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Kumari R, Saha T, Kumar P, Singh AK. CRISPR/Cas9-mediated genome editing technique to control fall armyworm ( Spodoptera frugiperda) in crop plants with special reference to maize. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:1161-1173. [PMID: 39100879 PMCID: PMC11291824 DOI: 10.1007/s12298-024-01486-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/29/2024] [Accepted: 07/04/2024] [Indexed: 08/06/2024]
Abstract
Fall Armyworm imposes a major risk to agricultural losses. Insecticides have historically been used to manage its infestations, but it eventually becomes resistant to them. To combat the pest, a more recent strategy based on the use of transgenic maize that expresses Bt proteins such as Cry1F from the bacteria has been used. Nonetheless, there have been numerous reports of Cry1F maize resistance in FAW populations. Nowadays, the more effective and less time-consuming genome editing method known as CRISPR/Cas9 technology has gradually supplanted these various breeding techniques. This method successfully edits the genomes of various insects, including Spodoptera frugiperda. On the other hand, this new technique can change an insect's DNA to overcome its tolerance to specific insecticides or to generate a gene drive. The production of plant cultivars resistant to fall armyworms holds great potential for the sustainable management of this pest, given the swift advancement of CRISPR/Cas9 technology and its varied uses. Thus, this review article discussed and critically assessed the use of CRISPR/Cas9 genome-editing technology in long-term fall armyworm pest management. However, this review study focuses primarily on the mechanism of the CRISPR-Cas9 system in both crop plants and insects for FAW management.
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Affiliation(s)
- Rima Kumari
- Division of Plant Biotechnology, College of Agricultural Biotechnology, Bihar Agricultural University, Sabour, Bihar 813210 India
| | - Tamoghna Saha
- Department of Entomology, Bihar Agricultural University, Sabour, Bihar 813210 India
| | - Pankaj Kumar
- Department of Molecular Biology and Genetic Engineering, Bihar Agricultural University, Sabour, Bihar 813210 India
| | - A. K. Singh
- Bihar Agricultural University, Sabour, 813210 Bihar India
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2
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Deem KD, Halfon MS, Tomoyasu Y. A new suite of reporter vectors and a novel landing site survey system to study cis-regulatory elements in diverse insect species. Sci Rep 2024; 14:10078. [PMID: 38698030 PMCID: PMC11066043 DOI: 10.1038/s41598-024-60432-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/23/2024] [Indexed: 05/05/2024] Open
Abstract
Comparative analyses between traditional model organisms, such as the fruit fly Drosophila melanogaster, and more recent model organisms, such as the red flour beetle Tribolium castaneum, have provided a wealth of insight into conserved and diverged aspects of gene regulation. While the study of trans-regulatory components is relatively straightforward, the study of cis-regulatory elements (CREs, or enhancers) remains challenging outside of Drosophila. A central component of this challenge has been finding a core promoter suitable for enhancer-reporter assays in diverse insect species. Previously, we demonstrated that a Drosophila Synthetic Core Promoter (DSCP) functions in a cross-species manner in Drosophila and Tribolium. Given the over 300 million years of divergence between the Diptera and Coleoptera, we reasoned that DSCP-based reporter constructs will be useful when studying cis-regulation in a variety of insect models across the holometabola and possibly beyond. To this end, we sought to create a suite of new DSCP-based reporter vectors, leveraging dual compatibility with piggyBac and PhiC31-integration, the 3xP3 universal eye marker, GATEWAY cloning, different colors of reporters and markers, as well as Gal4-UAS binary expression. While all constructs functioned properly with a Tc-nub enhancer in Drosophila, complications arose with tissue-specific Gal4-UAS binary expression in Tribolium. Nevertheless, the functionality of these constructs across multiple holometabolous orders suggests a high potential compatibility with a variety of other insects. In addition, we present the piggyLANDR (piggyBac-LoxP AttP Neutralizable Destination Reporter) platform for the establishment of proper PhiC31 landing sites free from position effects. As a proof-of-principle, we demonstrated the workflow for piggyLANDR in Drosophila. The potential utility of these tools ranges from molecular biology research to pest and disease-vector management, and will help advance the study of gene regulation beyond traditional insect models.
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Affiliation(s)
- Kevin D Deem
- Department of Biology, Miami University, Oxford, OH, 45056, USA
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Marc S Halfon
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, NY, 14203, USA
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3
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De Castro V, Galaine J, Loyon R, Godet Y. CRISPR-Cas gene knockouts to optimize engineered T cells for cancer immunotherapy. Cancer Gene Ther 2024:10.1038/s41417-024-00771-x. [PMID: 38609574 DOI: 10.1038/s41417-024-00771-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024]
Abstract
While CAR-T and tgTCR-T therapies have exhibited noteworthy and promising outcomes in hematologic and solid tumors respectively, a set of distinct challenges remains. Consequently, the quest for novel strategies has become imperative to safeguard and more effectively release the full functions of engineered T cells. These factors are intricately linked to the success of adoptive cell therapy. Recently, CRISPR-based technologies have emerged as a major breakthrough for maintaining T cell functions. These technologies have allowed the discovery of T cells' negative regulators such as specific cell-surface receptors, cell-signaling proteins, and transcription factors that are involved in the development or maintenance of T cell dysfunction. By employing a CRISPR-genic invalidation approach to target these negative regulators, it has become possible to prevent the emergence of hypofunctional T cells. This review revisits the establishment of the dysfunctional profile of T cells before delving into a comprehensive summary of recent CRISPR-gene invalidations, with each invalidation contributing to the enhancement of engineered T cells' antitumor capacities. The narrative unfolds as we explore how these advancements were discovered and identified, marking a significant advancement in the pursuit of superior adoptive cell therapy.
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Affiliation(s)
- Valentine De Castro
- Université de Franche-Comté, EFS, INSERM, UMR RIGHT, F-25000, Besançon, France
| | - Jeanne Galaine
- Université de Franche-Comté, EFS, INSERM, UMR RIGHT, F-25000, Besançon, France
| | - Romain Loyon
- Université de Franche-Comté, EFS, INSERM, UMR RIGHT, F-25000, Besançon, France
| | - Yann Godet
- Université de Franche-Comté, EFS, INSERM, UMR RIGHT, F-25000, Besançon, France.
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4
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Jung WJ, Park SJ, Cha S, Kim K. Factors affecting the cleavage efficiency of the CRISPR-Cas9 system. Anim Cells Syst (Seoul) 2024; 28:75-83. [PMID: 38440123 PMCID: PMC10911232 DOI: 10.1080/19768354.2024.2322054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 02/17/2024] [Indexed: 03/06/2024] Open
Abstract
The CRISPR-Cas system stands out as a promising genome editing tool due to its cost-effectiveness and time efficiency compared to other methods. This system has tremendous potential for treating various diseases, including genetic disorders and cancer, and promotes therapeutic research for a wide range of genetic diseases. Additionally, the CRISPR-Cas system simplifies the generation of animal models, offering a more accessible alternative to traditional methods. The CRISPR-Cas9 system can be used to cleave target DNA strands that need to be corrected, causing double-strand breaks (DSBs). DNA with DSBs can then be recovered by the DNA repair pathway that the CRISPR-Cas9 system uses to edit target gene sequences. High cleavage efficiency of the CRISPR-Cas9 system is thus imperative for effective gene editing. Herein, we explore several factors affecting the cleavage efficiency of the CRISPR-Cas9 system. These factors include the GC content of the protospacer-adjacent motif (PAM) proximal and distal regions, single-guide RNA (sgRNA) properties, and chromatin state. These considerations contribute to the efficiency of genome editing.
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Affiliation(s)
- Won Jun Jung
- Department of Physiology, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Soo-Ji Park
- Department of Physiology, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seongkwang Cha
- Department of Physiology, Korea University College of Medicine, Seoul, Republic of Korea
- Neuroscience Research Institute, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kyoungmi Kim
- Department of Physiology, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
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Strobl F, Ratke J, Krämer F, Utta A, Becker S, Stelzer EHK. Next generation marker-based vector concepts for rapid and unambiguous identification of single and double homozygous transgenic organisms. Biol Open 2023; 12:bio060015. [PMID: 37855381 PMCID: PMC10602009 DOI: 10.1242/bio.060015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/15/2023] [Indexed: 10/20/2023] Open
Abstract
For diploid model organisms, the actual transgenesis processes require subsequent periods of transgene management, which are challenging in emerging model organisms due to the lack of suitable methodology. We used the red flour beetle Tribolium castaneum, a stored-grain pest, to perform a comprehensive functional evaluation of our AClashOfStrings (ACOS) and the combined AGameOfClones/AClashOfStrings (AGOC/ACOS) vector concepts, which use four clearly distinguishable markers to provide full visual control over up to two independent transgenes. We achieved comprehensive statistical validation of our approach by systematically creating seventeen novel single and double homozygous sublines intended for fluorescence live imaging, including several sublines in which the microtubule cytoskeleton is labeled. During the mating procedures, we genotyped more than 20,000 individuals in less than 80 working hours, which corresponds to about 10 to 15 s per individual. We also confirm the functionality of our combined concept in two double transgene special cases, i.e. integration of both transgenes in close proximity on the same chromosome and integration of one transgene on the X allosome. Finally, we discuss our vector concepts regarding performance, genotyping accuracy, throughput, resource saving potential, fluorescent protein choice, modularity, adaptation to other diploid model organisms and expansion capability.
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Affiliation(s)
- Frederic Strobl
- Physical Biology / Physikalische Biologie (IZN, FB 15), Buchmann Institute for Molecular Life Sciences (BMLS), Cluster of Excellence Frankfurt – Macromolecular Complexes (CEF – MC), Goethe-Universität Frankfurt am Main (Campus Riedberg),Max-von-Laue-Straße 15, D-60438 Frankfurt am Main, Germany
| | - Julia Ratke
- Physical Biology / Physikalische Biologie (IZN, FB 15), Buchmann Institute for Molecular Life Sciences (BMLS), Cluster of Excellence Frankfurt – Macromolecular Complexes (CEF – MC), Goethe-Universität Frankfurt am Main (Campus Riedberg),Max-von-Laue-Straße 15, D-60438 Frankfurt am Main, Germany
| | - Franziska Krämer
- Physical Biology / Physikalische Biologie (IZN, FB 15), Buchmann Institute for Molecular Life Sciences (BMLS), Cluster of Excellence Frankfurt – Macromolecular Complexes (CEF – MC), Goethe-Universität Frankfurt am Main (Campus Riedberg),Max-von-Laue-Straße 15, D-60438 Frankfurt am Main, Germany
| | - Ana Utta
- Physical Biology / Physikalische Biologie (IZN, FB 15), Buchmann Institute for Molecular Life Sciences (BMLS), Cluster of Excellence Frankfurt – Macromolecular Complexes (CEF – MC), Goethe-Universität Frankfurt am Main (Campus Riedberg),Max-von-Laue-Straße 15, D-60438 Frankfurt am Main, Germany
| | - Sigrun Becker
- Physical Biology / Physikalische Biologie (IZN, FB 15), Buchmann Institute for Molecular Life Sciences (BMLS), Cluster of Excellence Frankfurt – Macromolecular Complexes (CEF – MC), Goethe-Universität Frankfurt am Main (Campus Riedberg),Max-von-Laue-Straße 15, D-60438 Frankfurt am Main, Germany
| | - Ernst H. K. Stelzer
- Physical Biology / Physikalische Biologie (IZN, FB 15), Buchmann Institute for Molecular Life Sciences (BMLS), Cluster of Excellence Frankfurt – Macromolecular Complexes (CEF – MC), Goethe-Universität Frankfurt am Main (Campus Riedberg),Max-von-Laue-Straße 15, D-60438 Frankfurt am Main, Germany
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6
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Halstead IN, Boehnke JR, Lewis GJ. Heterogeneous attitudinal profiles towards gene editing: Evidence from latent class analysis. PUBLIC UNDERSTANDING OF SCIENCE (BRISTOL, ENGLAND) 2023; 32:159-174. [PMID: 36003037 DOI: 10.1177/09636625221114608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Advances in gene-editing technology have important implications for the treatment and prevention of disease. Accordingly, it is important to understand public perceptions towards gene editing, as the public's willingness to endorse gene editing may be as important as technological breakthroughs themselves. Previous research has almost exclusively examined attitudes towards gene editing on specific issues, but has not addressed how attitudes towards gene editing across a range of issues coalesce in individuals: that is, the degree to which discrete, heterogeneous attitudinal profiles exist versus a simple support/oppose continuum. Here, we addressed this issue using latent class analysis on data from The Pew Research Center (N = 4726; US residents) across a wide range of gene-editing topics. We found that attitudes towards gene editing cohere into 10 distinct latent classes that showed some evidence of a support/oppose continuum, but also for clear qualitative differences between each class, even with support or oppose classes, on a number of issues. The most opposed classes significantly differed from the supporter classes in age, sex, political ideology and self-rated knowledge. These findings provide evidence that attitudes towards gene editing are heterogeneous and public discourse, as well as policy making need to consider a range of arguments when evaluating this technology.
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7
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Núñez-Pascual V, Calleja F, Pardo RV, Sarrazin AF, Irles P. The ring-legged earwig Euborellia annulipes as a new model for oogenesis and development studies in insects. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2023; 340:18-33. [PMID: 35167178 DOI: 10.1002/jez.b.23121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 12/23/2021] [Accepted: 01/03/2022] [Indexed: 12/16/2022]
Abstract
Insects are the dominant group of animals on Earth. Despite this abundance, most of our knowledge about many aspects of their biology and development come from a unique model, the vinegar fly, Drosophila melanogaster. Nevertheless, in the last years, the advances in molecular tools and imaging techniques have allowed the emergence of new insect models, adding valuable information to decipher the morphogenetic bases behind the formation and evolution of the vast diversity of shapes, sizes, and patterns that characterize them. Earwigs belong to Dermaptera which is a small order clustered in the Polyneopteran group. They are hemimetabolous insects with a flattened body, characteristic abdominal pincers, and maternal care behavior. This last feature and their role in agroecosystems have been studied in cosmopolitan species such as Forficula auricularia and Euborellia annulipes; however, their reproduction and embryonic development have been poorly addressed in laboratory conditions. In response, here we describe the ring-legged earwig Euborellia annulipes embryogenesis and life cycle from nymphal to adult stages, its reproduction, and essential morphological and behavioral characters. Additionally, using confocal and transmission electron microscopy we analyzed in detail the morphogenesis of its peculiar meroistic polytrophic ovary. Our aim is to provide an emerging model system to perform comparative studies on insect oogenesis, development, and morphological evolution.
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Affiliation(s)
- Valentina Núñez-Pascual
- CoDe-Lab, Instituto de Química, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile.,Institute of Agri-food, Animal and Environmental Sciences (ICA3), Universidad de O'Higgins, Rancagua, Chile
| | - Felipe Calleja
- Institute of Agri-food, Animal and Environmental Sciences (ICA3), Universidad de O'Higgins, Rancagua, Chile
| | - Renato V Pardo
- CoDe-Lab, Instituto de Química, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Andres F Sarrazin
- CoDe-Lab, Instituto de Química, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Paula Irles
- Institute of Agri-food, Animal and Environmental Sciences (ICA3), Universidad de O'Higgins, Rancagua, Chile
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8
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CRISPR-Cas Genome Editing for Insect Pest Stress Management in Crop Plants. STRESSES 2022. [DOI: 10.3390/stresses2040034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Global crop yield and food security are being threatened by phytophagous insects. Innovative methods are required to increase agricultural output while reducing reliance on hazardous synthetic insecticides. Using the revolutionary CRISPR-Cas technology to develop insect-resistant plants appears to be highly efficient at lowering production costs and increasing farm profitability. The genomes of both a model insect, Drosophila melanogaster, and major phytophagous insect genera, viz. Spodoptera, Helicoverpa, Nilaparvata, Locusta, Tribolium, Agrotis, etc., were successfully edited by the CRISPR-Cas toolkits. This new method, however, has the ability to alter an insect’s DNA in order to either induce a gene drive or overcome an insect’s tolerance to certain insecticides. The rapid progress in the methodologies of CRISPR technology and their diverse applications show a high promise in the development of insect-resistant plant varieties or other strategies for the sustainable management of insect pests to ensure food security. This paper reviewed and critically discussed the use of CRISPR-Cas genome-editing technology in long-term insect pest management. The emphasis of this review was on the prospective uses of the CRISPR-Cas system for insect stress management in crop production through the creation of genome-edited crop plants or insects. The potential and the difficulties of using CRISPR-Cas technology to reduce pest stress in crop plants were critically examined and discussed.
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9
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Functional genomic tools for emerging model species. Trends Ecol Evol 2022; 37:1104-1115. [PMID: 35914975 DOI: 10.1016/j.tree.2022.07.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 01/12/2023]
Abstract
Most studies in the field of ecology and evolution aiming to connect genotype to phenotype rarely validate identified loci using functional tools. Recent developments in RNA interference (RNAi) and clustered regularly interspaced palindromic repeats (CRISPR)-Cas genome editing have dramatically increased the feasibility of functional validation. However, these methods come with specific challenges when applied to emerging model organisms, including limited spatial control of gene silencing, low knock-in efficiencies, and low throughput of functional validation. Moreover, many functional studies to date do not recapitulate ecologically relevant variation, and this limits their scope for deeper insights into evolutionary processes. We therefore argue that increased use of gene editing by allelic replacement through homology-directed repair (HDR) would greatly benefit the field of ecology and evolution.
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Schulz NKE, Mohamed FF, Lo LK, Peuß R, de Buhr MF, Kurtz J. Paternal knockdown of tRNA(cytosine-5-)-methyltransferase (Dnmt2) increases offspring susceptibility to infection in red flour beetles. INSECT MOLECULAR BIOLOGY 2022; 31:711-721. [PMID: 35790040 DOI: 10.1111/imb.12798] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Intergenerational effects from fathers to offspring are increasingly reported from diverse organisms, but the underlying mechanisms remain speculative. Paternal trans-generational immune priming (TGIP) was demonstrated in the red flour beetle Tribolium castaneum: non-infectious bacterial exposure of fathers protects their offspring against an infectious challenge for at least two generations. Epigenetic processes, such as cytosine methylation of nucleic acids, have been proposed to enable transfer of information from fathers to offspring. Here we studied a potential role in TGIP of the Dnmt2 gene (renamed as Trdmt1 in humans), which encodes a highly conserved enzyme that methylates different RNAs, including specific cytosines of a set of tRNAs. Dnmt2 has previously been reported to be involved in intergenerational epigenetic inheritance in mice and protection against viruses in fruit flies. We first studied gene expression and found that Dnmt2 is expressed in various life history stages and tissues of T. castaneum, with high expression in the reproductive organs. RNAi-mediated knockdown of Dnmt2 in fathers was systemic, slowed down offspring larval development and increased mortality of the adult offspring upon bacterial infection. However, these effects were independent of bacterial exposure of the fathers. In conclusion, our results point towards a role of Dnmt2 for paternal effects, while elucidation of the mechanisms behind paternal TGIP needs further studies.
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Affiliation(s)
- Nora K E Schulz
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Fakry F Mohamed
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Institute of Virology Muenster, Center for Molecular Biology of Inflammation (ZMBE), University Hospital Muenster, Muenster, Germany
| | - Lai Ka Lo
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Robert Peuß
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Maike F de Buhr
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Joachim Kurtz
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
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Rasheed A, Barqawi AA, Mahmood A, Nawaz M, Shah AN, Bay DH, Alahdal MA, Hassan MU, Qari SH. CRISPR/Cas9 is a powerful tool for precise genome editing of legume crops: a review. Mol Biol Rep 2022; 49:5595-5609. [PMID: 35585381 DOI: 10.1007/s11033-022-07529-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/15/2022] [Accepted: 04/26/2022] [Indexed: 10/18/2022]
Abstract
Legumes are an imperative source of food and proteins across the globe. They also improve soil fertility through symbiotic nitrogen fixation (SNF). Genome editing (GE) is now a novel way of developing desirable traits in legume crops. Genome editing tools like clustered regularly interspaced short palindromic repeats (CRISPR) system permits a defined genome alteration to improve crop performance. This genome editing tool is reliable, cost-effective, and versatile, and it has to deepen in terms of use compared to other tools. Recently, many novel variations have drawn the attention of plant geneticists, and efforts are being made to develop trans-gene-free cultivars for ensuring biosafety measures. This review critically elaborates on the recent development in genome editing of major legumes crops. We hope this updated review will provide essential informations for the researchers working on legumes genome editing. In general, the CRISPR/Cas9 novel GE technique can be integrated with other techniques like omics approaches and next-generation tools to broaden the range of gene editing and develop any desired legumes traits. Regulatory ethics of CRISPR/Cas9 are also discussed.
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Affiliation(s)
- Adnan Rasheed
- Key Laboratory of Crops Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, Jiangxi Agricultural University, 330045, Nanchang, China
| | - Aminah A Barqawi
- Department of Chemistry, Al-Leith University College, Umm Al Qura University, Makkah, Saudi Arabia
| | - Athar Mahmood
- Department of Agronomy, University of Agriculture Faisalabad, 38040, Faisalabad, Pakistan
| | - Muhammad Nawaz
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, 64200, Punjab, Pakistan
| | - Adnan Noor Shah
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, 64200, Punjab, Pakistan.
| | - Daniyah H Bay
- Department of Biology, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Maryam A Alahdal
- Biology Department Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Muhammad Umair Hassan
- Research Center on Ecological Sciences, Jiangxi Agricultural University, 330045, Nanchang, China
| | - Sameer H Qari
- Department of Biology, Al-Jumum University College, Umm Al-Qura University, 21955, Makkah, Saudi Arabia.
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Christian A. Addressing Conflicts of Interest and Conflicts of Commitment in Public Advocacy and Policy Making on CRISPR/Cas-Based Human Genome Editing. Front Res Metr Anal 2022; 7:775336. [PMID: 35572153 PMCID: PMC9094628 DOI: 10.3389/frma.2022.775336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 03/17/2022] [Indexed: 11/24/2022] Open
Abstract
Leading experts on CRISPR/Cas-based genome editing—such as 2020 Nobel laureates Jennifer Doudna and Emmanuelle Charpentier—are not only renowned specialists in their fields, but also public advocates for upcoming regulatory frameworks on CRISPR/Cas. These frameworks will affect large portions of biomedical research on human genome editing. In advocating for particular ways of handling the risks and prospects of this technology, high-profile scientists not only serve as scientific experts, but also as moral advisers. The majority of them currently intend to bring about a “responsible pathway” toward human genome interventions in clinical therapy. Engaging in advocacy for such a pathway, they issue moral judgments on the risks and benefits of this new technology. They declare that there actually is a responsible pathway, they draft resolutions on temporary moratoria, they make judgments on which groups and individuals are credible and should participate in public and semi-public debates, so they also set the standards for deciding who counts as well-informed, as well as the standards of evidence for adopting or rejecting research policies. This degree of influence on public debates and policy making is, at the very least, noteworthy. This contribution sounds a note of caution with regard to the endeavor of a responsible pathway to human genome editing and in particular scrutinizes the legitimacy of expert-driven research policies given commercial conflicts of interest and conflicts of commitment among first-rank scholars.
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13
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McDonald JMC, Reed RD. Patterns of selection across gene regulatory networks. Semin Cell Dev Biol 2022; 145:60-67. [PMID: 35474149 DOI: 10.1016/j.semcdb.2022.03.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 01/31/2022] [Accepted: 03/23/2022] [Indexed: 12/29/2022]
Abstract
Gene regulatory networks (GRNs) are the core engine of organismal development. If we would like to understand the origin and diversification of phenotypes, it is necessary to consider the structure of GRNs in order to reconstruct the links between genetic mutations and phenotypic change. Much of the progress in evolutionary developmental biology, however, has occurred without a nuanced consideration of the evolution of functional relationships between genes, especially in the context of their broader network interactions. Characterizing and comparing GRNs across traits and species in a more detailed way will allow us to determine how network position influences what genes drive adaptive evolution. In this perspective paper, we consider the architecture of developmental GRNs and how positive selection strength may vary across a GRN. We then propose several testable models for these patterns of selection and experimental approaches to test these models.
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Affiliation(s)
- Jeanne M C McDonald
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States.
| | - Robert D Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States.
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14
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Dobreva MP, Camacho J, Abzhanov A. Time to synchronize our clocks: Connecting developmental mechanisms and evolutionary consequences of heterochrony. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2022; 338:87-106. [PMID: 34826199 DOI: 10.1002/jez.b.23103] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 09/27/2021] [Accepted: 10/12/2021] [Indexed: 06/13/2023]
Abstract
Heterochrony, defined as a change in the timing of developmental events altering the course of evolution, was first recognized by Ernst Haeckel in 1866. Haeckel's original definition was meant to explain the observed parallels between ontogeny and phylogeny, but the interpretation of his work became a source of controversy over time. Heterochrony took its modern meaning following the now classical work in the 1970-80s by Steven J. Gould, Pere Alberch, and co-workers. Predicted and described heterochronic scenarios emphasize the many ways in which developmental changes can influence evolution. However, while important examples of heterochrony detected with comparative morphological methods have multiplied, the more mechanistic understanding of this phenomenon lagged conspicuously behind. Considering the rapid progress in imaging and molecular tools available now for developmental biologists, this review aims to stress the need to take heterochrony research to the next level. It is time to synchronize the different levels of heterochrony research into a single analysis flow: from studies on organismal-level morphology to cells to molecules and genes, using complementary techniques. To illustrate how to achieve a more comprehensive understanding of phyletic morphological diversification associated with heterochrony, we discuss several recent case studies at various phylogenetic scales that combine morphological, cellular, and molecular analyses. Such a synergistic approach offers to more fully integrate phylogenetic and ontogenetic dimensions of the fascinating evolutionary phenomenon of heterochrony.
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Affiliation(s)
| | - Jasmin Camacho
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Arkhat Abzhanov
- Department of Life Sciences, Imperial College London, Ascot, UK
- Department of Life Sciences, Natural History Museum, London, UK
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15
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Rasoulinejad SA, Maroufi F. CRISPR-Based Genome Editing as a New Therapeutic Tool in Retinal Diseases. Mol Biotechnol 2021; 63:768-779. [PMID: 34057656 DOI: 10.1007/s12033-021-00345-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 05/19/2021] [Indexed: 12/26/2022]
Abstract
Retinal diseases are the primary reasons for severe visual defects and irreversible blindness. Retinal diseases are also inherited and acquired. Both of them are caused by mutations in genes or disruptions in specific gene expression, which can be treated by gene-editing therapy. Clustered regularly interspaced short palindromic repeats (CRISPR-Cas9) system is a frontier of gene-editing tools with great potential for therapeutic applications in the ophthalmology field to modify abnormal genes and treat the genome or epigenome-related retinal diseases. The CRISPR system is able to edit and trim the gene include deletion, insertion, inhibition, activation, replacing, remodeling, epigenetic alteration, and modify the gene expression. CRISPR-based genome editing techniques have indicated the enormous potential to treat retinal diseases that previous treatment was not available for them. Also, recent CRISPR genome surgery experiments have shown the improvement of patient's vision who suffered from severe visual loss. In this article, we review the applications of the CRISPR-Cas9 system in human or animal models for treating retinal diseases such as retinitis pigmentosa (RP), Leber congenital amaurosis (LCA), age-related macular degeneration (AMD), proliferative diabetic retinopathy (PDR), and proliferative vitreoretinopathy (PVR), then we survey limitations of CRISPR system for clinical therapy.
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Affiliation(s)
- Seyed Ahmad Rasoulinejad
- Department of Ophthalmology, Ayatollah Rouhani Hospital, Babol University of Medical Sciences, Babol, Iran.
| | - Faezeh Maroufi
- Department of Medical Laboratory Sciences, Faculty of Allied Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
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16
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Gene Therapies for Transfusion-Dependent β-Thalassemia. Indian Pediatr 2021. [DOI: 10.1007/s13312-021-2263-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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17
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Bing RG, Sulis DB, Wang JP, Adams MW, Kelly RM. Thermophilic microbial deconstruction and conversion of natural and transgenic lignocellulose. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:272-293. [PMID: 33684253 PMCID: PMC10519370 DOI: 10.1111/1758-2229.12943] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/25/2021] [Accepted: 02/28/2021] [Indexed: 06/12/2023]
Abstract
The potential to convert renewable plant biomasses into fuels and chemicals by microbial processes presents an attractive, less environmentally intense alternative to conventional routes based on fossil fuels. This would best be done with microbes that natively deconstruct lignocellulose and concomitantly form industrially relevant products, but these two physiological and metabolic features are rarely and simultaneously observed in nature. Genetic modification of both plant feedstocks and microbes can be used to increase lignocellulose deconstruction capability and generate industrially relevant products. Separate efforts on plants and microbes are ongoing, but these studies lack a focus on optimal, complementary combinations of these disparate biological systems to obtain a convergent technology. Improving genetic tools for plants have given rise to the generation of low-lignin lines that are more readily solubilized by microorganisms. Most focus on the microbiological front has involved thermophilic bacteria from the genera Caldicellulosiruptor and Clostridium, given their capacity to degrade lignocellulose and to form bio-products through metabolic engineering strategies enabled by ever-improving molecular genetics tools. Bioengineering plant properties to better fit the deconstruction capabilities of candidate consolidated bioprocessing microorganisms has potential to achieve the efficient lignocellulose deconstruction needed for industrial relevance.
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Affiliation(s)
- Ryan G. Bing
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695
| | - Daniel B. Sulis
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695
| | - Jack P. Wang
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695
| | - Michael W.W. Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695
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18
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Kuo DH, De-Miguel FF, Heath-Heckman EAC, Szczupak L, Todd K, Weisblat DA, Winchell CJ. A tale of two leeches: Toward the understanding of the evolution and development of behavioral neural circuits. Evol Dev 2020; 22:471-493. [PMID: 33226195 DOI: 10.1111/ede.12358] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 10/23/2020] [Accepted: 11/02/2020] [Indexed: 11/29/2022]
Abstract
In the animal kingdom, behavioral traits encompass a broad spectrum of biological phenotypes that have critical roles in adaptive evolution, but an EvoDevo approach has not been broadly used to study behavior evolution. Here, we propose that, by integrating two leech model systems, each of which has already attained some success in its respective field, it is possible to take on behavioral traits with an EvoDevo approach. We first identify the developmental changes that may theoretically lead to behavioral evolution and explain why an EvoDevo study of behavior is challenging. Next, we discuss the pros and cons of the two leech model species, Hirudo, a classic model for invertebrate neurobiology, and Helobdella, an emerging model for clitellate developmental biology, as models for behavioral EvoDevo research. Given the limitations of each leech system, neither is particularly strong for behavioral EvoDevo. However, the two leech systems are complementary in their technical accessibilities, and they do exhibit some behavioral similarities and differences. By studying them in parallel and together with additional leech species such as Haementeria, it is possible to explore the different levels of behavioral development and evolution.
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Affiliation(s)
- Dian-Han Kuo
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Francisco F De-Miguel
- Instituto de Fisiología Celular - Neurociencias, Universidad Nacional Autónoma de México, México City, México
| | | | - Lidia Szczupak
- Departamento de Fisiología Biología Molecular y Celular, Universidad de Buenos Aires, and IFIBYNE UBA-CONICET, Buenos Aires, Argentina
| | - Krista Todd
- Department of Neuroscience, Westminster College, Salt Lake City, Utah, USA
| | - David A Weisblat
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Christopher J Winchell
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
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Polkoff KM, Chung J, Simpson SG, Gleason K, Piedrahita JA. In Vitro Validation of Transgene Expression in Gene-Edited Pigs Using CRISPR Transcriptional Activators. CRISPR J 2020; 3:409-418. [PMID: 33095051 PMCID: PMC7580606 DOI: 10.1089/crispr.2020.0037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The use of CRISPR-Cas and RNA-guided endonucleases has drastically changed research strategies for understanding and exploiting gene function, particularly for the generation of gene-edited animal models. This has resulted in an explosion in the number of gene-edited species, including highly biomedically relevant pig models. However, even with error-free DNA insertion or deletion, edited genes are occasionally not expressed and/or translated as expected. Therefore, there is a need to validate the expression outcomes gene modifications in vitro before investing in the costly generation of a gene-edited animal. Unfortunately, many gene targets are tissue specific and/or not expressed in cultured primary cells, making validation difficult without generating an animal. In this study, using pigs as a proof of concept, we show that CRISPR-dCas9 transcriptional activators can be used to validate functional transgene insertion in nonexpressing easily cultured cells such as fibroblasts. This is a tool that can be used across disciplines and animal species to save time and resources by verifying expected outcomes of gene edits before generating live animals.
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Affiliation(s)
- Kathryn M. Polkoff
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, USA
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Jaewook Chung
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, USA
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Sean G. Simpson
- Deparment of Animal and Avian Sciences, University of Maryland, College Park, Maryland, USA
- RenOVAte Biosciences, Inc., Reisterstown, Maryland, USA
| | - Katherine Gleason
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, USA
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Jorge A. Piedrahita
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, USA
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
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20
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Soni S. Gene therapies for transfusion dependent β-thalassemia: Current status and critical criteria for success. Am J Hematol 2020; 95:1099-1112. [PMID: 32562290 DOI: 10.1002/ajh.25909] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 05/30/2020] [Accepted: 06/16/2020] [Indexed: 01/19/2023]
Abstract
Thalassemia is one of the most prevalent monogenic diseases usually caused by quantitative defects in the production of β-globin leading to severe anemia. Technological advances in genome sequencing, stem cell selection, viral vector development, transduction and gene editing strategies now allow for efficient exvivo genetic manipulation of human stem cells that can lead to production of hemoglobin, leading to a meaningful clinical benefit in thalassemia patients. In this review, the status of the gene-therapy approaches available for transfusion dependent thalassemia are discussed, along with the critical criteria that affect efficacy and lessons that have been learned from the early phase clinical trials. Salient steps necessary for the clinical development, manufacturing, and regulatory approvals of gene therapies for thalassemia are also highlighted, so that the potential of these therapies can be realized. It is highly anticipated that gene therapies will soon become a treatment option for patients lacking compatible donors for hematopoietic stem cell transplant and will offer an alternative for definitive treatment of β-thalassemia.
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Affiliation(s)
- Sandeep Soni
- Division of Pediatric Stem Cell Transplant and RM Lucile Packard Children's Hospital, Stanford University Palo Alto California
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21
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Gene knockdown via electroporation of short hairpin RNAs in embryos of the marine hydroid Hydractinia symbiolongicarpus. Sci Rep 2020; 10:12806. [PMID: 32732955 PMCID: PMC7393174 DOI: 10.1038/s41598-020-69489-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/13/2020] [Indexed: 11/08/2022] Open
Abstract
Analyzing gene function in a broad range of research organisms is crucial for understanding the biological functions of genes and their evolution. Recent studies have shown that short hairpin RNAs (shRNAs) can induce gene-specific knockdowns in two cnidarian species. We have developed a detailed, straightforward, and scalable method to deliver shRNAs into fertilized eggs of the hydrozoan cnidarian Hydractinia symbiolongicarpus via electroporation, yielding effective gene-targeted knockdowns that can last throughout embryogenesis. Our electroporation protocol allows for the transfection of shRNAs into hundreds of fertilized H. symbiolongicarpus eggs simultaneously with minimal embryo death and no long-term harmful consequences on the developing animals. We show RT-qPCR and detailed phenotypic evidence of our method successfully inducing effective knockdowns of an exogenous gene (eGFP) and an endogenous gene (Nanos2), as well as knockdown confirmation by RT-qPCR of two other endogenous genes. We also provide visual confirmation of successful shRNA transfection inside embryos through electroporation. Our detailed protocol for electroporation of shRNAs in H. symbiolongicarpus embryos constitutes an important experimental resource for the hydrozoan community while also serving as a successful model for the development of similar methods for interrogating gene function in other marine invertebrates.
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22
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Booth DS, King N. Genome editing enables reverse genetics of multicellular development in the choanoflagellate Salpingoeca rosetta. eLife 2020; 9:56193. [PMID: 32496191 PMCID: PMC7314544 DOI: 10.7554/elife.56193] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 06/03/2020] [Indexed: 12/20/2022] Open
Abstract
In a previous study, we established a forward genetic screen to identify genes required for multicellular development in the choanoflagellate, Salpingoeca rosetta (Levin et al., 2014). Yet, the paucity of reverse genetic tools for choanoflagellates has hampered direct tests of gene function and impeded the establishment of choanoflagellates as a model for reconstructing the origin of their closest living relatives, the animals. Here we establish CRISPR/Cas9-mediated genome editing in S. rosetta by engineering a selectable marker to enrich for edited cells. We then use genome editing to disrupt the coding sequence of a S. rosetta C-type lectin gene, rosetteless, and thereby demonstrate its necessity for multicellular rosette development. This work advances S. rosetta as a model system in which to investigate how genes identified from genetic screens and genomic surveys function in choanoflagellates and evolved as critical regulators of animal biology.
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Affiliation(s)
- David S Booth
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Nicole King
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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23
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Pende M, Vadiwala K, Schmidbaur H, Stockinger AW, Murawala P, Saghafi S, Dekens MPS, Becker K, Revilla-i-Domingo R, Papadopoulos SC, Zurl M, Pasierbek P, Simakov O, Tanaka EM, Raible F, Dodt HU. A versatile depigmentation, clearing, and labeling method for exploring nervous system diversity. SCIENCE ADVANCES 2020; 6:eaba0365. [PMID: 32523996 PMCID: PMC7259959 DOI: 10.1126/sciadv.aba0365] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/27/2020] [Indexed: 06/11/2023]
Abstract
Tissue clearing combined with deep imaging has emerged as a powerful alternative to classical histological techniques. Whereas current techniques have been optimized for imaging selected nonpigmented organs such as the mammalian brain, natural pigmentation remains challenging for most other biological specimens of larger volume. We have developed a fast DEpigmEntation-Plus-Clearing method (DEEP-Clear) that is easily incorporated in existing workflows and combines whole system labeling with a spectrum of detection techniques, ranging from immunohistochemistry to RNA in situ hybridization, labeling of proliferative cells (EdU labeling) and visualization of transgenic markers. With light-sheet imaging of whole animals and detailed confocal studies on pigmented organs, we provide unprecedented insight into eyes, whole nervous systems, and subcellular structures in animal models ranging from worms and squids to axolotls and zebrafish. DEEP-Clear thus paves the way for the exploration of species-rich clades and developmental stages that are largely inaccessible by regular imaging approaches.
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Affiliation(s)
- Marko Pende
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, building CH, 1040 Vienna, Austria
- Section for Bioelectronics, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria
| | - Karim Vadiwala
- Max Perutz Labs and Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria
| | - Hannah Schmidbaur
- Department of Neuroscience and Development, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Alexander W. Stockinger
- Max Perutz Labs and Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria
| | - Prayag Murawala
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Saiedeh Saghafi
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, building CH, 1040 Vienna, Austria
| | - Marcus P. S. Dekens
- Max Perutz Labs and Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria
| | - Klaus Becker
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, building CH, 1040 Vienna, Austria
- Section for Bioelectronics, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria
| | - Roger Revilla-i-Domingo
- Max Perutz Labs and Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria
| | - Sofia-Christina Papadopoulos
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, building CH, 1040 Vienna, Austria
| | - Martin Zurl
- Max Perutz Labs and Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria
| | - Pawel Pasierbek
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Oleg Simakov
- Department of Neuroscience and Development, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Elly M. Tanaka
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Florian Raible
- Max Perutz Labs and Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria
| | - Hans-Ulrich Dodt
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, building CH, 1040 Vienna, Austria
- Section for Bioelectronics, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria
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24
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CRISPR/Cas9-Mediated Mutagenesis of RCO in Cardamine hirsuta. PLANTS 2020; 9:plants9020268. [PMID: 32085527 PMCID: PMC7076481 DOI: 10.3390/plants9020268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 11/17/2022]
Abstract
The small crucifer Cardamine hirsuta bears complex leaves divided into leaflets. This is in contrast to its relative, the reference plant Arabidopsis thaliana, which has simple leaves. Comparative studies between these species provide attractive opportunities to study the diversification of form. Here, we report on the implementation of the CRISPR/Cas9 genome editing methodology in C. hirsuta and with it the generation of novel alleles in the RCO gene, which was previously shown to play a major role in the diversification of form between the two species. Thus, genome editing can now be deployed in C. hirsuta, thereby increasing its versatility as a model system to study gene function and evolution.
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25
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Tomoyasu Y, Halfon MS. How to study enhancers in non-traditional insect models. ACTA ACUST UNITED AC 2020; 223:223/Suppl_1/jeb212241. [PMID: 32034049 DOI: 10.1242/jeb.212241] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Transcriptional enhancers are central to the function and evolution of genes and gene regulation. At the organismal level, enhancers play a crucial role in coordinating tissue- and context-dependent gene expression. At the population level, changes in enhancers are thought to be a major driving force that facilitates evolution of diverse traits. An amazing array of diverse traits seen in insect morphology, physiology and behavior has been the subject of research for centuries. Although enhancer studies in insects outside of Drosophila have been limited, recent advances in functional genomic approaches have begun to make such studies possible in an increasing selection of insect species. Here, instead of comprehensively reviewing currently available technologies for enhancer studies in established model organisms such as Drosophila, we focus on a subset of computational and experimental approaches that are likely applicable to non-Drosophila insects, and discuss the pros and cons of each approach. We discuss the importance of validating enhancer function and evaluate several possible validation methods, such as reporter assays and genome editing. Key points and potential pitfalls when establishing a reporter assay system in non-traditional insect models are also discussed. We close with a discussion of how to advance enhancer studies in insects, both by improving computational approaches and by expanding the genetic toolbox in various insects. Through these discussions, this Review provides a conceptual framework for studying the function and evolution of enhancers in non-traditional insect models.
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Affiliation(s)
| | - Marc S Halfon
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
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26
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Kowalko J. Utilizing the blind cavefish Astyanax mexicanus to understand the genetic basis of behavioral evolution. J Exp Biol 2020; 223:223/Suppl_1/jeb208835. [DOI: 10.1242/jeb.208835] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
ABSTRACT
Colonization of novel habitats often results in the evolution of diverse behaviors. Comparisons between individuals from closely related populations that have evolved divergent behaviors in different environments can be used to investigate behavioral evolution. However, until recently, functionally connecting genotypes to behavioral phenotypes in these evolutionarily relevant organisms has been difficult. The development of gene editing tools will facilitate functional genetic analysis of genotype–phenotype connections in virtually any organism, and has the potential to significantly transform the field of behavioral genetics when applied to ecologically and evolutionarily relevant organisms. The blind cavefish Astyanax mexicanus provides a remarkable example of evolution associated with colonization of a novel habitat. These fish consist of a single species that includes sighted surface fish that inhabit the rivers of Mexico and southern Texas and at least 29 populations of blind cavefish from the Sierra Del Abra and Sierra de Guatemala regions of Northeast Mexico. Although eye loss and albinism have been studied extensively in A. mexicanus, derived behavioral traits including sleep loss, alterations in foraging and reduction in social behaviors are now also being investigated in this species to understand the genetic and neural basis of behavioral evolution. Astyanax mexicanus has emerged as a powerful model system for genotype–phenotype mapping because surface and cavefish are interfertile. Further, the molecular basis of repeated trait evolution can be examined in this species, as multiple cave populations have independently evolved the same traits. A sequenced genome and the implementation of gene editing in A. mexicanus provides a platform for gene discovery and identification of the contributions of naturally occurring variation to behaviors. This review describes the current knowledge of behavioral evolution in A. mexicanus with an emphasis on the molecular and genetic underpinnings of evolved behaviors. Multiple avenues of new research that can be pursued using gene editing tools are identified, and how these will enhance our understanding of behavioral evolution is discussed.
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Affiliation(s)
- Johanna Kowalko
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter, FL 33458, USA
- Program of Neurogenetics, Florida Atlantic University, Jupiter, FL 33458, USA
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27
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Barman A, Deb B, Chakraborty S. A glance at genome editing with CRISPR–Cas9 technology. Curr Genet 2019; 66:447-462. [DOI: 10.1007/s00294-019-01040-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/18/2019] [Accepted: 10/21/2019] [Indexed: 12/16/2022]
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28
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Gilles AF, Schinko JB, Schacht MI, Enjolras C, Averof M. Clonal analysis by tunable CRISPR-mediated excision. Development 2019; 146:dev.170969. [PMID: 30552128 DOI: 10.1242/dev.170969] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 11/26/2018] [Indexed: 01/05/2023]
Abstract
Clonal marking techniques based on the Cre/lox and Flp/FRT systems are widely used in multicellular model organisms to mark individual cells and their progeny, in order to study their morphology, growth properties and developmental fates. The same tools can be adapted to introduce specific genetic changes in a subset of cells within the body, i.e. to perform mosaic genetic analysis. Marking and manipulating distinct cell clones requires control over the frequency of clone induction, which is sometimes difficult to achieve. Here, we present Valcyrie, a new method that replaces the conventional Cre or Flp recombinase-mediated excision of a marker cassette by CRISPR-mediated excision. A major advantage of this approach is that CRISPR efficiency can be tuned in a predictable fashion by manipulating the degree of sequence complementarity between the CRISPR guide RNA and its targets. We establish the method in the beetle Tribolium castaneum We demonstrate that clone marking frequency can be tuned to generate embryos that carry single marked clones. The Valcyrie approach can be applied to a wide range of experimental settings, for example to modulate clone frequency with existing tools in established model organisms and to introduce clonal analysis in emerging experimental models.
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Affiliation(s)
- Anna F Gilles
- Institut de Génomique Fonctionnelle de Lyon (IGFL), École Normale Supérieure de Lyon, 32 avenue Tony Garnier, 69007 Lyon, France .,BMIC graduate programme, Université Claude Bernard/Lyon 1, France.,TriGenes gUG, Biberach University of Applied Sciences, Hubertus-Liebrecht-Str. 35, 88400 Biberach/Riss, Germany
| | - Johannes B Schinko
- Institut de Génomique Fonctionnelle de Lyon (IGFL), École Normale Supérieure de Lyon, 32 avenue Tony Garnier, 69007 Lyon, France .,TriGenes gUG, Biberach University of Applied Sciences, Hubertus-Liebrecht-Str. 35, 88400 Biberach/Riss, Germany.,Centre National de la Recherche Scientifique (CNRS), France
| | - Magdalena I Schacht
- Institut de Génomique Fonctionnelle de Lyon (IGFL), École Normale Supérieure de Lyon, 32 avenue Tony Garnier, 69007 Lyon, France.,Department of Evolutionary Developmental Genetics, Universität Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Camille Enjolras
- Institut de Génomique Fonctionnelle de Lyon (IGFL), École Normale Supérieure de Lyon, 32 avenue Tony Garnier, 69007 Lyon, France.,Centre National de la Recherche Scientifique (CNRS), France
| | - Michalis Averof
- Institut de Génomique Fonctionnelle de Lyon (IGFL), École Normale Supérieure de Lyon, 32 avenue Tony Garnier, 69007 Lyon, France .,Centre National de la Recherche Scientifique (CNRS), France
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Konstantinides N, Degabriel S, Desplan C. Neuro-evo-devo in the single cell sequencing era. CURRENT OPINION IN SYSTEMS BIOLOGY 2018; 11:32-40. [PMID: 30886939 PMCID: PMC6419771 DOI: 10.1016/j.coisb.2018.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The nervous system represents the most complex tissue in animals. How this complexity evolved has been a challenging question to address. The explosion in single cell sequencing techniques, the development of new algorithms to cluster single cells into cell types, along with powerful tools for drawing developmental trajectories offer a unique opportunity to compare homologous cell types between species. They further permit the identification of key developmental points and transcription factors that can lead to the evolution of new cell types. At the same time, the ease of use and efficiency of CRISPR genome editing technology allow validation of predicted regulators. This promises exciting developments in the next few years in the field of neuronal evolution and development.
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Affiliation(s)
| | - Sophie Degabriel
- Department of Biology, New York University, New York, NY 10003, USA
| | - Claude Desplan
- Department of Biology, New York University, New York, NY 10003, USA
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, UAE
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30
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Shah T, Andleeb T, Lateef S, Noor MA. Genome editing in plants: Advancing crop transformation and overview of tools. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 131:12-21. [PMID: 29754773 DOI: 10.1016/j.plaphy.2018.05.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 04/03/2018] [Accepted: 05/05/2018] [Indexed: 05/22/2023]
Abstract
Genome manipulation technology is one of emerging field which brings real revolution in genetic engineering and biotechnology. Targeted editing of genomes pave path to address a wide range of goals not only to improve quality and productivity of crops but also permit to investigate the fundamental roots of biological systems. These goals includes creation of plants with valued compositional properties and with characters that confer resistance to numerous biotic and abiotic stresses. Numerous novel genome editing systems have been introduced during the past few years; these comprise zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas9). Genome editing technique is consistent for improving average yield to achieve the growing demands of the world's existing food famine and to launch a feasible and environmentally safe agriculture scheme, to more specific, productive, cost-effective and eco-friendly. These exciting novel methods, concisely reviewed herein, have verified themselves as efficient and reliable tools for the genetic improvement of plants.
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Affiliation(s)
- Tariq Shah
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Key laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agriculture, Wuhan, 430062, China.
| | - Tayyaba Andleeb
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-e-azam University, Islamabad, Pakistan
| | - Sadia Lateef
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-e-azam University, Islamabad, Pakistan
| | - Mehmood Ali Noor
- Instiute of Crop Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Crop Physiology and Ecology, Ministry of Agriculture, Beijing, 100081, China
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31
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Wang G, Dong Y, Liu X, Yao G, Yu X, Yang M. The Current Status and Development of Insect-Resistant Genetically Engineered Poplar in China. FRONTIERS IN PLANT SCIENCE 2018; 9:1408. [PMID: 30298085 PMCID: PMC6160562 DOI: 10.3389/fpls.2018.01408] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 09/05/2018] [Indexed: 05/03/2023]
Abstract
Poplar is one of the main afforestation tree species in China, and the use of a single, or only a few, clones with low genetic diversity in poplar plantations has led to increasing problems with insect pests. The use of genetic engineering to cultivate insect-resistant poplar varieties has become a hot topic. Over the past 20 years, there have been remarkable achievements in this area. To date, nearly 22 insect-resistant poplar varieties have been created and approved for small-scale field testing, environmental release, or pilot-scale production. Here, we comprehensively review the development of insect-resistant genetically modified (GM) poplars in China. This review mostly addresses issues surrounding the regulation and commercialization of Bt poplar in China, the various insecticidal genes used, the effects of transgenic poplars on insects, toxic protein expression, multigene transformation, the stability of insect resistance, and biosafety. The efficacy of GM poplars for pest control differed among different transgenic poplar clones, larval instars, and insect species. The Bt protein analysis revealed that the expression level of Cry3A was significantly higher than that of Cry1Ac. Temporal and spatial studies of Bt protein showed that its expression varied with the developmental stage and tissue. The inheritance and expression of the exogenous gene were reviewed in transgenic hybrid poplar progeny lines and grafted sections. Biosafety issues, in terms of transgene stability and the effects on soil microorganisms, natural enemies of insects, and arthropod communities are also discussed.
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Affiliation(s)
- Guiying Wang
- Institute of Forest Biotechnology, Forestry College, Agricultural University of Hebei, Baoding, China
- Langfang Academy of Agriculture and Forestry Sciences, Langfang, China
| | - Yan Dong
- Institute of Forest Biotechnology, Forestry College, Agricultural University of Hebei, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - Xiaojie Liu
- Langfang Academy of Agriculture and Forestry Sciences, Langfang, China
| | - Guosheng Yao
- Langfang Academy of Agriculture and Forestry Sciences, Langfang, China
| | - Xiaoyue Yu
- Institute of Forest Biotechnology, Forestry College, Agricultural University of Hebei, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - Minsheng Yang
- Institute of Forest Biotechnology, Forestry College, Agricultural University of Hebei, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
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32
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HIV-1 inhibition in cells with CXCR4 mutant genome created by CRISPR-Cas9 and piggyBac recombinant technologies. Sci Rep 2018; 8:8573. [PMID: 29872154 PMCID: PMC5988798 DOI: 10.1038/s41598-018-26894-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 05/22/2018] [Indexed: 01/15/2023] Open
Abstract
The C-X-C chemokine receptor type 4 (CXCR4) is one of the major co-receptors for human immunodeficiency virus type 1 (HIV-1) entry and is considered an important therapeutic target. However, its function in maintaining the development of hematopoietic stem cells (HSC) makes it difficult to be used for HIV-1 gene therapy with HSC transplantation. A previous report showed that the natural CXCR4 P191A mutant inhibits HIV-1 infection without any defect in HSC differentiation, which could provide a basis for the development of new approaches for HIV-1 gene therapy. In the present study, we used CRISPR-Cas9 combined with the piggyBac transposon technologies to efficiently induce the expression of the CXCR4 P191A mutant in an HIV-1 reporter cell line, leading to no detectable exogenous sequences. In addition, no off-target effects were detected in the genome-edited cells. The decline of HIV-1 replication in biallelic CXCR4 gene-edited cells suggests that individuals equipped with homologous recombination of the CXCR4 P191A mutant could prevent or reduce HIV-1 infection. This study provides an effective approach to create a CXCR4 mutation with HIV-1 infection inhibition function and without leaving any genetic footprint inside cells, thereby shedding light on an application in HIV-1 gene therapy and avoiding side effects caused by deficiency or destruction of CXCR4 function.
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33
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Cleves PA, Strader ME, Bay LK, Pringle JR, Matz MV. CRISPR/Cas9-mediated genome editing in a reef-building coral. Proc Natl Acad Sci U S A 2018; 115:5235-5240. [PMID: 29695630 PMCID: PMC5960312 DOI: 10.1073/pnas.1722151115] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Reef-building corals are critically important species that are threatened by anthropogenic stresses including climate change. In attempts to understand corals' responses to stress and other aspects of their biology, numerous genomic and transcriptomic studies have been performed, generating a variety of hypotheses about the roles of particular genes and molecular pathways. However, it has not generally been possible to test these hypotheses rigorously because of the lack of genetic tools for corals. Here, we demonstrate efficient genome editing using the CRISPR/Cas9 system in the coral Acropora millepora We targeted the genes encoding fibroblast growth factor 1a (FGF1a), green fluorescent protein (GFP), and red fluorescent protein (RFP). After microinjecting CRISPR/Cas9 ribonucleoprotein complexes into fertilized eggs, we detected induced mutations in the targeted genes using changes in restriction-fragment length, Sanger sequencing, and high-throughput Illumina sequencing. We observed mutations in ∼50% of individuals screened, and the proportions of wild-type and various mutant gene copies in these individuals indicated that mutation induction continued for at least several cell cycles after injection. Although multiple paralogous genes encoding green fluorescent proteins are present in A. millepora, appropriate design of the guide RNA allowed us to induce mutations simultaneously in more than one paralog. Because A. millepora larvae can be induced to settle and begin colony formation in the laboratory, CRISPR/Cas9-based gene editing should allow rigorous tests of gene function in both larval and adult corals.
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Affiliation(s)
- Phillip A Cleves
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Marie E Strader
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
| | - Line K Bay
- Australian Institute of Marine Science, Townsville, QLD 4810, Australia
| | - John R Pringle
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305;
| | - Mikhail V Matz
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712;
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34
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Guiding Lights in Genome Editing for Inherited Retinal Disorders: Implications for Gene and Cell Therapy. Neural Plast 2018; 2018:5056279. [PMID: 29853845 PMCID: PMC5964415 DOI: 10.1155/2018/5056279] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/18/2018] [Indexed: 12/26/2022] Open
Abstract
Inherited retinal dystrophies (IRDs) are a leading cause of visual impairment in the developing world. These conditions present an irreversible dysfunction or loss of neural retinal cells, which significantly impacts quality of life. Due to the anatomical accessibility and immunoprivileged status of the eye, ophthalmological research has been at the forefront of innovative and advanced gene- and cell-based therapies, both of which represent great potential as therapeutic treatments for IRD patients. However, due to a genetic and clinical heterogeneity, certain IRDs are not candidates for these approaches. New advances in the field of genome editing using Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated protein (Cas) have provided an accurate and efficient way to edit the human genome and represent an appealing alternative for treating IRDs. We provide a brief update on current gene augmentation therapies for retinal dystrophies. Furthermore, we discuss recent advances in the field of genome editing and stem cell technologies, which together enable precise and personalized therapies for patients. Lastly, we highlight current technological limitations and barriers that need to be overcome before this technology can become a viable treatment option for patients.
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35
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Strobl F, Anderl A, Stelzer EHK. A universal vector concept for a direct genotyping of transgenic organisms and a systematic creation of homozygous lines. eLife 2018; 7:e31677. [PMID: 29543587 PMCID: PMC5854464 DOI: 10.7554/elife.31677] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 01/29/2018] [Indexed: 12/25/2022] Open
Abstract
Diploid transgenic organisms are either hemi- or homozygous. Genetic assays are, therefore, required to identify the genotype. Our AGameOfClones vector concept uses two clearly distinguishable transformation markers embedded in interweaved, but incompatible Lox site pairs. Cre-mediated recombination leads to hemizygous individuals that carry only one marker. In the following generation, heterozygous descendants are identified by the presence of both markers and produce homozygous progeny that are selected by the lack of one marker. We prove our concept in Tribolium castaneum by systematically creating multiple functional homozygous transgenic lines suitable for long-term fluorescence live imaging. Our approach saves resources and simplifies transgenic organism handling. Since the concept relies on the universal Cre-Lox system, it is expected to work in all diploid model organisms, for example, insects, zebrafish, rodents and plants. With appropriate adaptions, it can be used in knock-out assays to preselect homozygous individuals and thus minimize the number of wasted animals.
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Affiliation(s)
- Frederic Strobl
- Physical Biology, BMLS, CEF-MCGoethe UniversitätFrankfurt am MainGermany
| | - Anita Anderl
- Physical Biology, BMLS, CEF-MCGoethe UniversitätFrankfurt am MainGermany
| | - Ernst HK Stelzer
- Physical Biology, BMLS, CEF-MCGoethe UniversitätFrankfurt am MainGermany
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36
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Tiricz H, Nagy B, Ferenc G, Török K, Nagy I, Dudits D, Ayaydin F. Relaxed chromatin induced by histone deacetylase inhibitors improves the oligonucleotide-directed gene editing in plant cells. JOURNAL OF PLANT RESEARCH 2018; 131:179-189. [PMID: 28836127 DOI: 10.1007/s10265-017-0975-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 07/26/2017] [Indexed: 06/07/2023]
Abstract
Improving efficiency of oligonucleotide-directed mutagenesis (ODM) is a prerequisite for wide application of this gene-editing approach in plant science and breeding. Here we have tested histone deacetylase inhibitor treatments for induction of relaxed chromatin and for increasing the efficiency of ODM in cultured maize cells. For phenotypic assay we produced transgenic maize cell lines expressing the non-functional Green Fluorescent Protein (mGFP) gene carrying a TAG stop codon. These transgenic cells were bombarded with corrective oligonucleotide as editing reagent to recover GFP expression. Repair of green fluorescent protein function was monitored by confocal fluorescence microscopy and flow cytometry was used for quantification of correction events. Sequencing PCR fragments of the GFP gene from corrected cells indicated a nucleotide exchange in the stop codon (TAG) from T to G nucleotide that resulted in the restoration of GFP function. We show that pretreatment of maize cells with sodium butyrate (5-10 mM) and nicotinamide (1-5 mM) as known inhibitors of histone deacetylases can cause elevated chromatin sensitivity to DNase I that was visualized in agarose gels and confirmed by the reduced presence of intact PCR template for the inserted exogenous mGFP gene. Maize cells with more relaxed chromatin could serve as an improved recipient for targeted nucleotide exchange as indicated by an average of 2.67- to 3.62-fold increase in GFP-positive cells. Our results stimulate further studies on the role of the condition of the recipient cells in ODM and testing the application of chromatin modifying agents in other, programmable nuclease-based genome-editing techniques in higher plants.
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Affiliation(s)
- Hilda Tiricz
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Bettina Nagy
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Györgyi Ferenc
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Katalin Török
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - István Nagy
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
- SeqOmics Biotechnology Ltd., Mórahalom, Hungary
| | - Dénes Dudits
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary.
| | - Ferhan Ayaydin
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
- Laboratory of Cellular Imaging, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
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37
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Novel and innovative approaches for treatment of β-thalassemia. PEDIATRIC HEMATOLOGY ONCOLOGY JOURNAL 2017. [DOI: 10.1016/j.phoj.2017.11.153] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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38
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Schlosser G, Musser J, Arendt D. Editorial - Development and evolution of sensory cells and organs. Dev Biol 2017; 431:1-2. [PMID: 28889956 DOI: 10.1016/j.ydbio.2017.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Gerhard Schlosser
- School of Natural Sciences, National University of Ireland, Galway, Biosciences Research Building, Newcastle Road, Galway, Ireland.
| | - Jacob Musser
- European Molecular Biology Laboratory, Developmental Biology Unit, 69117 Heidelberg, Germany.
| | - Detlev Arendt
- European Molecular Biology Laboratory, Developmental Biology Unit, 69117 Heidelberg, Germany.
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39
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Sun D, Guo Z, Liu Y, Zhang Y. Progress and Prospects of CRISPR/Cas Systems in Insects and Other Arthropods. Front Physiol 2017; 8:608. [PMID: 28932198 PMCID: PMC5592444 DOI: 10.3389/fphys.2017.00608] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/07/2017] [Indexed: 01/03/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated gene Cas9 represent an invaluable system for the precise editing of genes in diverse species. The CRISPR/Cas9 system is an adaptive mechanism that enables bacteria and archaeal species to resist invading viruses and phages or plasmids. Compared with zinc finger nucleases and transcription activator-like effector nucleases, the CRISPR/Cas9 system has the advantage of requiring less time and effort. This efficient technology has been used in many species, including diverse arthropods that are relevant to agriculture, forestry, fisheries, and public health; however, there is no review that systematically summarizes its successful application in the editing of both insect and non-insect arthropod genomes. Thus, this paper seeks to provide a comprehensive and impartial overview of the progress of the CRISPR/Cas9 system in different arthropods, reviewing not only fundamental studies related to gene function exploration and experimental optimization but also applied studies in areas such as insect modification and pest control. In addition, we also describe the latest research advances regarding two novel CRISPR/Cas systems (CRISPR/Cpf1 and CRISPR/C2c2) and discuss their future prospects for becoming crucial technologies in arthropods.
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Affiliation(s)
- Dan Sun
- Longping Branch, Graduate School of Hunan UniversityChangsha, China.,Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Zhaojiang Guo
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Yong Liu
- Longping Branch, Graduate School of Hunan UniversityChangsha, China
| | - Youjun Zhang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
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40
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Rebeiz M, Tsiantis M. Enhancer evolution and the origins of morphological novelty. Curr Opin Genet Dev 2017; 45:115-123. [PMID: 28527813 DOI: 10.1016/j.gde.2017.04.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 03/25/2017] [Accepted: 04/27/2017] [Indexed: 01/07/2023]
Abstract
A central goal of evolutionary biology is to understand the genetic origin of morphological novelties-i.e. anatomical structures unique to a taxonomic group. Elaboration of morphology during development depends on networks of regulatory genes that activate patterned gene expression through transcriptional enhancer regions. We summarize recent case studies and genome-wide investigations that have uncovered diverse mechanisms though which new enhancers arise. We also discuss how these enhancer-originating mechanisms have clarified the history of genetic networks underlying diversification of genital structures in flies, limbs and neural crest in chordates, and plant leaves. These studies have identified enhancers that were pivotal for morphological divergence and highlighted how novel genetic networks shaping form emerged from pre-existing ones.
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Affiliation(s)
- Mark Rebeiz
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15215, USA.
| | - Miltos Tsiantis
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829 Köln, Germany.
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41
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Taning CNT, Van Eynde B, Yu N, Ma S, Smagghe G. CRISPR/Cas9 in insects: Applications, best practices and biosafety concerns. JOURNAL OF INSECT PHYSIOLOGY 2017; 98:245-257. [PMID: 28108316 DOI: 10.1016/j.jinsphys.2017.01.007] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/28/2016] [Accepted: 01/12/2017] [Indexed: 05/13/2023]
Abstract
Discovered as a bacterial adaptive immune system, CRISPR/Cas9 (clustered, regularly interspaced, short palindromic repeat/CRISPR associated) is being developed as an attractive tool in genome editing. Due to its high specificity and applicability, CRISPR/Cas9-mediated gene editing has been employed in a multitude of organisms and cells, including insects, for not only fundamental research such as gene function studies, but also applied research such as modification of organisms of economic importance. Despite the rapid increase in the use of CRISPR in insect genome editing, results still differ from each study, principally due to existing differences in experimental parameters, such as the Cas9 and guide RNA form, the delivery method, the target gene and off-target effects. Here, we review current reports on the successes of CRISPR/Cas9 applications in diverse insects and insect cells. We furthermore summarize several best practices to give a useful checklist of CRISPR/Cas9 experimental setup in insects for beginners. Lastly, we discuss the biosafety concerns related to the release of CRISPR/Cas9-edited insects into the environment.
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Affiliation(s)
- Clauvis Nji Tizi Taning
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium.
| | - Benigna Van Eynde
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Na Yu
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
| | - Sanyuan Ma
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Guy Smagghe
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium.
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Abstract
Although the insect wing is a textbook example of morphological novelty, the origin of insect wings remains a mystery and is regarded as a chief conundrum in biology. Centuries of debates have culminated into two prominent hypotheses: the tergal origin hypothesis and the pleural origin hypothesis. However, between these two hypotheses, there is little consensus in regard to the origin tissue of the wing as well as the evolutionary route from the origin tissue to the functional flight device. Recent evolutionary developmental (evo-devo) studies have shed new light on the origin of insect wings. A key concept in these studies is “serial homology”. In this review, we discuss how the wing serial homologs identified in recent evo-devo studies have provided a new angle through which this century-old conundrum can be explored. We also review what we have learned so far from wing serial homologs and discuss what we can do to go beyond simply identifying wing serial homologs and delve further into the developmental and genetic mechanisms that have facilitated the evolution of insect wings.
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Affiliation(s)
- Yoshinori Tomoyasu
- Department of Biology, Miami University, Pearson Hall, 700E High Street, Oxford, OH 45056, USA
| | - Takahiro Ohde
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, 38 Nishigonaka Myodaiji, Okazaki 444-8585, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 38 Nishigonaka Myodaiji, Okazaki 444-8585, Japan
| | - Courtney Clark-Hachtel
- Department of Biology, Miami University, Pearson Hall, 700E High Street, Oxford, OH 45056, USA
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43
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Genome Editing in Plants: An Overview of Tools and Applications. INTERNATIONAL JOURNAL OF AGRONOMY 2017. [DOI: 10.1155/2017/7315351] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The emergence of genome manipulation methods promises a real revolution in biotechnology and genetic engineering. Targeted editing of the genomes of living organisms not only permits investigations into the understanding of the fundamental basis of biological systems but also allows addressing a wide range of goals towards improving productivity and quality of crops. This includes the creation of plants with valuable compositional properties and with traits that confer resistance to various biotic and abiotic stresses. During the past few years, several novel genome editing systems have been developed; these include zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas9). These exciting new methods, briefly reviewed herein, have proved themselves as effective and reliable tools for the genetic improvement of plants.
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44
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Sanger TJ, Kircher BK. Model Clades Versus Model Species: Anolis Lizards as an Integrative Model of Anatomical Evolution. Methods Mol Biol 2017; 1650:285-297. [PMID: 28809029 DOI: 10.1007/978-1-4939-7216-6_19] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Anolis lizards , known for their replicated patterns of morphological diversification, are widely studied in the fields of evolution and ecology. As a textbook example of adaptive radiation, this genus has supported decades of intense study in natural history, behavior, morphological evolution, and systematics. Following the publication of the A. carolinensis genome, research on Anolis lizards has expanded into new areas, toward obtaining an understanding the developmental and genetic bases of anole diversity. Here, we discuss recent progress in these areas and the burgeoning methodological toolkit that has been used to elucidate the genetic mechanisms underlying anatomical variation in this group. We also highlight the growing number of studies that have used A. carolinensis as the representative squamate in large-scale comparison of amniote evolution and development . Finally, we address one of the largest technical challenges biologists are facing in making Anolis a model for integrative studies of ecology, evolution, development , and genetics, the development of ex-ovo culturing techniques that have broad utility. Ultimately, with the power to ask questions across all biological scales in this diverse genus full, anoles are rapidly becoming a uniquely integrative and powerful biological system.
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Affiliation(s)
- Thomas J Sanger
- Department of Biology, Loyola University Chicago, Chicago, IL, 60660, USA.
| | - Bonnie K Kircher
- Department of Biology, University of Florida, Gainesville, FL, 32601, USA
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45
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Rutkauskas M, Krivoy A, Szczelkun MD, Rouillon C, Seidel R. Single-Molecule Insight Into Target Recognition by CRISPR-Cas Complexes. Methods Enzymol 2016; 582:239-273. [PMID: 28062037 DOI: 10.1016/bs.mie.2016.10.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Ribonucleoprotein (RNP) complexes from CRISPR-Cas systems have attracted enormous interest since they can be easily and flexibly reprogrammed to target any desired locus for genome engineering and gene regulation applications. Basis for the programmability is a short RNA (crRNA) inside these complexes that recognizes the target nucleic acid by base pairing. For CRISPR-Cas systems that target double-stranded DNA this results in local DNA unwinding and formation of a so-called R-loop structure. Here we provide an overview how this target recognition mechanism can be dissected in great detail at the level of a single molecule. Specifically, we demonstrate how magnetic tweezers are applied to measure the local DNA unwinding at the target in real time. To this end we introduce the technique and the measurement principle. By studying modifications of the consensus target sequence, we show how different sequence elements contribute to the target recognition mechanism. From these data, a unified target recognition mechanism can be concluded for the RNPs Cascade and Cas9 from types I and II CRISPR-Cas systems. R-loop formation is hereby initiated on the target at an upstream element, called protospacer adjacent motif (PAM), from which the R-loop structure zips directionally toward the PAM-distal end of the target. At mismatch positions, the R-loop propagation stalls and further propagation competes with collapse of the structure. Upon full R-loop zipping conformational changes within the RNPs trigger degradation of the DNA target. This represents a shared labor mechanism in which zipping between nucleic acid strands is the actual target recognition mechanism while sensing of the R-loop arrival at the PAM-distal end just verifies the success of the full zipping.
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Affiliation(s)
- M Rutkauskas
- Molecular Biophysics Group, Institute for Experimental Physics I, Universität Leipzig, Leipzig, Germany
| | - A Krivoy
- Molecular Biophysics Group, Institute for Experimental Physics I, Universität Leipzig, Leipzig, Germany; Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - M D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - C Rouillon
- Molecular Biophysics Group, Institute for Experimental Physics I, Universität Leipzig, Leipzig, Germany.
| | - R Seidel
- Molecular Biophysics Group, Institute for Experimental Physics I, Universität Leipzig, Leipzig, Germany.
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46
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Evans TA. Embryonic axon guidance: insights from Drosophila and other insects. CURRENT OPINION IN INSECT SCIENCE 2016; 18:11-16. [PMID: 27939705 DOI: 10.1016/j.cois.2016.08.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/10/2016] [Accepted: 08/15/2016] [Indexed: 06/06/2023]
Abstract
During embryonic development, growing axons are guided by cellular signaling pathways that control a series of individual axon guidance decisions. In Drosophila, two major pathways (Netrin-Frazzled/DCC and Slit-Robo) regulate axon guidance in the embryonic ventral nerve cord, including the critical decision of whether or not to cross the midline. Studies in the fruit fly have revealed a complex picture of precise regulation and cross-talk between these pathways. In addition, Robo receptors in Drosophila have diversified their activities to regulate additional axon guidance decisions in the developing embryo. Here, I discuss recent advances in understanding roles and regulation of the Net-Fra and Slit-Robo signaling pathways in Drosophila, and examine the evolutionary conservation of these signaling mechanisms across insects and other arthropods.
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Affiliation(s)
- Timothy A Evans
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, United States.
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47
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Kao D, Lai AG, Stamataki E, Rosic S, Konstantinides N, Jarvis E, Di Donfrancesco A, Pouchkina-Stancheva N, Sémon M, Grillo M, Bruce H, Kumar S, Siwanowicz I, Le A, Lemire A, Eisen MB, Extavour C, Browne WE, Wolff C, Averof M, Patel NH, Sarkies P, Pavlopoulos A, Aboobaker A. The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion. eLife 2016; 5:20062. [PMID: 27849518 PMCID: PMC5111886 DOI: 10.7554/elife.20062] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 10/19/2016] [Indexed: 12/17/2022] Open
Abstract
The amphipod crustacean Parhyale hawaiensis is a blossoming model system for studies of developmental mechanisms and more recently regeneration. We have sequenced the genome allowing annotation of all key signaling pathways, transcription factors, and non-coding RNAs that will enhance ongoing functional studies. Parhyale is a member of the Malacostraca clade, which includes crustacean food crop species. We analysed the immunity related genes of Parhyale as an important comparative system for these species, where immunity related aquaculture problems have increased as farming has intensified. We also find that Parhyale and other species within Multicrustacea contain the enzyme sets necessary to perform lignocellulose digestion ('wood eating'), suggesting this ability may predate the diversification of this lineage. Our data provide an essential resource for further development of Parhyale as an experimental model. The first malacostracan genome will underpin ongoing comparative work in food crop species and research investigating lignocellulose as an energy source. DOI:http://dx.doi.org/10.7554/eLife.20062.001 The marine crustacean known as Parhyale hawaiensis is related to prawns, shrimps and crabs and is found at tropical coastlines around the world. This species has recently attracted scientific interest as a possible new model to study how animal embryos develop before birth and, because Parhyale can rapidly regrow lost limbs, how tissues and organs regenerate. Indeed, Parhyale has many characteristics that make it a good model organism, being small, fast-growing and easy to keep and care for in the laboratory. Several research tools have already been developed to make it easier to study Parhyale. This includes the creation of a system for using the popular gene editing technology, CRISPR, in this animal. However, one critical resource that is available for most model organisms was missing; the complete sequence of all the genetic information of this crustacean, also known as its genome, was not available. Kao, Lai, Stamataki et al. have now compiled the Parhyale genome – which is slightly larger than the human genome – and studied its genetics. Analysis revealed that Parhyale has genes that allow it to fully digest plant material. This is unusual because most animals that do this rely upon the help of bacteria. Kao, Lai, Stamataki et al. also identified genes that provide some of the first insights into the immune system of crustaceans, which protects these creatures from diseases. Kao, Lai, Stamataki et al. have provided a resource and findings that could help to establish Parhyale as a popular model organism for studying several ideas in biology, including organ regeneration and embryonic development. Understanding how Parhyale digests plant matter, for example, could progress the biofuel industry towards efficient production of greener energy. Insights from its immune system could also be adapted to make farmed shrimp and prawns more resistant to infections, boosting seafood production. DOI:http://dx.doi.org/10.7554/eLife.20062.002
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Affiliation(s)
- Damian Kao
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Alvina G Lai
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Evangelia Stamataki
- Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States
| | - Silvana Rosic
- MRC Clinical Sciences Centre, Imperial College London, London, United Kingdom.,Clinical Sciences, Imperial College London, London, United Kingdom
| | - Nikolaos Konstantinides
- Institut de Gé nomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and É cole Normale Supé rieure de Lyon, Lyon, France
| | - Erin Jarvis
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
| | | | | | - Marie Sémon
- Institut de Gé nomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and É cole Normale Supé rieure de Lyon, Lyon, France
| | - Marco Grillo
- Institut de Gé nomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and É cole Normale Supé rieure de Lyon, Lyon, France
| | - Heather Bruce
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
| | - Suyash Kumar
- Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States
| | - Igor Siwanowicz
- Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States
| | - Andy Le
- Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States
| | - Andrew Lemire
- Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States
| | - Michael B Eisen
- Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, United States
| | - Cassandra Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States
| | - William E Browne
- Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, Washington, United States
| | - Carsten Wolff
- Vergleichende Zoologie, Institut fur Biologie,Humboldt-Universitat zu Berlin, Berlin, Germany
| | - Michalis Averof
- Institut de Gé nomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and É cole Normale Supé rieure de Lyon, Lyon, France
| | - Nipam H Patel
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
| | - Peter Sarkies
- MRC Clinical Sciences Centre, Imperial College London, London, United Kingdom.,Clinical Sciences, Imperial College London, London, United Kingdom
| | | | - Aziz Aboobaker
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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48
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Sengillo JD, Justus S, Tsai YT, Cabral T, Tsang SH. Gene and cell-based therapies for inherited retinal disorders: An update. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2016; 172:349-366. [PMID: 27862925 DOI: 10.1002/ajmg.c.31534] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Retinal degenerations present a unique challenge as disease progression is irreversible and the retina has little regenerative potential. No current treatments for inherited retinal disease have the ability to reverse blindness, and current dietary supplement recommendations only delay disease progression with varied results. However, the retina is anatomically accessible and capable of being monitored at high resolution in vivo. This, in addition to the immune-privileged status of the eye, has put ocular disease at the forefront of advances in gene- and cell-based therapies. This review provides an update on gene therapies and randomized control trials for inherited retinal disease, including Leber congenital amaurosis, choroideremia, retinitis pigmentosa, Usher syndrome, X-linked retinoschisis, Leber hereditary optic neuropathy, and achromatopsia. New gene-modifying and cell-based strategies are also discussed. © 2016 Wiley Periodicals, Inc.
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49
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Heppert JK, Dickinson DJ, Pani AM, Higgins CD, Steward A, Ahringer J, Kuhn JR, Goldstein B. Comparative assessment of fluorescent proteins for in vivo imaging in an animal model system. Mol Biol Cell 2016; 27:3385-3394. [PMID: 27385332 PMCID: PMC5221575 DOI: 10.1091/mbc.e16-01-0063] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 06/27/2016] [Accepted: 06/28/2016] [Indexed: 11/11/2022] Open
Abstract
Fluorescent protein tags are fundamental tools used to visualize gene products and analyze their dynamics in vivo. Recent advances in genome editing have expedited the precise insertion of fluorescent protein tags into the genomes of diverse organisms. These advances expand the potential of in vivo imaging experiments and facilitate experimentation with new, bright, photostable fluorescent proteins. Most quantitative comparisons of the brightness and photostability of different fluorescent proteins have been made in vitro, removed from biological variables that govern their performance in cells or organisms. To address the gap, we quantitatively assessed fluorescent protein properties in vivo in an animal model system. We generated transgenic Caenorhabditis elegans strains expressing green, yellow, or red fluorescent proteins in embryos and imaged embryos expressing different fluorescent proteins under the same conditions for direct comparison. We found that mNeonGreen was not as bright in vivo as predicted based on in vitro data but is a better tag than GFP for specific kinds of experiments, and we report on optimal red fluorescent proteins. These results identify ideal fluorescent proteins for imaging in vivo in C. elegans embryos and suggest good candidate fluorescent proteins to test in other animal model systems for in vivo imaging experiments.
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Affiliation(s)
- Jennifer K Heppert
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Daniel J Dickinson
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Ariel M Pani
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Christopher D Higgins
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Annette Steward
- Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Julie Ahringer
- Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Jeffrey R Kuhn
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712
| | - Bob Goldstein
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
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50
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Grillo M, Konstantinides N, Averof M. Old questions, new models: unraveling complex organ regeneration with new experimental approaches. Curr Opin Genet Dev 2016; 40:23-31. [DOI: 10.1016/j.gde.2016.05.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Revised: 05/12/2016] [Accepted: 05/13/2016] [Indexed: 10/21/2022]
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