic of Korea
| | - Seung Young Shin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, Daejeon, Republic of Korea
| | - Soo Min Lee
- Center for Eco-Friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Gyung Ja Choi
- Center for Eco-Friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Sang-Gyu Kim
- Department of Biological Sciences, Korea Advanced Institute for Science and Technology, Daejeon, Republic of Korea
| | - Hye Sun Cho
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Jae-Heung Jeon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Yong-Sam Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- GenKOre, Daejeon, Republic of Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
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5
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Abstract
CRISPR/Cas-based genome editing technologies have the potential to fast-track large-scale crop breeding programs. However, the rigid cell wall limits the delivery of CRISPR/Cas components into plant cells, decreasing genome editing efficiency. Established methods, such as Agrobacterium tumefaciens-mediated or biolistic transformation have been used to integrate genetic cassettes containing CRISPR components into the plant genome. Although efficient, these methods pose several problems, including 1) The transformation process requires laborious and time-consuming tissue culture and regeneration steps; 2) many crop species and elite varieties are recalcitrant to transformation; 3) The segregation of transgenes in vegetatively propagated or highly heterozygous crops, such as pineapple, is either difficult or impossible; and 4) The production of a genetically modified first generation can lead to public controversy and onerous government regulations. The development of transgene-free genome editing technologies can address many problems associated with transgenic-based approaches. Transgene-free genome editing have been achieved through the delivery of preassembled CRISPR/Cas ribonucleoproteins, although its application is limited. The use of viral vectors for delivery of CRISPR/Cas components has recently emerged as a powerful alternative but it requires further exploration. In this review, we discuss the different strategies, principles, applications, and future directions of transgene-free genome editing methods.
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Affiliation(s)
- Zheng Gong
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Science, The University of Queensland, Brisbane, QLD, Australia
| | - Ming Cheng
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Science, The University of Queensland, Brisbane, QLD, Australia
| | - Jose R Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Science, The University of Queensland, Brisbane, QLD, Australia
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6
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Scintilla S, Salvagnin U, Giacomelli L, Zeilmaker T, Malnoy MA, Rouppe van der Voort J, Moser C. Regeneration of non-chimeric plants from DNA-free edited grapevine protoplasts. Front Plant Sci 2022; 13:1078931. [PMID: 36531381 DOI: 10.1101/2021.07.16.452503] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 11/16/2022] [Indexed: 05/20/2023]
Abstract
The application of New Breeding Techniques (NBTs) in Vitis vinifera is highly desirable to introduce valuable traits while preserving the genotype of the elite cultivars. However, a broad application of NBTs through standard DNA-based transformation is poorly accepted by public opinion and law regulations in Europe and other countries due to the stable integration of exogenous DNA, which leads to transgenic plants possibly affected by chimerism. A single-cell based approach, coupled with a DNA-free transfection of the CRISPR/Cas editing machinery, constitutes a powerful tool to overcome these problems and maintain the original genetic make-up in the whole organism. We here describe a successful single-cell based, DNA-free methodology to obtain edited grapevine plants, regenerated from protoplasts isolated from embryogenic callus of two table grapevine varieties (V. vinifera cv. Crimson seedless and Sugraone). The regenerated, non-chimeric plants were edited on the downy- and powdery-mildew susceptibility genes, VviDMR6 and VviMlo6 respectively, either as single or double mutants.
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Affiliation(s)
- Simone Scintilla
- Centro Ricerca ed Innovazione, Fondazione E. Mach. Via E. Mach 1, San Michele all'Adige, Trento, Italy
| | - Umberto Salvagnin
- Centro Ricerca ed Innovazione, Fondazione E. Mach. Via E. Mach 1, San Michele all'Adige, Trento, Italy
- Consorzio Innovazione Vite (CIVIT), Trento, TN, Italy
| | - Lisa Giacomelli
- Centro Ricerca ed Innovazione, Fondazione E. Mach. Via E. Mach 1, San Michele all'Adige, Trento, Italy
- Scienza Biotechnologies BV., Enkhuizen, Netherlands
| | | | - Mickael A Malnoy
- Centro Ricerca ed Innovazione, Fondazione E. Mach. Via E. Mach 1, San Michele all'Adige, Trento, Italy
| | | | - Claudio Moser
- Centro Ricerca ed Innovazione, Fondazione E. Mach. Via E. Mach 1, San Michele all'Adige, Trento, Italy
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7
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Scintilla S, Salvagnin U, Giacomelli L, Zeilmaker T, Malnoy MA, Rouppe van der Voort J, Moser C. Regeneration of non-chimeric plants from DNA-free edited grapevine protoplasts. Front Plant Sci 2022; 13:1078931. [PMID: 36531381 PMCID: PMC9752144 DOI: 10.3389/fpls.2022.1078931] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 11/16/2022] [Indexed: 05/19/2023]
Abstract
The application of New Breeding Techniques (NBTs) in Vitis vinifera is highly desirable to introduce valuable traits while preserving the genotype of the elite cultivars. However, a broad application of NBTs through standard DNA-based transformation is poorly accepted by public opinion and law regulations in Europe and other countries due to the stable integration of exogenous DNA, which leads to transgenic plants possibly affected by chimerism. A single-cell based approach, coupled with a DNA-free transfection of the CRISPR/Cas editing machinery, constitutes a powerful tool to overcome these problems and maintain the original genetic make-up in the whole organism. We here describe a successful single-cell based, DNA-free methodology to obtain edited grapevine plants, regenerated from protoplasts isolated from embryogenic callus of two table grapevine varieties (V. vinifera cv. Crimson seedless and Sugraone). The regenerated, non-chimeric plants were edited on the downy- and powdery-mildew susceptibility genes, VviDMR6 and VviMlo6 respectively, either as single or double mutants.
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Affiliation(s)
- Simone Scintilla
- Centro Ricerca ed Innovazione, Fondazione E. Mach. Via E. Mach 1, San Michele all’Adige, Trento, Italy
- *Correspondence: Simone Scintilla, ; Claudio Moser,
| | - Umberto Salvagnin
- Centro Ricerca ed Innovazione, Fondazione E. Mach. Via E. Mach 1, San Michele all’Adige, Trento, Italy
- Consorzio Innovazione Vite (CIVIT), Trento, TN, Italy
| | - Lisa Giacomelli
- Centro Ricerca ed Innovazione, Fondazione E. Mach. Via E. Mach 1, San Michele all’Adige, Trento, Italy
- Scienza Biotechnologies BV., Enkhuizen, Netherlands
| | | | - Mickael A. Malnoy
- Centro Ricerca ed Innovazione, Fondazione E. Mach. Via E. Mach 1, San Michele all’Adige, Trento, Italy
| | | | - Claudio Moser
- Centro Ricerca ed Innovazione, Fondazione E. Mach. Via E. Mach 1, San Michele all’Adige, Trento, Italy
- *Correspondence: Simone Scintilla, ; Claudio Moser,
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Shaukat AN, Kaliatsi EG, Skeparnias I, Stathopoulos C. The Dynamic Network of RNP RNase P Subunits. Int J Mol Sci 2021; 22:ijms221910307. [PMID: 34638646 PMCID: PMC8509007 DOI: 10.3390/ijms221910307] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 11/17/2022] Open
Abstract
Ribonuclease P (RNase P) is an important ribonucleoprotein (RNP), responsible for the maturation of the 5′ end of precursor tRNAs (pre-tRNAs). In all organisms, the cleavage activity of a single phosphodiester bond adjacent to the first nucleotide of the acceptor stem is indispensable for cell viability and lies within an essential catalytic RNA subunit. Although RNase P is a ribozyme, its kinetic efficiency in vivo, as well as its structural variability and complexity throughout evolution, requires the presence of one protein subunit in bacteria to several protein partners in archaea and eukaryotes. Moreover, the existence of protein-only RNase P (PRORP) enzymes in several organisms and organelles suggests a more complex evolutionary timeline than previously thought. Recent detailed structures of bacterial, archaeal, human and mitochondrial RNase P complexes suggest that, although apparently dissimilar enzymes, they all recognize pre-tRNAs through conserved interactions. Interestingly, individual protein subunits of the human nuclear and mitochondrial holoenzymes have additional functions and contribute to a dynamic network of elaborate interactions and cellular processes. Herein, we summarize the role of each RNase P subunit with a focus on the human nuclear RNP and its putative role in flawless gene expression in light of recent structural studies.
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Cai Z, So BR, Dreyfuss G. Comprehensive RNP profiling in cells identifies U1 snRNP complexes with cleavage and polyadenylation factors active in telescripting. Methods Enzymol 2021; 655:325-347. [PMID: 34183128 DOI: 10.1016/bs.mie.2021.04.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Full-length transcription in the majority of protein-coding and other genes transcribed by RNA polymerase II in complex eukaryotes requires U1 snRNP (U1) to co-transcriptionally suppress transcription-terminating premature 3'-end cleavage and polyadenylation (PCPA) from cryptic polyadenylation signals (PASs). This U1 activity, termed telescripting, requires U1 to base-pair with the nascent RNA and inhibit usage of a downstream PAS. Here we describe experimental methods to determine the mechanism of U1 telescripting, involving mapping of U1 and CPA factors (CPAFs) binding locations in relation to PCPA sites, and identify U1 and CPAFs interactomes. The methods which utilizes rapid reversible protein-RNA and protein-protein chemical crosslinking, immunoprecipitations (XLIPs) of components of interest, and RNA-seq and quantitative proteomic mass spectrometry, captured U1-CPAFs complexes in cells, providing important insights into telescripting mechanism. XLIP profiling can be used for comprehensive molecular definition of diverse RNPs.
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Affiliation(s)
- Zhiqiang Cai
- Department of Biochemistry and Biophysics, School of Medicine, Howard Hughes Medical Institute, University of Pennsylvania, Philadelphia, PA, United States
| | - Byung Ran So
- Department of Biochemistry and Biophysics, School of Medicine, Howard Hughes Medical Institute, University of Pennsylvania, Philadelphia, PA, United States
| | - Gideon Dreyfuss
- Department of Biochemistry and Biophysics, School of Medicine, Howard Hughes Medical Institute, University of Pennsylvania, Philadelphia, PA, United States.
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Kurtz S, Lucas-Hahn A, Schlegelberger B, Göhring G, Niemann H, Mettenleiter TC, Petersen B. Knockout of the HMG domain of the porcine SRY gene causes sex reversal in gene-edited pigs. Proc Natl Acad Sci U S A 2021; 118:e2008743118. [PMID: 33443157 DOI: 10.1073/pnas.2008743118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The present work characterizes the porcine sex-determining region on the Y chromosome (SRY) gene and demonstrates its pivotal role in sex determination. We provide evidence that genetically male pigs with a knockout of the SRY gene undergo sex reversal of the external and internal genitalia. This discovery of SRY as the main switch for sex determination in pigs may provide an alternative for surgical castration in pig production, preventing boar taint. As the pig shares many genetic, physiological, and anatomical similarities with humans, it also provides a suitable large animal model for human sex reversal syndromes, allowing for the development of new interventions for human sex disorders. The sex-determining region on the Y chromosome (SRY) is thought to be the central genetic element of male sex development in mammals. Pathogenic modifications within the SRY gene are associated with a male-to-female sex reversal syndrome in humans and other mammalian species, including rabbits and mice. However, the underlying mechanisms are largely unknown. To understand the biological function of the SRY gene, a site-directed mutational analysis is required to investigate associated phenotypic changes at the molecular, cellular, and morphological level. Here, we successfully generated a knockout of the porcine SRY gene by microinjection of two CRISPR-Cas ribonucleoproteins, targeting the centrally located “high mobility group” (HMG), followed by a frameshift mutation of the downstream SRY sequence. This resulted in the development of genetically male (XY) pigs with complete external and internal female genitalia, which, however, were significantly smaller than in 9-mo-old age-matched control females. Quantitative digital PCR analysis revealed a duplication of the SRY locus in Landrace pigs similar to the known palindromic duplication in Duroc breeds. Our study demonstrates the central role of the HMG domain in the SRY gene in male porcine sex determination. This proof-of-principle study could assist in solving the problem of sex preference in agriculture to improve animal welfare. Moreover, it establishes a large animal model that is more comparable to humans with regard to genetics, physiology, and anatomy, which is pivotal for longitudinal studies to unravel mammalian sex determination and relevant for the development of new interventions for human sex development disorders.
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Mujagić A, Marushima A, Nagasaki Y, Hosoo H, Hirayama A, Puentes S, Takahashi T, Tsurushima H, Suzuki K, Matsui H, Ishikawa E, Matsumaru Y, Matsumura A. Antioxidant nanomedicine with cytoplasmic distribution in neuronal cells shows superior neurovascular protection properties. Brain Res 2020; 1743:146922. [PMID: 32504549 DOI: 10.1016/j.brainres.2020.146922] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 05/20/2020] [Accepted: 06/01/2020] [Indexed: 01/15/2023]
Abstract
This study investigated whether nitroxide radical (4-amino-TEMPOL)-containing nanoparticles (RNPs; antioxidant nanomedicine) can prevent neurovascular unit impairment caused by reactive oxygen species (ROS) after cerebral ischemia-reperfusion. C57BL/6J mice underwent transient middle cerebral artery occlusion (tMCAO). The mice were randomly divided and administered intra-arterial RNPs injection (9 mg/kg, 7 μM/kg), edaravone (3 mg/kg, 17 μM/kg), or phosphate-buffered saline (control group). Survival rate and neurological score were evaluated 24 h post-injection. RNPs distribution was determined using immunofluorescence staining and blood-brain barrier (BBB) disruption using Evans blue extravasation assay. Effect of RNPs and edaravone on microglia polarization into microglia M1 and M2 was evaluated. We also determined multiple ROS-scavenging activities in brain homogenates of RNPs- and edaravone-treated animals using an electron spin resonance-based spin-trapping method. Compared with edaravone, RNPs significantly improved the survival rate and neurological deficit, inhibited BBB disruption and supported polarization of microglia into M2 microglia. RNPs were localized in endothelial cells, the perivascular space, neuronal cell cytoplasm, astrocytes, and microglia. Scavenging capacities of hydroxyl, alkoxyl, and peroxyl radicals were significantly higher in the RNPs-treated group. RNPs show promising results as a future neuroprotective nanomedicine approach for cerebral ischemia-reperfusion injury.
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Affiliation(s)
- Arnela Mujagić
- Department of Neurosurgery, Faculty of Medicine, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan; Department of Neurosurgery, Graduate School of Comprehensive Human Science, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan
| | - Aiki Marushima
- Department of Neurosurgery, Faculty of Medicine, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan; Department of Neurosurgery, Graduate School of Comprehensive Human Science, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan.
| | - Yukio Nagasaki
- Graduate School of Pure and Applied Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan
| | - Hisayuki Hosoo
- Department of Neurosurgery, Faculty of Medicine, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan; Department of Neurosurgery, Graduate School of Comprehensive Human Science, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan
| | - Aki Hirayama
- Center for Integrative Medicine, Tsukuba University of Technology, Kasuga 4-12-7, Tsukuba, Ibaraki, Japan
| | - Sandra Puentes
- Graduate School of Systems and Information Engineering, University of Tsukuba, Tennodai 1-1-1, Ibaraki, Japan
| | - Toshihide Takahashi
- Department of Neurosurgery, Faculty of Medicine, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan; Department of Neurosurgery, Graduate School of Comprehensive Human Science, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan
| | - Hideo Tsurushima
- Department of Neurosurgery, Faculty of Medicine, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan; Department of Neurosurgery, Graduate School of Comprehensive Human Science, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan
| | - Kensuke Suzuki
- Department of Neurosurgery, Saitama Medical Center, Dokkyo Medical University, Minami-Koshigaya 2-1-50, Koshigaya, Saitama, Japan
| | - Hirofumi Matsui
- Department of Gastroenterology, Faculty of Medicine, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan
| | - Eiichi Ishikawa
- Department of Neurosurgery, Faculty of Medicine, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan; Department of Neurosurgery, Graduate School of Comprehensive Human Science, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan
| | - Yuji Matsumaru
- Department of Neurosurgery, Faculty of Medicine, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan; Department of Neurosurgery, Graduate School of Comprehensive Human Science, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan
| | - Akira Matsumura
- Department of Neurosurgery, Faculty of Medicine, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan; Department of Neurosurgery, Graduate School of Comprehensive Human Science, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan
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12
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Abstract
Cajal bodies (CBs) are nuclear membraneless bodies composed of proteins and RNA. Although it is known that CBs play a role in RNA metabolism and the formation of functional ribonucleoprotein (RNP) particles, the whole breadth of CB functions is far from being fully elucidated. In this short review, we will summarize and discuss the growing body of evidence pointing to an involvement of this subnuclear compartment in plant-virus interactions.
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Affiliation(s)
- Yi Ding
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai 201602, China;
- Center for Excellence in Molecular Plant Science, Chinese Academy of Sciences, Shanghai 201602, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Rosa Lozano-Durán
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai 201602, China;
- Center for Excellence in Molecular Plant Science, Chinese Academy of Sciences, Shanghai 201602, China
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13
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Remenyi R, Li R, Harris M. On-demand Labeling of SNAP-tagged Viral Protein for Pulse-Chase Imaging, Quench-Pulse-Chase Imaging, and Nanoscopy-based Inspection of Cell Lysates. Bio Protoc 2019; 9:e3177. [PMID: 30886879 DOI: 10.21769/bioprotoc.3177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Advanced labeling technologies allow researchers to study protein turnover inside intact cells and to track the labeled protein in downstream applications. In the context of a viral infection, the combination of imaging and fluorescent labeling of viral proteins sheds light on their biological activity and interaction with the host cell. Initial approaches have fused fluorescent proteins such as green fluorescent protein (GFP) to the viral protein-of-interest. In contrast, self-labeling enzyme tags such as the commercial SNAP-tag, a modified version of human O6-alkylguanine-DNA-alkyltransferase, covalently link synthetic ligands, which users can add on demand. The first two protocols presented here build on previously published protocols for fluorescent labeling in pulse-chase and quench-pulse-chase experiments; the combination of fluorescent labeling with advanced light microscopy visualizes the dynamic turnover of the SNAP-tagged viral protein in intact mammalian cells. A third protocol also outlines how to inspect cellular lysates microscopically for detergent-resistant assemblies of the labeled viral protein. These protocols showcase the flexibility of the SNAP-based labeling system for tracking a viral protein-of-interest in live cells, intact fixed cells, and cell lysates. Moreover, the protocols employ recently developed commercial microscopes (e.g., Airyscan microscopy) that balance resolution, speed, phototoxicity, photobleaching, and ease-of-use.
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Affiliation(s)
- Roland Remenyi
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Raymond Li
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Mark Harris
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
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14
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Montagna C, Petris G, Casini A, Maule G, Franceschini GM, Zanella I, Conti L, Arnoldi F, Burrone OR, Zentilin L, Zacchigna S, Giacca M, Cereseto A. VSV-G-Enveloped Vesicles for Traceless Delivery of CRISPR-Cas9. Mol Ther Nucleic Acids 2018; 12:453-462. [PMID: 30195783 PMCID: PMC6041463 DOI: 10.1016/j.omtn.2018.05.010] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 04/16/2018] [Accepted: 05/14/2018] [Indexed: 02/07/2023]
Abstract
The method of delivery of CRISPR-Cas9 into target cells is a strong determinant of efficacy and specificity in genome editing. Even though high efficiency of Cas9 delivery is necessary for optimal editing, its long-term and high levels of expression correlate with increased off-target activity. We developed vesicles (VEsiCas) carrying CRISPR-SpCas9 ribonucleoprotein complexes (RNPs) that are efficiently delivered into target cells through the fusogenic glycoprotein of the vesicular stomatitis virus (VSV-G). A crucial step for VEsiCas production is the synthesis of the single guide RNA (sgRNA) mediated by the T7 RNA polymerase in the cytoplasm of producing cells as opposed to canonical U6-driven Pol III nuclear transcription. In VEsiCas, the absence of DNA encoding SpCas9 and sgRNA allows rapid clearance of the nuclease components in target cells, which correlates with reduced genome-wide off-target cleavages. Compared with SpCas9 RNPs electroporation, which is currently the method of choice to obtain transient SpCas9 activity, VEsiCas deliver the nuclease with higher efficiency and lower toxicity. We show that a wide variety of cells can be edited through VEsiCas, including a variety of transformed cells, induced pluripotent stem cells (iPSCs), and cardiomyocytes, in vivo. VEsiCas is a traceless CRISPR-Cas9 delivery tool for efficient and safe genome editing that represents a further advancement toward the therapeutic use of the CRISPR-Cas9 technology.
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Affiliation(s)
- Claudia Montagna
- Laboratory of Molecular Virology, University of Trento, Centre for Integrative Biology, 38123 Trento, Italy
| | - Gianluca Petris
- Laboratory of Molecular Virology, University of Trento, Centre for Integrative Biology, 38123 Trento, Italy.
| | - Antonio Casini
- Laboratory of Molecular Virology, University of Trento, Centre for Integrative Biology, 38123 Trento, Italy
| | - Giulia Maule
- Laboratory of Molecular Virology, University of Trento, Centre for Integrative Biology, 38123 Trento, Italy
| | - Gian Marco Franceschini
- Laboratory of Molecular Virology, University of Trento, Centre for Integrative Biology, 38123 Trento, Italy
| | - Ilaria Zanella
- Laboratory of Molecular Virology, University of Trento, Centre for Integrative Biology, 38123 Trento, Italy
| | - Luciano Conti
- Laboratory of Stem Cell Biology, University of Trento, Centre for Integrative Biology, 38123 Trento, Italy
| | - Francesca Arnoldi
- International Centre for Genetic Engineering and Biotechnology (ICGEB), AREA Science Park, Padriciano 99, 34149 Trieste, Italy; Department of Medicine, Surgery and Health Sciences, University of Trieste, 34149 Trieste, Italy
| | - Oscar R Burrone
- International Centre for Genetic Engineering and Biotechnology (ICGEB), AREA Science Park, Padriciano 99, 34149 Trieste, Italy
| | - Lorena Zentilin
- International Centre for Genetic Engineering and Biotechnology (ICGEB), AREA Science Park, Padriciano 99, 34149 Trieste, Italy
| | - Serena Zacchigna
- International Centre for Genetic Engineering and Biotechnology (ICGEB), AREA Science Park, Padriciano 99, 34149 Trieste, Italy; Department of Medicine, Surgery and Health Sciences, University of Trieste, 34149 Trieste, Italy
| | - Mauro Giacca
- International Centre for Genetic Engineering and Biotechnology (ICGEB), AREA Science Park, Padriciano 99, 34149 Trieste, Italy; Department of Medicine, Surgery and Health Sciences, University of Trieste, 34149 Trieste, Italy
| | - Anna Cereseto
- Laboratory of Molecular Virology, University of Trento, Centre for Integrative Biology, 38123 Trento, Italy.
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15
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Metje-Sprink J, Menz J, Modrzejewski D, Sprink T. DNA-Free Genome Editing: Past, Present and Future. Front Plant Sci 2018; 9:1957. [PMID: 30693009 PMCID: PMC6339908 DOI: 10.3389/fpls.2018.01957] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/17/2018] [Indexed: 05/18/2023]
Abstract
Genome Editing using engineered endonuclease (GEEN) systems rapidly took over the field of plant science and plant breeding. So far, Genome Editing techniques have been applied in more than fifty different plants; including model species like Arabidopsis; main crops like rice, maize or wheat as well as economically less important crops like strawberry, peanut and cucumber. These techniques have been used for basic research as proof-of-concept or to investigate gene functions in most of its applications. However, several market-oriented traits have been addressed including enhanced agronomic characteristics, improved food and feed quality, increased tolerance to abiotic and biotic stress and herbicide tolerance. These technologies are evolving at a tearing pace and especially the field of CRISPR based Genome Editing is advancing incredibly fast. CRISPR-Systems derived from a multitude of bacterial species are being used for targeted Gene Editing and many modifications have already been applied to the existing CRISPR-Systems such as (i) alter their protospacer adjacent motif (ii) increase their specificity (iii) alter their ability to cut DNA and (iv) fuse them with additional proteins. Besides, the classical transformation system using Agrobacteria tumefaciens or Rhizobium rhizogenes, other transformation technologies have become available and additional methods are on its way to the plant sector. Some of them are utilizing solely proteins or protein-RNA complexes for transformation, making it possible to alter the genome without the use of recombinant DNA. Due to this, it is impossible that foreign DNA is being incorporated into the host genome. In this review we will present the recent developments and techniques in the field of DNA-free Genome Editing, its advantages and pitfalls and give a perspective on technologies which might be available in the future for targeted Genome Editing in plants. Furthermore, we will discuss these techniques in the light of existing- and potential future regulations.
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16
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Fuster-García C, García-García G, González-Romero E, Jaijo T, Sequedo MD, Ayuso C, Vázquez-Manrique RP, Millán JM, Aller E. USH2A Gene Editing Using the CRISPR System. Mol Ther Nucleic Acids 2017; 8:529-541. [PMID: 28918053 PMCID: PMC5573797 DOI: 10.1016/j.omtn.2017.08.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 08/09/2017] [Accepted: 08/09/2017] [Indexed: 01/06/2023]
Abstract
Usher syndrome (USH) is a rare autosomal recessive disease and the most common inherited form of combined visual and hearing impairment. Up to 13 genes are associated with this disorder, with USH2A being the most prevalent, due partially to the recurrence rate of the c.2299delG mutation. Excluding hearing aids or cochlear implants for hearing impairment, there are no medical solutions available to treat USH patients. The repair of specific mutations by gene editing is, therefore, an interesting strategy that can be explored using the CRISPR/Cas9 system. In this study, this method of gene editing is used to target the c.2299delG mutation on fibroblasts from an USH patient carrying the mutation in homozygosis. Successful in vitro mutation repair was demonstrated using locus-specific RNA-Cas9 ribonucleoproteins with subsequent homologous recombination repair induced by an engineered template supply. Effects on predicted off-target sites in the CRISPR-treated cells were discarded after a targeted deep-sequencing screen. The proven effectiveness and specificity of these correction tools, applied to the c.2299delG pathogenic variant of USH2A, indicates that the CRISPR system should be considered to further explore a potential treatment of USH.
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Affiliation(s)
- Carla Fuster-García
- Grupo de Investigación en Biomedicina Molecular, Celular y Genómica, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
| | - Gema García-García
- Grupo de Investigación en Biomedicina Molecular, Celular y Genómica, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain; CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Elisa González-Romero
- Grupo de Investigación en Biomedicina Molecular, Celular y Genómica, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
| | - Teresa Jaijo
- Grupo de Investigación en Biomedicina Molecular, Celular y Genómica, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain; CIBER de Enfermedades Raras (CIBERER), Madrid, Spain; Unidad de Genética y Diagnóstico Prenatal, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - María D Sequedo
- Grupo de Investigación en Biomedicina Molecular, Celular y Genómica, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain; CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Carmen Ayuso
- CIBER de Enfermedades Raras (CIBERER), Madrid, Spain; Servicio de Genética, Fundación Jiménez Díaz, University Hospital, Instituto de Investigación Sanitaria Fundación Jiménez Díaz IIS-FJD, UAM, Madrid, Spain
| | - Rafael P Vázquez-Manrique
- Grupo de Investigación en Biomedicina Molecular, Celular y Genómica, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain; CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - José M Millán
- Grupo de Investigación en Biomedicina Molecular, Celular y Genómica, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain; CIBER de Enfermedades Raras (CIBERER), Madrid, Spain.
| | - Elena Aller
- Grupo de Investigación en Biomedicina Molecular, Celular y Genómica, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain; CIBER de Enfermedades Raras (CIBERER), Madrid, Spain; Unidad de Genética y Diagnóstico Prenatal, Hospital Universitario y Politécnico La Fe, Valencia, Spain
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17
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Abstract
Organelles without membranes are found in all types of cells and typically contain RNA and protein. RNA and protein are the constituents of ribosomes, one of the most ancient cellular structures. It is reasonable to propose that organelles without membranes preceded protocells and other membrane-bound structures at the origins of life. Such membraneless organelles would be well sheltered in the spaces between mica sheets, which have many advantages as a site for the origins of life.
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18
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Abstract
Proteins and RNA are often found in ribonucleoprotein particles (RNPs), where they function in cellular processes to synthesize proteins (the ribosome), chemically modify RNAs (small nucleolar RNPs), splice pre-mRNAs (the spliceosome), and, on a larger scale, sequester RNAs, degrade them, or process them (P bodies, Cajal bodies, and nucleoli). Each RNA–protein interaction is a story in itself, as both molecules can change conformation, compete for binding sites, and regulate cellular functions. Recent studies of Xist long non-coding RNP, the U4/5/6 tri-small nuclear RNP complex, and an activated state of a spliceosome reveal new features of RNA interactions with proteins, and, although their stories are incomplete, they are already fascinating.
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Affiliation(s)
- Kathleen B Hall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, 63110, USA
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19
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Gallagher JR, Torian U, McCraw DM, Harris AK. Structural studies of influenza virus RNPs by electron microscopy indicate molecular contortions within NP supra-structures. J Struct Biol 2016; 197:294-307. [PMID: 28007449 DOI: 10.1016/j.jsb.2016.12.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 11/19/2016] [Accepted: 12/16/2016] [Indexed: 12/29/2022]
Abstract
Ribonucleoprotein (RNP) complexes of influenza viruses are composed of multiple copies of the viral nucleoprotein (NP) that can form filamentous supra-structures. RNPs package distinct viral genomic RNA segments of different lengths into pleomorphic influenza virions. RNPs also function in viral RNA transcription and replication. Different RNP segments have varying lengths, but all must be incorporated into virions during assembly and then released during viral entry for productive infection cycles. RNP structures serve varied functions in the viral replication cycle, therefore understanding their molecular organization and flexibility is essential to understanding these functions. Here, we show using electron tomography and image analyses that isolated RNP filaments are not rigid helical structures, but instead display variations in lengths, curvatures, and even tolerated kinks and local unwinding. Additionally, we observed NP rings within RNP preparations, which were commonly composed of 5, 6, or 7 NP molecules and were of similar widths to filaments, suggesting plasticity in NP-NP interactions mediate RNP structural polymorphism. To demonstrate that NP alone could generate rings of variable oligomeric state, we performed 2D single particle image analysis on recombinant NP and found that rings of 4 and 5 protomers dominated, but rings of all compositions up to 7 were directly observed with variable frequency. This structural flexibility may be needed as RNPs carry out the interactions and conformational changes required for RNP assembly and genome packaging as well as virus uncoating.
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Affiliation(s)
- John R Gallagher
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Room 6351, Bethesda, MD 20892, USA
| | - Udana Torian
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Room 6351, Bethesda, MD 20892, USA
| | - Dustin M McCraw
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Room 6351, Bethesda, MD 20892, USA
| | - Audray K Harris
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Room 6351, Bethesda, MD 20892, USA.
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