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      Intimate functional interactions between  TGS1 and the Smn complex revealed by an analysis of the Drosophila eye development

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          Abstract

          Trimethylguanosine synthase 1 (TGS1) is a conserved enzyme that mediates formation of the trimethylguanosine cap on several RNAs, including snRNAs and telomerase RNA. Previous studies have shown that TGS1 binds the Survival Motor Neuron (SMN) protein, whose deficiency causes spinal muscular atrophy (SMA). Here, we analyzed the roles of the Drosophila orthologs of the human TGS1 and SMN genes. We show that the Drosophila TGS1 protein (dTgs1) physically interacts with all subunits of the Drosophila Smn complex (Smn, Gem2, Gem3, Gem4 and Gem5), and that a human TGS1 transgene rescues the mutant phenotype caused by dTgs1 loss. We demonstrate that both dTgs1 and Smn are required for viability of retinal progenitor cells and that downregulation of these genes leads to a reduced eye size. Importantly, overexpression of dTgs1 partially rescues the eye defects caused by Smn depletion, and vice versa. These results suggest that the Drosophila eye model can be exploited for screens aimed at the identification of genes and drugs that modify the phenotypes elicited by Tgs1 and Smn deficiency. These modifiers could help to understand the molecular mechanisms underlying SMA pathogenesis and devise new therapies for this genetic disease.

          Author summary

          We explored the functional relationships between TGS1 and SMN using Drosophila as model organism. TGS1 is an enzyme that modifies the structure of the 5’-end of several RNAs, including telomerase RNA and the small nuclear RNAs (snRNAs) that are required for messenger RNA maturation. The SMN protein regulates snRNAs biogenesis and mutations in human SMN cause Spinal Muscular Atrophy (SMA), a devastating disorder characterized by neurodegeneration, progressive paralysis and death. We show that mutations in the Drosophila TGS1 ( dTgs1) gene cause lethality, which is rescued by a human TGS1 transgene. We also show that the dTgs1 protein physically interacts with all subunits of the Smn complex, and that downregulation of either dTgs1 or Smn leads to a reduced Drosophila eye size. Notably, overexpression of dTgs1 partially rescues the eye defects caused by Smn knockdown, and vice versa, indicating that these genes cooperate in eye development. These results suggest that the eye model can be exploited for screens aimed at detection of chemical and genetic modifiers of the eye mutant phenotype elicited by dTgs1 and Smn deficiency, providing new clues about SMA pathogenesis and potential therapies.

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          Most cited references77

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          An optimized transgenesis system for Drosophila using germ-line-specific phiC31 integrases.

          Germ-line transformation via transposable elements is a powerful tool to study gene function in Drosophila melanogaster. However, some inherent characteristics of transposon-mediated transgenesis limit its use for transgene analysis. Here, we circumvent these limitations by optimizing a phiC31-based integration system. We generated a collection of lines with precisely mapped attP sites that allow the insertion of transgenes into many different predetermined intergenic locations throughout the fly genome. By using regulatory elements of the nanos and vasa genes, we established endogenous sources of the phiC31 integrase, eliminating the difficulties of coinjecting integrase mRNA and raising the transformation efficiency. Moreover, to discriminate between specific and rare nonspecific integration events, a white gene-based reconstitution system was generated that enables visual selection for precise attP targeting. Finally, we demonstrate that our chromosomal attP sites can be modified in situ, extending their scope while retaining their properties as landing sites. The efficiency, ease-of-use, and versatility obtained here with the phiC31-based integration system represents an important advance in transgenesis and opens up the possibility of systematic, high-throughput screening of large cDNA sets and regulatory elements.
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            Optimized CRISPR/Cas tools for efficient germline and somatic genome engineering in Drosophila.

            The type II clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system has emerged recently as a powerful method to manipulate the genomes of various organisms. Here, we report a toolbox for high-efficiency genome engineering of Drosophila melanogaster consisting of transgenic Cas9 lines and versatile guide RNA (gRNA) expression plasmids. Systematic evaluation reveals Cas9 lines with ubiquitous or germ-line-restricted patterns of activity. We also demonstrate differential activity of the same gRNA expressed from different U6 snRNA promoters, with the previously untested U6:3 promoter giving the most potent effect. An appropriate combination of Cas9 and gRNA allows targeting of essential and nonessential genes with transmission rates ranging from 25-100%. We also demonstrate that our optimized CRISPR/Cas tools can be used for offset nicking-based mutagenesis. Furthermore, in combination with oligonucleotide or long double-stranded donor templates, our reagents allow precise genome editing by homology-directed repair with rates that make selection markers unnecessary. Last, we demonstrate a novel application of CRISPR/Cas-mediated technology in revealing loss-of-function phenotypes in somatic cells following efficient biallelic targeting by Cas9 expressed in a ubiquitous or tissue-restricted manner. Our CRISPR/Cas tools will facilitate the rapid evaluation of mutant phenotypes of specific genes and the precise modification of the genome with single-nucleotide precision. Our results also pave the way for high-throughput genetic screening with CRISPR/Cas.
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              Genome Engineering of Drosophila with the CRISPR RNA-Guided Cas9 Nuclease

              We have adapted a bacterial CRISPR RNA/Cas9 system to precisely engineer the Drosophila genome and report that Cas9-mediated genomic modifications are efficiently transmitted through the germline. This RNA-guided Cas9 system can be rapidly programmed to generate targeted alleles for probing gene function in Drosophila.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Investigation
                Role: Investigation
                Role: Investigation
                Role: Investigation
                Role: Investigation
                Role: Investigation
                Role: Investigation
                Role: Investigation
                Role: Investigation
                Role: Investigation
                Role: Investigation
                Role: Formal analysisRole: Investigation
                Role: ConceptualizationRole: Funding acquisitionRole: Writing – original draft
                Role: ConceptualizationRole: Funding acquisitionRole: InvestigationRole: Writing – original draft
                Role: Editor
                Journal
                PLoS Genet
                PLoS Genet
                plos
                plosgen
                PLoS Genetics
                Public Library of Science (San Francisco, CA USA )
                1553-7390
                1553-7404
                26 May 2020
                May 2020
                : 16
                : 5
                : e1008815
                Affiliations
                [1 ] Dipartimento di Biologia e Biotecnologie “C Darwin”, Sapienza University of Rome, Rome, Italy
                [2 ] Istituto di Biologia e Patologia Molecolari (IBPM) del CNR, Rome, Italy
                [3 ] Dipartimento di Biologia Ambientale, Sapienza University of Rome, Rome, Italy
                [4 ] Fondazione Cenci Bolognetti, Istituto Pasteur, Rome, Italy
                [5 ] Biosciences/Living Systems Institute, College of Life and Environmental Sciences, University of Exeter, United Kingdom
                Geisel School of Medicine at Dartmouth, UNITED STATES
                Author notes

                The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0001-5212-0803
                http://orcid.org/0000-0002-3971-7872
                http://orcid.org/0000-0002-9628-1411
                http://orcid.org/0000-0002-0817-1862
                http://orcid.org/0000-0003-3777-300X
                http://orcid.org/0000-0002-5072-5240
                Article
                PGENETICS-D-20-00213
                10.1371/journal.pgen.1008815
                7289441
                32453722
                74b55ad3-c6ca-4a71-b1e6-54c1b47fd062
                © 2020 Maccallini et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 13 February 2020
                : 30 April 2020
                Page count
                Figures: 6, Tables: 0, Pages: 24
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100002426, Fondazione Telethon;
                Award ID: GPP13147
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100004588, Istituto Pasteur-Fondazione Cenci Bolognetti;
                Award ID: under 40
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100005010, Associazione Italiana per la Ricerca sul Cancro;
                Award ID: AIRC, IG 20528
                Award Recipient :
                This work was supported by grants from Telethon (GPP13147; https://www.telethon.it/) and Fondazione Cenci Bolognetti ( http://www.istitutopasteuritalia.it/) to G.D.R., and Associazione Italiana Ricerca sul Cancro (AIRC, IG 20528; https://www.airc.it/) to M.G. G.N. was supported by fellowships from Regione Lazio (Torno Subito 2018; http://www.tornosubito.laziodisu.it/) and from Sapienza, University of Rome ( https://www.uniroma1.it). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Anatomy
                Head
                Eyes
                Medicine and Health Sciences
                Anatomy
                Head
                Eyes
                Biology and Life Sciences
                Anatomy
                Ocular System
                Eyes
                Medicine and Health Sciences
                Anatomy
                Ocular System
                Eyes
                Research and Analysis Methods
                Animal Studies
                Experimental Organism Systems
                Model Organisms
                Drosophila Melanogaster
                Research and Analysis Methods
                Model Organisms
                Drosophila Melanogaster
                Research and Analysis Methods
                Animal Studies
                Experimental Organism Systems
                Animal Models
                Drosophila Melanogaster
                Biology and Life Sciences
                Organisms
                Eukaryota
                Animals
                Invertebrates
                Arthropoda
                Insects
                Drosophila
                Drosophila Melanogaster
                Biology and life sciences
                Genetics
                Epigenetics
                RNA interference
                Biology and life sciences
                Genetics
                Gene expression
                RNA interference
                Biology and life sciences
                Genetics
                Genetic interference
                RNA interference
                Biology and life sciences
                Biochemistry
                Nucleic acids
                RNA
                RNA interference
                Biology and Life Sciences
                Developmental Biology
                Life Cycles
                Larvae
                Biology and Life Sciences
                Genetics
                Phenotypes
                Biology and life sciences
                Biochemistry
                Nucleic acids
                RNA
                Non-coding RNA
                Small nuclear RNA
                Biology and Life Sciences
                Developmental Biology
                Organism Development
                Organogenesis
                Sense Organ Development
                Eye Development
                Biology and Life Sciences
                Developmental Biology
                Morphogenesis
                Imaginal Discs
                Custom metadata
                vor-update-to-uncorrected-proof
                2020-06-11
                All relevant data are within the manuscript and its Supporting Information files.

                Genetics
                Genetics

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