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Kutnowski N, Ghanim GE, Lee Y, Rio DC. Activity of zebrafish THAP9 transposase and zebrafish P element-like transposons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586318. [PMID: 38562726 PMCID: PMC10983969 DOI: 10.1101/2024.03.22.586318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Transposable elements are mobile DNA segments that are found ubiquitously across the three domains of life. One family of transposons, called P elements, were discovered in the fruit fly Drosophila melanogaster. Since their discovery, P element transposase-homologous genes (called THAP-domain containing 9 or THAP9) have been discovered in other animal genomes. Here, we show that the zebrafish (Danio rerio) genome contains both an active THAP9 transposase (zfTHAP9) and mobile P-like transposable elements (called Pdre). zfTHAP9 transposase can excise one of its own elements (Pdre2) and Drosophila P elements. Drosophila P element transposase (DmTNP) is also able to excise the zebrafish Pdre2 element, even though it's distinct from the Drosophila P element. However, zfTHAP9 cannot transpose Pdre2 or Drosophila P elements, indicating partial transposase activity. Characterization of the N-terminal THAP DNA binding domain of zfTHAP9 shows distinct DNA binding site preferences from DmTNP and mutation of the zfTHAP9, based on known mutations in DmTNP, generated a hyperactive protein,. These results define an active vertebrate THAP9 transposase that can act on the endogenous zebrafish Pdre and Drosophila P elements.
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Affiliation(s)
- Nitzan Kutnowski
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
| | - George E Ghanim
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
| | - Yeon Lee
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
| | - Donald C Rio
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
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2
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Duan Q, Estrella R, Carson A, Chen Y, Volkan PC. The effect of Drosophila attP40 background on the glomerular organization of Or47b olfactory receptor neurons. G3 (BETHESDA, MD.) 2023; 13:jkad022. [PMID: 36695023 PMCID: PMC10085800 DOI: 10.1093/g3journal/jkad022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/26/2023]
Abstract
Bacteriophage integrase-directed insertion of transgenic constructs into specific genomic loci has been widely used by Drosophila community. The attP40 landing site located on the second chromosome gained popularity because of its high inducible transgene expression levels. Here, unexpectedly, we found that homozygous attP40 chromosome disrupts normal glomerular organization of Or47b olfactory receptor neuron (ORN) class in Drosophila. This effect is not likely to be caused by the loss of function of Msp300, where the attP40 docking site is inserted. Moreover, the attP40 background seems to genetically interact with the second chromosome Or47b-GAL4 driver, which results in a similar glomerular defect. Whether the ORN phenotype is caused by the neighbouring genes around Msp300 locus in the presence of attP40-based insertions or a second unknown mutation in the attP40 background remains elusive. Our findings tell a cautionary tale about using this popular transgenic landing site, highlighting the importance of rigorous controls to rule out the attP40 landing site-associated background effects.
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Affiliation(s)
- Qichen Duan
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Rachel Estrella
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Allison Carson
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Yang Chen
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Pelin C Volkan
- Department of Biology, Duke University, Durham, NC 27708, USA
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3
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Hu X, Fan Y, Mao C, Chen H, Wang Q. Application of transposon insertion site sequencing method in the exploration of gene function in microalgae. Front Microbiol 2023; 14:1111794. [PMID: 36819037 PMCID: PMC9936982 DOI: 10.3389/fmicb.2023.1111794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/06/2023] [Indexed: 02/05/2023] Open
Abstract
Microalgae are a large group of organisms that can produce various useful substances through photosynthesis. Microalgae need to be genetically modified at the molecular level to become "Chassis Cells" for food, medicine, energy, and environmental protection and, consequently, obtain benefits from microalgae resources. Insertional mutagenesis of microalgae using transposons is a practical possibility for understanding the function of microalgae genes. Theoretical and technical support is provided in this manuscript for applying transposons to microalgae gene function by summarizing the sequencing method of transposon insertion sites.
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Affiliation(s)
- Xiaobing Hu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China,School of Environmental Engineering, Yellow River Conservancy Technical Institute, Kaifeng, China
| | - Yulong Fan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Chengfeng Mao
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Hui Chen
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Qiang Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China,Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, China,*Correspondence: Qiang Wang, ✉
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4
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Escobedo SE, Shah A, Easton AN, Hall H, Weake VM. Characterizing a gene expression toolkit for eye- and photoreceptor-specific expression in Drosophila. Fly (Austin) 2021; 15:73-88. [PMID: 33899690 PMCID: PMC8078738 DOI: 10.1080/19336934.2021.1915683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 03/16/2021] [Accepted: 04/08/2021] [Indexed: 10/21/2022] Open
Abstract
Binary expression systems are a powerful tool for tissue- and cell-specific research. Many of the currently available Drosophila eye-specific drivers have not been systematically characterized for their expression level and cell-type specificity in the adult eye or during development. Here, we used a luciferase reporter to measure expression levels of different drivers in the adult Drosophila eye, and characterized the cell type-specificity of each driver using a fluorescent reporter in live 10-day-old adult males. We also further characterized the expression pattern of these drivers in various developmental stages. We compared several Gal4 drivers from the Bloomington Drosophila Stock Center (BDSC) including GMR-Gal4, longGMR-Gal4 and Rh1-Gal4 with newly developed Gal4 and QF2 drivers that are specific to different cell types in the adult eye. In addition, we generated drug-inducible Rh1-GSGal4 lines and compared their induced expression with an available GMR-GSGal4 line. Although both lines had significant induction of gene expression measured by luciferase activity, Rh1-GSGal4 was expressed at levels below the detection of the fluorescent reporter by confocal microscopy, while GMR-GSGal4 showed substantial reporter expression in the absence of drug by microscopy. Overall, our study systematically characterizes and compares a large toolkit of eye- and photoreceptor-specific drivers, while also uncovering some of the limitations of currently available expression systems in the adult eye.
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Affiliation(s)
| | - Aashka Shah
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Alyssa N. Easton
- Department of Agriculture and Biological Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Hana Hall
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Vikki M. Weake
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
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Alquezar‐Planas DE, Löber U, Cui P, Quedenau C, Chen W, Greenwood AD. DNA sonication inverse PCR for genome scale analysis of uncharacterized flanking sequences. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13497] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- David E. Alquezar‐Planas
- Department of Wildlife Diseases Leibniz Institute for Zoo and Wildlife Research Berlin Germany
- Australian Museum Research InstituteAustralian Museum Sydney NSW Australia
| | - Ulrike Löber
- Department of Wildlife Diseases Leibniz Institute for Zoo and Wildlife Research Berlin Germany
- The Berlin Center for Genomics in Biodiversity Research Berlin Germany
- Experimental and Clinical Research Center A Cooperation of Charité – Universitätsmedizin Berlin and Max Delbruck Center for Molecular Medicine Berlin Germany
| | - Pin Cui
- Department of Wildlife Diseases Leibniz Institute for Zoo and Wildlife Research Berlin Germany
| | - Claudia Quedenau
- Genomics Max Delbrück Center for Molecular Medicine Berlin Germany
| | - Wei Chen
- Berlin Institute for Medical Systems BiologyMax‐Delbrück Center for Molecular Medicine Berlin Germany
| | - Alex D. Greenwood
- Department of Wildlife Diseases Leibniz Institute for Zoo and Wildlife Research Berlin Germany
- Department of Veterinary Medicine Freie Universität Berlin Berlin Germany
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6
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Palladino J, Chavan A, Sposato A, Mason TD, Mellone BG. Targeted De Novo Centromere Formation in Drosophila Reveals Plasticity and Maintenance Potential of CENP-A Chromatin. Dev Cell 2020; 52:379-394.e7. [PMID: 32049040 DOI: 10.1016/j.devcel.2020.01.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 10/17/2019] [Accepted: 01/06/2020] [Indexed: 11/25/2022]
Abstract
Centromeres are essential for accurate chromosome segregation and are marked by centromere protein A (CENP-A) nucleosomes. Mis-targeted CENP-A chromatin has been shown to seed centromeres at non-centromeric DNA. However, the requirements for such de novo centromere formation and transmission in vivo remain unknown. Here, we employ Drosophila melanogaster and the LacI/lacO system to investigate the ability of targeted de novo centromeres to assemble and be inherited through development. De novo centromeres form efficiently at six distinct genomic locations, which include actively transcribed chromatin and heterochromatin, and cause widespread chromosomal instability. During tethering, de novo centromeres sometimes prevail, causing the loss of the endogenous centromere via DNA breaks and HP1-dependent epigenetic inactivation. Transient induction of de novo centromeres and chromosome healing in early embryogenesis show that, once established, these centromeres can be maintained through development. Our results underpin the ability of CENP-A chromatin to establish and sustain mitotic centromere function in Drosophila.
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Affiliation(s)
- Jason Palladino
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Ankita Chavan
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Anthony Sposato
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Timothy D Mason
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Barbara G Mellone
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA.
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Buchman A, Gamez S, Li M, Antoshechkin I, Li HH, Wang HW, Chen CH, Klein MJ, Duchemin JB, Crowe JE, Paradkar PN, Akbari OS. Broad dengue neutralization in mosquitoes expressing an engineered antibody. PLoS Pathog 2020; 16:e1008103. [PMID: 31945137 PMCID: PMC6964813 DOI: 10.1371/journal.ppat.1008103] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 09/23/2019] [Indexed: 12/11/2022] Open
Abstract
With dengue virus (DENV) becoming endemic in tropical and subtropical regions worldwide, there is a pressing global demand for effective strategies to control the mosquitoes that spread this disease. Recent advances in genetic engineering technologies have made it possible to create mosquitoes with reduced vector competence, limiting their ability to acquire and transmit pathogens. Here we describe the development of Aedes aegypti mosquitoes synthetically engineered to impede vector competence to DENV. These mosquitoes express a gene encoding an engineered single-chain variable fragment derived from a broadly neutralizing DENV human monoclonal antibody and have significantly reduced viral infection, dissemination, and transmission rates for all four major antigenically distinct DENV serotypes. Importantly, this is the first engineered approach that targets all DENV serotypes, which is crucial for effective disease suppression. These results provide a compelling route for developing effective genetic-based DENV control strategies, which could be extended to curtail other arboviruses.
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Affiliation(s)
- Anna Buchman
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, United States of America
| | - Stephanie Gamez
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, United States of America
| | - Ming Li
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, United States of America
| | - Igor Antoshechkin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Hsing-Han Li
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Zhunan, Taiwan
| | - Hsin-Wei Wang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Zhunan, Taiwan
| | - Chun-Hong Chen
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Zhunan, Taiwan
| | - Melissa J. Klein
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, VIC, Australia
| | - Jean-Bernard Duchemin
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, VIC, Australia
| | - James E. Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Departments of Pediatrics, Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Prasad N. Paradkar
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, VIC, Australia
| | - Omar S. Akbari
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, United States of America
- Tata Institute for Genetics and Society-UCSD, La Jolla, California, United States of America
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8
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Bui M, Shyong J, Lutz EK, Yang T, Li M, Truong K, Arvidson R, Buchman A, Riffell JA, Akbari OS. Live calcium imaging of Aedes aegypti neuronal tissues reveals differential importance of chemosensory systems for life-history-specific foraging strategies. BMC Neurosci 2019; 20:27. [PMID: 31208328 PMCID: PMC6580577 DOI: 10.1186/s12868-019-0511-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 06/10/2019] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The mosquito Aedes aegypti has a wide variety of sensory pathways that have supported its success as a species as well as a highly competent vector of numerous debilitating infectious pathogens. Investigations into mosquito sensory systems and their effects on behavior are valuable resources for the advancement of mosquito control strategies. Numerous studies have elucidated key aspects of mosquito sensory systems, however there remains critical gaps within the field. In particular, compared to that of the adult form, there has been a lack of studies directed towards the immature life stages. Additionally, although numerous studies have pinpointed specific sensory receptors as well as responding motor outputs, there has been a lack of studies able to monitor both concurrently. RESULTS To begin filling aforementioned gaps, here we engineered Ae. aegypti to ubiquitously express a genetically encoded calcium indicator, GCaMP6s. Using this strain, combined with advanced microscopy, we simultaneously measured live stimulus-evoked calcium responses in both neuronal and muscle cells with a wide spatial range and resolution. CONCLUSIONS By coupling in vivo live calcium imaging with behavioral assays we were able to gain functional insights into how stimulus-evoked neural and muscle activities are represented, modulated, and transformed in mosquito larvae enabling us to elucidate mosquito sensorimotor properties important for life-history-specific foraging strategies.
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Affiliation(s)
- Michelle Bui
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093 USA
| | - Jennifer Shyong
- Department of Entomology and Riverside Center for Disease Vector Research, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521 USA
| | - Eleanor K. Lutz
- Department of Biology, University of Washington, Seattle, WA 98195 USA
| | - Ting Yang
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093 USA
| | - Ming Li
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093 USA
| | - Kenneth Truong
- Department of Entomology and Riverside Center for Disease Vector Research, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521 USA
| | - Ryan Arvidson
- Department of Entomology and Riverside Center for Disease Vector Research, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521 USA
| | - Anna Buchman
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093 USA
| | | | - Omar S. Akbari
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093 USA
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA 92093 USA
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Maharjan M, Maeda RK, Karch F, Hart CM. Using a phiC31 "Disintegrase" to make new attP sites in the Drosophila genome at locations showing chromosomal position effects. PLoS One 2018; 13:e0205538. [PMID: 30296303 PMCID: PMC6175522 DOI: 10.1371/journal.pone.0205538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 09/26/2018] [Indexed: 12/31/2022] Open
Abstract
An engineered phiC31 “Disintegrase” able to make an attP site in Drosophila out of an attR-attL pair is described. This was used to generate attP sites at genomic locations where a mini-white (mini-w) transgene was subject to chromosomal position effects (CPE). The first step was random genomic integration of a P-element-based transposon with an insulated mini-w transgene. We then removed the upstream insulator using FLP recombinase to detect CPE. Next mini-w and the downstream insulator were “dis-integrated” leaving behind an attP site. The location is marked by a yellow+ transgene that is flanked by loxP sites, so it can also be removed. Using this system, we generated 10 new attP landing platforms. Three of these showing strong activating CPE were selected for further analysis. We show that the attP sites are functional by integrating in plasmids with attB sites. The CPE is recapitulated and can be blocked by insulators. We show that a dimerized 215 bp fragment of the 500 bp BEAF-dependent scs’ insulator containing a high affinity BEAF binding site blocks the CPE, while a monomer of the sequence is less effective. This indicates that two BEAF binding sites make a stronger insulator than a single site. This system could be useful for generating attP sites at prescreened sites for other purposes, such as studying CPE in embryos or other tissues or for use with “trapped” enhancers of interest.
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Affiliation(s)
- Mukesh Maharjan
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Robert K. Maeda
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - François Karch
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Craig M. Hart
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
- * E-mail:
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Zou S, Wang H, Li Y, Kong Z, Tang D. The NB-LRR gene Pm60 confers powdery mildew resistance in wheat. THE NEW PHYTOLOGIST 2018; 218:298-309. [PMID: 29281751 DOI: 10.1111/nph.14964] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 11/20/2017] [Indexed: 05/18/2023]
Abstract
Powdery mildew is one of the most devastating diseases of wheat. To date, few powdery mildew resistance genes have been cloned from wheat due to the size and complexity of the wheat genome. Triticum urartu is the progenitor of the A genome of wheat and is an important source for powdery mildew resistance genes. Using molecular markers designed from scaffolds of the sequenced T. urartu accession and standard map-based cloning, a powdery mildew resistance locus was mapped to a 356-kb region, which contains two nucleotide-binding and leucine-rich repeat domain (NB-LRR) protein-encoding genes. Virus-induced gene silencing, single-cell transient expression, and stable transformation assays demonstrated that one of these two genes, designated Pm60, confers resistance to powdery mildew. Overexpression of full-length Pm60 and two allelic variants in Nicotiana benthamiana leaves induced hypersensitive cell death response, but expression of the coiled-coil domain alone was insufficient to induce hypersensitive response. Yeast two-hybrid, bimolecular fluorescence complementation and luciferase complementation imaging assays showed that Pm60 protein interacts with its neighboring NB-containing protein, suggesting that they might be functionally related. The identification and cloning of this novel wheat powdery mildew resistance gene will facilitate breeding for disease resistance in wheat.
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Affiliation(s)
- Shenghao Zou
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Development Biology, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huan Wang
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Development Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiwen Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Development Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhaosheng Kong
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dingzhong Tang
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Development Biology, Chinese Academy of Sciences, Beijing, 100101, China
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11
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Callens M, Watanabe H, Kato Y, Miura J, Decaestecker E. Microbiota inoculum composition affects holobiont assembly and host growth in Daphnia. MICROBIOME 2018; 6:56. [PMID: 29566771 PMCID: PMC5863831 DOI: 10.1186/s40168-018-0444-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 03/13/2018] [Indexed: 05/24/2023]
Abstract
BACKGROUND Host-associated microbiota is often acquired by horizontal transmission of microbes present in the environment. It is hypothesized that differences in the environmental pool of colonizers can influence microbiota community assembly on the host and as such affect holobiont composition and host fitness. To investigate this hypothesis, the host-associated microbiota of the invertebrate eco(toxico)logical model Daphnia was experimentally disturbed using different concentrations of the antibiotic oxytetracycline. The community assembly and host-microbiota interactions when Daphnia were colonized by the disturbed microbiota were investigated by inoculating germ-free individuals with the microbiota. RESULTS Antibiotic-induced disturbance of the microbiota had a strong effect on the subsequent colonization of Daphnia by affecting ecological interactions between members of the microbiota. This resulted in differences in community assembly which, in turn, affected Daphnia growth. CONCLUSIONS These results show that the composition of the pool of colonizing microbiota can be an important structuring factor of the microbiota assembly on Daphnia, affecting holobiont composition and host growth. These findings contribute to a better understanding of how the microbial environment can shape the holobiont composition and affect host-microbiota interactions.
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Affiliation(s)
- Martijn Callens
- Aquatic Biology, Science and Technology, IRF Life Sciences, KU Leuven, Campus Kortrijk, E. Sabbelaan 53, 8500, Kortrijk, Belgium
- Centre d'Ecologie Fonctionelle Evolutive, CNRS Montpellier, UMR 5175, 1919 route de Mende, 34293, Montpellier CEDEX 5, France
| | - Hajime Watanabe
- Bioenvironmental Science, Osaka University, Yamadaoka, Suita, Osaka, 565 0871, Japan
| | - Yasuhiko Kato
- Bioenvironmental Science, Osaka University, Yamadaoka, Suita, Osaka, 565 0871, Japan
| | - Jun Miura
- Bioenvironmental Science, Osaka University, Yamadaoka, Suita, Osaka, 565 0871, Japan
| | - Ellen Decaestecker
- Aquatic Biology, Science and Technology, IRF Life Sciences, KU Leuven, Campus Kortrijk, E. Sabbelaan 53, 8500, Kortrijk, Belgium.
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12
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Li M, Bui M, Yang T, Bowman CS, White BJ, Akbari OS. Germline Cas9 expression yields highly efficient genome engineering in a major worldwide disease vector, Aedes aegypti. Proc Natl Acad Sci U S A 2017; 114:E10540-E10549. [PMID: 29138316 PMCID: PMC5724270 DOI: 10.1073/pnas.1711538114] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The development of CRISPR/Cas9 technologies has dramatically increased the accessibility and efficiency of genome editing in many organisms. In general, in vivo germline expression of Cas9 results in substantially higher activity than embryonic injection. However, no transgenic lines expressing Cas9 have been developed for the major mosquito disease vector Aedes aegypti Here, we describe the generation of multiple stable, transgenic Ae. aegypti strains expressing Cas9 in the germline, resulting in dramatic improvements in both the consistency and efficiency of genome modifications using CRISPR. Using these strains, we disrupted numerous genes important for normal morphological development, and even generated triple mutants from a single injection. We have also managed to increase the rates of homology-directed repair by more than an order of magnitude. Given the exceptional mutagenic efficiency and specificity of the Cas9 strains we engineered, they can be used for high-throughput reverse genetic screens to help functionally annotate the Ae. aegypti genome. Additionally, these strains represent a step toward the development of novel population control technologies targeting Ae. aegypti that rely on Cas9-based gene drives.
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Affiliation(s)
- Ming Li
- Department of Entomology, University of California, Riverside, CA 92521
- Center for Disease Vector Research, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521
| | - Michelle Bui
- Department of Entomology, University of California, Riverside, CA 92521
- Center for Disease Vector Research, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521
| | - Ting Yang
- Department of Entomology, University of California, Riverside, CA 92521
- Center for Disease Vector Research, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521
| | - Christian S Bowman
- Department of Entomology, University of California, Riverside, CA 92521
- Center for Disease Vector Research, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521
| | - Bradley J White
- Department of Entomology, University of California, Riverside, CA 92521
- Center for Disease Vector Research, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521
| | - Omar S Akbari
- Department of Entomology, University of California, Riverside, CA 92521;
- Center for Disease Vector Research, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521
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13
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Sanchez-Díaz I, Rosales-Bravo F, Reyes-Taboada JL, Covarrubias AA, Narvaez-Padilla V, Reynaud E. The Esg Gene Is Involved in Nicotine Sensitivity in Drosophila melanogaster. PLoS One 2015; 10:e0133956. [PMID: 26222315 PMCID: PMC4519288 DOI: 10.1371/journal.pone.0133956] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 07/03/2015] [Indexed: 12/04/2022] Open
Abstract
In humans, there is a strong correlation between sensitivity to substances of abuse and addiction risk. This differential tolerance to drugs has a strong genetic component. The identification of human genetic factors that alter drug tolerance has been a difficult task. For this reason and taking advantage of the fact that Drosophila responds similarly to humans to many drugs, and that genetically it has a high degree of homology (sharing at least 70% of genes known to be involved in human genetic diseases), we looked for genes in Drosophila that altered their nicotine sensitivity. We developed an instantaneous nicotine vaporization technique that exposed flies in a reproducible way. The amount of nicotine sufficient to "knock out" half of control flies for 30 minutes was determined and this parameter was defined as Half Recovery Time (HRT). Two fly lines, L4 and L70, whose HRT was significantly longer than control´s were identified. The L4 insertion is a loss of function allele of the transcriptional factor escargot (esg), whereas L70 insertion causes miss-expression of the microRNA cluster miR-310-311-312-313 (miR-310c). In this work, we demonstrate that esg loss of function induces nicotine sensitivity possibly by altering development of sensory organs and neurons in the medial section of the thoracoabdominal ganglion. The ectopic expression of the miR-310c also induces nicotine sensitivity by lowering Esg levels thus disrupting sensory organs and possibly to the modulation of other miR-310c targets.
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Affiliation(s)
- Iván Sanchez-Díaz
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad, 2001, Apartado Postal, 510–3, Cuernavaca 62210, México
| | - Fernando Rosales-Bravo
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca, Morelos 62209, México
| | - José Luis Reyes-Taboada
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad, 2001, Apartado Postal, 510–3, Cuernavaca 62210, Mexico
| | - Alejandra A Covarrubias
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad, 2001, Apartado Postal, 510–3, Cuernavaca 62210, Mexico
| | - Verónica Narvaez-Padilla
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca, Morelos 62209, México
| | - Enrique Reynaud
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad, 2001, Apartado Postal, 510–3, Cuernavaca 62210, México
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14
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Weber M, Wey-Fabrizius AR, Podsiadlowski L, Witek A, Schill RO, Sugár L, Herlyn H, Hankeln T. Phylogenetic analyses of endoparasitic Acanthocephala based on mitochondrial genomes suggest secondary loss of sensory organs. Mol Phylogenet Evol 2012; 66:182-9. [PMID: 23044398 DOI: 10.1016/j.ympev.2012.09.017] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 09/06/2012] [Accepted: 09/17/2012] [Indexed: 11/27/2022]
Abstract
The metazoan taxon Syndermata (Monogononta, Bdelloidea, Seisonidea, Acanthocephala) comprises species with vastly different lifestyles. The focus of this study is on the phylogeny within the syndermatan subtaxon Acanthocephala (thorny-headed worms, obligate endoparasites). In order to investigate the controversially discussed phylogenetic relationships of acanthocephalan subtaxa we have sequenced the mitochondrial (mt) genomes of Echinorhynchus truttae (Palaeacanthocephala), Paratenuisentis ambiguus (Eoacanthocephala), Macracanthorhynchus hirudinaceus (Archiacanthocephala), and Philodina citrina (Bdelloidea). In doing so, we present the largest molecular phylogenetic dataset so far for this question comprising all major subgroups of Acanthocephala. Alongside with publicly available mt genome data of four additional syndermatans as well as 18 other lophotrochozoan (spiralian) taxa and one outgroup representative, the derived protein-coding sequences were used for Maximum Likelihood as well as Bayesian phylogenetic analyses. We achieved entirely congruent results, whereupon monophyletic Archiacanthocephala represent the sister taxon of a clade comprising Eoacanthocephala and monophyletic Palaeacanthocephala (Echinorhynchida). This topology suggests the secondary loss of lateral sensory organs (sensory pores) within Palaeacanthocephala and is further in line with the emergence of apical sensory organs in the stem lineage of Archiacanthocephala.
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Affiliation(s)
- Mathias Weber
- Institute of Molecular Genetics, Johannes Gutenberg-University Mainz, J-J Becherweg 30a, D-55099 Mainz, Germany.
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15
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Lang M, Murat S, Clark AG, Gouppil G, Blais C, Matzkin LM, Guittard É, Yoshiyama−Yanagawa T, Kataoka H, Niwa R, Lafont R, Dauphin−Villemant C, Orgogozo V. Mutations in the neverland gene turned Drosophila pachea into an obligate specialist species. Science 2012; 337:1658-61. [PMID: 23019649 PMCID: PMC4729188 DOI: 10.1126/science.1224829] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Most living species exploit a limited range of resources. However, little is known about how tight associations build up during evolution between such specialist species and the hosts they use. We examined the dependence of Drosophila pachea on its single host, the senita cactus. Several amino acid changes in the Neverland oxygenase rendered D. pachea unable to transform cholesterol into 7-dehydrocholesterol (the first reaction in the steroid hormone biosynthetic pathway in insects) and thus made D. pachea dependent on the uncommon sterols of its host plant. The neverland mutations increase survival on the cactus's unusual sterols and are in a genomic region that faced recent positive selection. This study illustrates how relatively few genetic changes in a single gene may restrict the ecological niche of a species.
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Affiliation(s)
- Michael Lang
- CNRS UMR7592, Univ Paris Diderot, Sorbonne Paris Cité, Institut Jacques Monod, 15 rue Hélène Brion, 75205 Paris cedex 13, France
| | - Sophie Murat
- CNRS UMR7592, Univ Paris Diderot, Sorbonne Paris Cité, Institut Jacques Monod, 15 rue Hélène Brion, 75205 Paris cedex 13, France
- UPMC, Univ Paris 06, CNRS, Bâtiment A, 7 quai Saint Bernard, 75005 Paris, France
| | - Andrew G. Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY USA
| | - Géraldine Gouppil
- CNRS UMR7592, Univ Paris Diderot, Sorbonne Paris Cité, Institut Jacques Monod, 15 rue Hélène Brion, 75205 Paris cedex 13, France
| | - Catherine Blais
- UPMC, Univ Paris 06, CNRS, Bâtiment A, 7 quai Saint Bernard, 75005 Paris, France
| | - Luciano M. Matzkin
- Department of Biological Sciences, University of Alabama in Huntsville, 301 Sparkman Drive, Huntsville AL 35899, USA
| | - Émilie Guittard
- UPMC, Univ Paris 06, CNRS, Bâtiment A, 7 quai Saint Bernard, 75005 Paris, France
| | - Takuji Yoshiyama−Yanagawa
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennoudai 1-1-1, Tsukuba, Ibaraki 305-8572, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Hiroshi Kataoka
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Ryusuke Niwa
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennoudai 1-1-1, Tsukuba, Ibaraki 305-8572, Japan
| | - René Lafont
- UPMC, Univ Paris 06, CNRS, Bâtiment A, 7 quai Saint Bernard, 75005 Paris, France
| | | | - Virginie Orgogozo
- CNRS UMR7592, Univ Paris Diderot, Sorbonne Paris Cité, Institut Jacques Monod, 15 rue Hélène Brion, 75205 Paris cedex 13, France
- UPMC, Univ Paris 06, CNRS, Bâtiment A, 7 quai Saint Bernard, 75005 Paris, France
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16
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Campbell JL, Gu Q, Guo D, Nash HA. Genetic effects in Drosophila on the potency of diverse general anesthetics: a distinctive pattern of altered sensitivity. J Neurogenet 2012; 23:412-21. [PMID: 19863272 DOI: 10.3109/01677060903177800] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Mutations that influence the sensitivity of an organism to a volatile general anesthetic can be divided into two classes. In one, sensitivity to all other volatile agents is affected to a similar degree. Although this class may contain mutations of interest for understanding anesthesia, it is also likely to contain mutations that merely alter general health. In the second class, mutations confer non-uniform effects on potency (NEP), i.e., larger effects for some volatile anesthetics than for others. Members of this class are of special interest for studies of arousal and its pharmacological suppression because they not only avoid the pitfall of effects on global health, but also imply the existence of drug targets that are preferentially affected by particular agents. In this work, we provide the first systematic investigation of the relative frequency and diversity of NEP mutations in Drosophila. As a first step, we isolated and characterized a set of P element insertion mutations that confer altered sensitivity of the fruit fly to the clinical anesthetic halothane. Then we tested the members of this collection for their effect on the sensitivity of flies to five other volatile agents. Not only do we find that most of the mutations show non-uniform effects, they also share a characteristic arrangement of altered potencies (halothane > >desflurane >or= enflurane approximately isoflurane approximately methoxyflurane > sevoflurane). From this result, although we do not know how direct or indirect are the effects of the mutations, we infer the existence of a biologically relevant target for anesthetic action that has a distinct preference for halothane over other agents. Intriguingly, P element insertions that co-map with several NEP loci have been shown to alter the fly's response to cocaine and ethanol, suggesting that common genetic elements are involved in the response to all three drugs.
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Affiliation(s)
- Joseph L Campbell
- Laboratory of Molecular Biology, National Institute of Mental Health, Bethesda, MD 20892-3736, USA
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17
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Tatevossian RG, Tang B, Dalton J, Forshew T, Lawson AR, Ma J, Neale G, Shurtleff SA, Bailey S, Gajjar A, Baker SJ, Sheer D, Ellison DW. MYB upregulation and genetic aberrations in a subset of pediatric low-grade gliomas. Acta Neuropathol 2010; 120:731-43. [PMID: 21046410 DOI: 10.1007/s00401-010-0763-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 10/16/2010] [Accepted: 10/19/2010] [Indexed: 12/18/2022]
Abstract
Recent studies of genetic abnormalities in pediatric low-grade gliomas (LGGs) have focused on activation of the ERK/MAPK pathway by KIAA1549-BRAF gene fusions in the majority of pilocytic astrocytomas (PAs) and by rare mutations in elements of the pathway across histopathologically diverse LGGs. This study reports that MYB, an oncogene not previously implicated in gliomagenesis, is activated in a diverse subset of pediatric LGGs. The study cohort comprised 57 pediatric LGGs and a comparative cohort of 59 pediatric high-grade gliomas (HGGs). The LGG cohort included 34 PAs and 23 diffuse gliomas; fibrillary astrocytomas (n = 14), oligodendroglial tumors (n = 7), and angiocentric gliomas (n = 2). MYB copy number abnormalities were disclosed using Affymetrix 6.0 SNP arrays and confirmed using interphase fluorescence in situ hybridization. Novel MYB amplifications that upregulate MYB RNA and protein expression were demonstrated in 2/14 diffuse astrocytomas. In addition, focal deletion of the terminal region of MYB was seen in 1 of 2 angiocentric gliomas (AGs). Increased expression of MYB was demonstrated by quantitative RT-PCR and immunohistochemistry. MYB upregulation at the protein level was demonstrated in a proportion of diffuse LGGs (60%), pilocytic astrocytomas (41%), and HGGs (19%), but abnormalities at the genomic level were only a feature of diffuse gliomas. Our data suggest that MYB may have a role in a subset of pediatric gliomas, through a variety of mechanisms in addition to MYB amplification and deletion.
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Affiliation(s)
- Ruth G Tatevossian
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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18
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Perturbation analysis of heterochromatin-mediated gene silencing and somatic inheritance. PLoS Genet 2010; 6:e1001095. [PMID: 20838586 PMCID: PMC2936522 DOI: 10.1371/journal.pgen.1001095] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Accepted: 07/27/2010] [Indexed: 12/15/2022] Open
Abstract
Repetitive sequences in eukaryotic genomes induce chromatin-mediated gene-silencing of juxtaposed genes. Many components that promote or antagonize silencing have been identified, but how heterochromatin causes variegated and heritable changes in gene expression remains mysterious. We have used inducible mis-expression in the Drosophila eye to recover new factors that alter silencing caused by the bwD allele, an insertion of repetitive satellite DNA that silences a bw+ allele on the homologous chromosome. Inducible modifiers allow perturbation of silencing at different times in development, and distinguish factors that affect establishment or maintenance of silencing. We find that diverse chromatin and RNA processing factors can de-repress silencing. Most factors are effective even in differentiated cells, implying that silent chromatin remains plastic. However, over-expression of the bantam microRNA or the crooked-legs (crol) zinc-finger protein only de-repress silencing when expressed in cycling cells. Over-expression of crol accelerates the cell cycle, and this is required for de-repression of silencing. Strikingly, continual over-expression of crol converts the speckled variegation pattern of bwD into sectored variegation, where de-repression is stably inherited through mitotic divisions. Over-expression of crol establishes an open chromatin state, but the factor is not needed to maintain this state. Our analysis reveals that active chromatin states can be efficiently inherited through cell divisions, with implications for the stable maintenance of gene expression patterns through development. Repetitive DNA and transposons are compacted into heterochromatin in eukaryotic genomes to silence potentially dangerous elements. Heterochromatic silencing is distinct from classical gene repression because affected genes randomly switch on and off during development, with varying degrees of somatic heritability. Here, we focus on the silencing of a reporter gene by a repetitive DNA satellite block on a homologous chromosome. Silencing in this system relies on long-range chromosomal interactions, but these are disrupted during mitosis and must be re-established every cell cycle. We employed an inducible system to identify factors that can alter silencing when over-expressed. The inducible nature of this system allows us to perturb silencing at different development stages, and distinguish factors that affect the establishment or maintenance of silencing. We identified a diverse collection of modifiers, and most can alter silenced chromatin even in differentiating cells. Strikingly, over-expression of one factor – the crol zinc-finger protein – establishes a de-repressed state that is somatically heritable. Our analysis of crol implicates cell cycle progression in the maintenance of silenced chromatin, and argues that active chromatin can be efficiently propagated through mitotic divisions. Our findings validate inducible modifiers as tools for the dissection of establishment and maintenance of chromatin states.
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Large-scale functional annotation and expanded implementations of the P{wHy} hybrid transposon in the Drosophila melanogaster genome. Genetics 2009; 182:653-60. [PMID: 19398769 DOI: 10.1534/genetics.109.103762] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Whole genome sequencing of the model organisms has created increased demand for efficient tools to facilitate the genome annotation efforts. Accordingly, we report the further implementations and analyses stemming from our publicly available P{wHy} library for Drosophila melanogaster. A two-step regime-large scale transposon mutagenesis followed by hobo-induced nested deletions-allows mutation saturation and provides significant enhancements to existing genomic coverage. We previously showed that, for a given starting insert, deletion saturation is readily obtained over a 60-kb interval; here, we perform a breakdown analysis of efficiency to identify rate-limiting steps in the process. Transrecombination, the hobo-induced recombination between two P{wHy} half molecules, was shown to further expand the P{wHy} mutational range, pointing to a potent, iterative process of transrecombination-reconstitution-transrecombination for alternating between very large and very fine-grained deletions in a self-contained manner. A number of strains also showed partial or complete repression of P{wHy} markers, depending on chromosome location, whereby asymmetric marker silencing allowed continuous phenotypic detection, indicating that P{wHy}-based saturational mutagenesis should be useful for the study of heterochromatin/positional effects.
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