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Lipaeva P, Karkossa I, Bedulina D, Schubert K, Luckenbach T. Cold-adapted amphipod species upon heat stress: Proteomic responses and their correlation with transcriptomic responses. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 45:101048. [PMID: 36525778 DOI: 10.1016/j.cbd.2022.101048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/15/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
The cellular heat shock response (HSR) comprises transcriptomic and proteomic reactions to thermal stress. It was here addressed, how the proteomic, together with the transcriptomic HSR, relate to the thermal sensitivities of three cold-adapted but differently thermo-sensitive freshwater amphipod species. The proteomes of thermosensitive Eulimnogammarus verrucosus and thermotolerant Eulimnogammarus cyaneus, both endemic to Lake Baikal, and of thermotolerant Holarctic Gammarus lacustris were investigated upon 24 h exposure to the species-specific 10 % lethal temperatures (LT10). Furthermore, correlations of heat stress induced changes in proteomes (this study) and transcriptomes (previous study with identical experimental design) were examined. Proteomes indicated that the HSR activated processes encompassed (i) proteostasis maintenance, (ii) maintenance of cell adhesion, (iii) oxygen transport, (iv) antioxidant response, and (v) regulation of protein synthesis. Thermo-sensitive E. verrucosus showed the most pronounced proteomic HSR and the lowest correlation of transcriptomic and proteomic HSRs. For proteins related to translation (ribosomal proteins, elongation factors), transcriptomic and proteomic changes were inconsistent: transcripts were downregulated in many cases, with levels of corresponding proteins remaining unchanged. In the Eulimnogammarus species, levels of hemocyanin protein but not transcript were increased upon heat stress, suggesting a HSR also directed to enhance oxygen transport. Thermosensitive E. verrucosus showed the most pronounced relocation of transcription/translation activity to proteostasis maintenance, which may indicate that the general species-specific stability of protein structure could be a fundamental determinant of thermotolerance. By combining transcriptomic and proteomic response data, this study provides a comprehensive picture of the cellular HSR components in the studied amphipods.
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Affiliation(s)
- Polina Lipaeva
- Department of Bioanalytical Ecotoxicology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.
| | - Isabel Karkossa
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Daria Bedulina
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Kristin Schubert
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Till Luckenbach
- Department of Bioanalytical Ecotoxicology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
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Wang J, Chen X, Hou X, Wang J, Yue W, Huang S, Xu G, Yan J, Lu G, Hofreiter M, Li C, Wang C. "Omics" data unveil early molecular response underlying limb regeneration in the Chinese mitten crab, Eriocheir sinensis. SCIENCE ADVANCES 2022; 8:eabl4642. [PMID: 36112682 PMCID: PMC9481118 DOI: 10.1126/sciadv.abl4642] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/01/2022] [Indexed: 05/22/2023]
Abstract
Limb regeneration is a fascinating and medically interesting trait that has been well preserved in arthropod lineages, particularly in crustaceans. However, the molecular mechanisms underlying arthropod limb regeneration remain largely elusive. The Chinese mitten crab Eriocheir sinensis shows strong regenerative capacity, a trait that has likely allowed it to become a worldwide invasive species. Here, we report a chromosome-level genome of E. sinensis as well as large-scale transcriptome data during the limb regeneration process. Our results reveal that arthropod-specific genes involved in signal transduction, immune response, histone methylation, and cuticle development all play fundamental roles during the regeneration process. Particularly, Innexin2-mediated signal transduction likely facilitates the early stage of the regeneration process, while an effective crustacean-specific prophenoloxidase system (ProPo-AS) plays crucial roles in the initial immune response. Collectively, our findings uncover novel genetic pathways pertaining to arthropod limb regeneration and provide valuable resources for studies on regeneration from a comparative perspective.
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Affiliation(s)
- Jun Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources certified by the Ministry of Agriculture and Rural Affairs/National Demonstration Center for Experimental Fisheries Science Education/Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Xiaowen Chen
- Key Laboratory of Freshwater Aquatic Genetic Resources certified by the Ministry of Agriculture and Rural Affairs/National Demonstration Center for Experimental Fisheries Science Education/Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Xin Hou
- Key Laboratory of Freshwater Aquatic Genetic Resources certified by the Ministry of Agriculture and Rural Affairs/National Demonstration Center for Experimental Fisheries Science Education/Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Jingan Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources certified by the Ministry of Agriculture and Rural Affairs/National Demonstration Center for Experimental Fisheries Science Education/Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Wucheng Yue
- Key Laboratory of Freshwater Aquatic Genetic Resources certified by the Ministry of Agriculture and Rural Affairs/National Demonstration Center for Experimental Fisheries Science Education/Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Shu Huang
- Key Laboratory of Freshwater Aquatic Genetic Resources certified by the Ministry of Agriculture and Rural Affairs/National Demonstration Center for Experimental Fisheries Science Education/Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Gangchun Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization certified by the Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Jizhou Yan
- Key Laboratory of Freshwater Aquatic Genetic Resources certified by the Ministry of Agriculture and Rural Affairs/National Demonstration Center for Experimental Fisheries Science Education/Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Guoqing Lu
- Department of Biology, University of Nebraska at Omaha, Omaha, NE 68182, USA
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
- Corresponding author. Email (M.H.); (C.L.); (C.W.)
| | - Chenhong Li
- Key Laboratory of Freshwater Aquatic Genetic Resources certified by the Ministry of Agriculture and Rural Affairs/National Demonstration Center for Experimental Fisheries Science Education/Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
- Corresponding author. Email (M.H.); (C.L.); (C.W.)
| | - Chenghui Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources certified by the Ministry of Agriculture and Rural Affairs/National Demonstration Center for Experimental Fisheries Science Education/Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
- Corresponding author. Email (M.H.); (C.L.); (C.W.)
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3
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Crain AT, Klusza S, Armstrong RL, Santa Rosa P, Temple BRS, Strahl BD, McKay DJ, Matera AG, Duronio RJ. Distinct developmental phenotypes result from mutation of Set8/KMT5A and histone H4 lysine 20 in Drosophila melanogaster. Genetics 2022; 221:iyac054. [PMID: 35404465 PMCID: PMC9157153 DOI: 10.1093/genetics/iyac054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/28/2022] [Indexed: 01/27/2023] Open
Abstract
Mono-methylation of histone H4 lysine 20 (H4K20me1) is catalyzed by Set8/KMT5A and regulates numerous aspects of genome organization and function. Loss-of-function mutations in Drosophila melanogaster Set8 or mammalian KMT5A prevent H4K20me1 and disrupt development. Set8/KMT5A also has non-histone substrates, making it difficult to determine which developmental functions of Set8/KMT5A are attributable to H4K20me1 and which to other substrates or to non-catalytic roles. Here, we show that human KMT5A can functionally substitute for Set8 during Drosophila development and that the catalytic SET domains of the two enzymes are fully interchangeable. We also uncovered a role in eye development for the N-terminal domain of Set8 that cannot be complemented by human KMT5A. Whereas Set820/20 null mutants are inviable, we found that an R634G mutation in Set8 predicted from in vitro experiments to ablate catalytic activity resulted in viable adults. Additionally, Set8(R634G) mutants retain significant, albeit reduced, H4K20me1, indicating that the R634G mutation does not eliminate catalytic activity in vivo and is functionally hypomorphic rather than null. Flies engineered to express only unmodifiable H4 histones (H4K20A) can also complete development, but are phenotypically distinct from H4K20R, Set820/20 null, and Set8R634G mutants. Taken together, our results demonstrate functional conservation of KMT5A and Set8 enzymes, as well as distinct roles for Set8 and H4K20me1 in Drosophila development.
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Affiliation(s)
- Aaron T Crain
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599 USA
| | - Stephen Klusza
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599 USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599 USA
| | - Robin L Armstrong
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599 USA
| | | | - Brenda R S Temple
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599 USA
| | - Brian D Strahl
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599 USA
| | - Daniel J McKay
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599 USA
| | - A Gregory Matera
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599 USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599 USA
| | - Robert J Duronio
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599 USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599 USA
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4
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Huang L, Nie L, Dai Z, Dong J, Jia X, Yang X, Yao L, Ma SC. The application of mass spectrometry imaging in traditional Chinese medicine: a review. Chin Med 2022; 17:35. [PMID: 35248086 PMCID: PMC8898510 DOI: 10.1186/s13020-022-00586-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/22/2022] [Indexed: 08/26/2023] Open
Abstract
AbstractMass spectrometry imaging is a frontier technique which connects classical mass spectrometry with ion imaging. Various types of chemicals could be visualized in their native tissues using mass spectrometry imaging. Up to now, the most commonly applied mass spectrometry imaging techniques are matrix assisted laser desorption ionization mass spectrometry imaging, desorption electrospray ionization mass spectrometry imaging and secondary ion mass spectrometry imaging. This review gives an introduction to the principles, development and applications of commonly applied mass spectrometry imaging techniques, and then illustrates the application of mass spectrometry imaging in the investigation of traditional Chinese medicine. Recently, mass spectrometry imaging has been adopted to explore the spatial distribution of endogenous metabolites in traditional Chinese medicine. Data collected from mass spectrometry imaging can be further utilized to search for marker components of traditional Chinese medicine, discover new compounds from traditional herbs, and differentiate between medicinal plants that are similar in botanical features. Moreover, mass spectrometry imaging also plays a role in revealing the pharmacological and toxicological mechanisms of traditional Chinese medicine.
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5
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Wang H, Jiang F, Liu X, Liu Q, Fu Y, Li R, Hou L, Zhang J, He J, Kang L. Piwi/piRNAs control food intake by promoting neuropeptide F expression in locusts. EMBO Rep 2022; 23:e50851. [PMID: 34985794 PMCID: PMC8892266 DOI: 10.15252/embr.202050851] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 12/08/2021] [Accepted: 12/16/2021] [Indexed: 11/18/2022] Open
Abstract
Animal feeding, which directly affects growth and metabolism, is an important physiological process. However, the contribution of PIWI proteins and PIWI‐interacting RNAs (piRNAs) to the regulatory mechanism of animal feeding is unknown. Here, we report a novel function of Piwi and piRNAs in regulating food intake in locusts. Our study shows that the locust can serve as a representative species for determining PIWI function in insects. Knockdown of Piwi1 expression suppresses anabolic processes and reduces food consumption and body weight. The reduction in food intake by knockdown of Piwi1 expression results from decreased expression of neuropeptide NPF1 in a piRNA‐dependent manner. Mechanistically, intronic piRNAs might enhance RNA splicing of NPF1 by preventing hairpin formation at the branch point sites. These results suggest a novel nuclear PIWI/piRNA‐mediated mechanism that controls food intake in the locust nervous system.
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Affiliation(s)
- Huimin Wang
- Beijing Institutes of Life Science Chinese Academy of Sciences Beijing China
- CAS Center for Excellence in Biotic Interactions University of Chinese Academy of Sciences Beijing China
| | - Feng Jiang
- Beijing Institutes of Life Science Chinese Academy of Sciences Beijing China
- CAS Center for Excellence in Biotic Interactions University of Chinese Academy of Sciences Beijing China
| | - Xiang Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Qing Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents Institute of Zoology Chinese Academy of Sciences Beijing China
- Sino‐Danish College University of Chinese Academy of Sciences Beijing China
| | - Yunyun Fu
- College of Life Science Hebei University Baoding China
| | - Ran Li
- Beijing Institutes of Life Science Chinese Academy of Sciences Beijing China
| | - Li Hou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Jie Zhang
- Beijing Institutes of Life Science Chinese Academy of Sciences Beijing China
| | - Jing He
- State Key Laboratory of Integrated Management of Pest Insects and Rodents Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Le Kang
- Beijing Institutes of Life Science Chinese Academy of Sciences Beijing China
- CAS Center for Excellence in Biotic Interactions University of Chinese Academy of Sciences Beijing China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents Institute of Zoology Chinese Academy of Sciences Beijing China
- College of Life Science Hebei University Baoding China
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6
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Polinski JM, Zimin AV, Clark KF, Kohn AB, Sadowski N, Timp W, Ptitsyn A, Khanna P, Romanova DY, Williams P, Greenwood SJ, Moroz LL, Walt DR, Bodnar AG. The American lobster genome reveals insights on longevity, neural, and immune adaptations. SCIENCE ADVANCES 2021; 7:7/26/eabe8290. [PMID: 34162536 PMCID: PMC8221624 DOI: 10.1126/sciadv.abe8290] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 05/07/2021] [Indexed: 05/30/2023]
Abstract
The American lobster, Homarus americanus, is integral to marine ecosystems and supports an important commercial fishery. This iconic species also serves as a valuable model for deciphering neural networks controlling rhythmic motor patterns and olfaction. Here, we report a high-quality draft assembly of the H. americanus genome with 25,284 predicted gene models. Analysis of the neural gene complement revealed extraordinary development of the chemosensory machinery, including a profound diversification of ligand-gated ion channels and secretory molecules. The discovery of a novel class of chimeric receptors coupling pattern recognition and neurotransmitter binding suggests a deep integration between the neural and immune systems. A robust repertoire of genes involved in innate immunity, genome stability, cell survival, chemical defense, and cuticle formation represents a diversity of defense mechanisms essential to thrive in the benthic marine environment. Together, these unique evolutionary adaptations contribute to the longevity and ecological success of this long-lived benthic predator.
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Affiliation(s)
| | - Aleksey V Zimin
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - K Fraser Clark
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, Nova Scotia B2N 5E3, Canada
| | - Andrea B Kohn
- The Whitney Laboratory for Marine Bioscience and Department of Neuroscience, University of Florida, Gainesville and St. Augustine, FL 32080-8623, USA
| | - Norah Sadowski
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Winston Timp
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Andrey Ptitsyn
- Gloucester Marine Genomics Institute, Gloucester, MA 01930, USA
| | - Prarthana Khanna
- Genetics Program, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Daria Y Romanova
- Institute of Higher Nervous Activity and Neurophysiology of RAS, Moscow 117485, Russia
| | - Peter Williams
- The Whitney Laboratory for Marine Bioscience and Department of Neuroscience, University of Florida, Gainesville and St. Augustine, FL 32080-8623, USA
| | - Spencer J Greenwood
- Department of Biomedical Sciences, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island C1A 4P3, Canada
| | - Leonid L Moroz
- The Whitney Laboratory for Marine Bioscience and Department of Neuroscience, University of Florida, Gainesville and St. Augustine, FL 32080-8623, USA
| | - David R Walt
- Gloucester Marine Genomics Institute, Gloucester, MA 01930, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA 02115, USA
| | - Andrea G Bodnar
- Gloucester Marine Genomics Institute, Gloucester, MA 01930, USA.
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Palli SR. Epigenetic regulation of post-embryonic development. CURRENT OPINION IN INSECT SCIENCE 2021; 43:63-69. [PMID: 33068783 PMCID: PMC8044252 DOI: 10.1016/j.cois.2020.09.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/09/2020] [Accepted: 09/18/2020] [Indexed: 05/02/2023]
Abstract
Modifications to DNA and core histones influence chromatin organization and expression of the genome. DNA methylation plays a significant role in the regulation of multiple biological processes that regulate behavior and caste differentiation in social insects. Histone modifications play significant roles in the regulation of development and reproduction in other insects. Genes coding for acetyltransferases, deacetylases, methyltransferases, and demethylases that modify core histones have been identified in genomes of multiple insects. Studies on the function and mechanisms of action of some of these enzymes uncovered their contribution to post-embryonic development. The results from studies on epigenetic modifiers could help in the identification of inhibitors of epigenetic modifiers that could be developed to control pests and disease vectors.
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Affiliation(s)
- Subba Reddy Palli
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, S225 Ag. Science N, Lexington, KY 40546, United States.
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8
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Berlandi J, Chaouch A, De Jay N, Tegeder I, Thiel K, Shirinian M, Kleinman CL, Jeibmann A, Lasko P, Jabado N, Hasselblatt M. Identification of genes functionally involved in the detrimental effects of mutant histone H3.3-K27M in Drosophila melanogaster. Neuro Oncol 2020; 21:628-639. [PMID: 30715493 DOI: 10.1093/neuonc/noz021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Recurrent specific mutations in evolutionarily conserved histone 3 (H3) variants drive pediatric high-grade gliomas (HGGs), but little is known about their downstream effects. The aim of this study was to identify genes involved in the detrimental effects of mutant H3.3-K27M, the main genetic driver in lethal midline HGG, in a transgenic Drosophila model. METHODS Mutant and wild-type histone H3.3-expressing flies were generated using a φC31-based integration system. Genetic modifier screens were performed by crossing H3.3-K27M expressing driver strains and 194 fly lines expressing short hairpin RNA targeting genes selected based on their potential role in the detrimental effects of mutant H3. Expression of the human orthologues of genes with functional relevance in the fly model was validated in H3-K27M mutant HGG. RESULTS Ubiquitous and midline glia-specific expression of H3.3-K27M but not wild-type H3.3 caused pupal lethality, morphological alterations, and decreased H3K27me3. Knockdown of 17 candidate genes shifted the lethal phenotype to later stages of development. These included histone modifying and chromatin remodeling genes as well as genes regulating cell differentiation and proliferation. Notably, several of these genes were overexpressed in mutant H3-K27M mutated HGG. CONCLUSIONS Rapid screening, identification, and validation of relevant targets in "oncohistone" mediated pathogenesis have proven a challenge and a barrier to providing novel therapies. Our results provide further evidence on the role of chromatin modifiers in the genesis of H3.3-K27M. Notably, they validate Drosophila as a model system for rapid identification of relevant genes functionally involved in the detrimental effects of H3.3-K27M mutagenesis.
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Affiliation(s)
- Johannes Berlandi
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Amel Chaouch
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Nicolas De Jay
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,The Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada
| | - Isabel Tegeder
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Katharina Thiel
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Margret Shirinian
- Department of Experimental Pathology, Immunology, and Microbiology Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Claudia L Kleinman
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,The Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada
| | - Astrid Jeibmann
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Paul Lasko
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Nada Jabado
- Department of Paediatrics, McGill University and the McGill University Health Center Research Institute, Montreal, Quebec, Canada
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
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9
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Jiang F, Zhang J, Liu Q, Liu X, Wang H, He J, Kang L. Long-read direct RNA sequencing by 5'-Cap capturing reveals the impact of Piwi on the widespread exonization of transposable elements in locusts. RNA Biol 2019; 16:950-959. [PMID: 30982421 PMCID: PMC6546357 DOI: 10.1080/15476286.2019.1602437] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 03/25/2019] [Accepted: 03/26/2019] [Indexed: 12/20/2022] Open
Abstract
The large genome of the migratory locust (Locusta migratoria) genome accumulates massive amount of accumulated transposable elements (TEs), which show intrinsic transcriptional activities. Hampering the ability to precisely determine full-length RNA transcript sequences are exonized TEs, which produce numerous highly similar fragments that are difficult to resolve using short-read sequencing technology. Here, we applied a 5'-Cap capturing method using Nanopore long-read direct RNA sequencing to characterize full-length transcripts in their native RNA form and to analyze the TE exonization pattern in the locust transcriptome. Our results revealed the widespread establishment of TE exonization and a substantial contribution of TEs to RNA splicing in the locust transcriptome. The results of the transcriptomic spectrum influenced by Piwi expression indicated that TE-derived sequences were the main targets of Piwi-mediated repression. Furthermore, our study showed that Piwi expression regulates the length of RNA transcripts containing TE-derived sequences, creating an alternative UTR usage. Overall, our results reveal the transcriptomic characteristics of TE exonization in the species characterized by large and repetitive genomes.
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Affiliation(s)
- Feng Jiang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jie Zhang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Qing Liu
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China
| | - Xiang Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Huimin Wang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Jing He
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Le Kang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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10
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Fellous A, Earley RL, Silvestre F. The Kdm/Kmt gene families in the self-fertilizing mangrove rivulus fish, Kryptolebias marmoratus, suggest involvement of histone methylation machinery in development and reproduction. Gene 2019; 687:173-187. [DOI: 10.1016/j.gene.2018.11.046] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 11/06/2018] [Accepted: 11/15/2018] [Indexed: 12/16/2022]
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11
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Jiang F, Liu Q, Wang Y, Zhang J, Wang H, Song T, Yang M, Wang X, Kang L. Comparative genomic analysis of SET domain family reveals the origin, expansion, and putative function of the arthropod-specific SmydA genes as histone modifiers in insects. Gigascience 2018; 6:1-16. [PMID: 28444351 PMCID: PMC5459927 DOI: 10.1093/gigascience/gix031] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 04/19/2017] [Indexed: 02/07/2023] Open
Abstract
The SET domain is an evolutionarily conserved motif present in histone lysine methyltransferases, which are important in the regulation of chromatin and gene expression in animals. In this study, we searched for SET domain–containing genes (SET genes) in all of the 147 arthropod genomes sequenced at the time of carrying out this experiment to understand the evolutionary history by which SET domains have evolved in insects. Phylogenetic and ancestral state reconstruction analysis revealed an arthropod-specific SET gene family, named SmydA, that is ancestral to arthropod animals and specifically diversified during insect evolution. Considering that pseudogenization is the most probable fate of the new emerging gene copies, we provided experimental and evolutionary evidence to demonstrate their essential functions. Fluorescence in situ hybridization analysis and in vitro methyltransferase activity assays showed that the SmydA-2 gene was transcriptionally active and retained the original histone methylation activity. Expression knockdown by RNA interference significantly increased mortality, implying that the SmydA genes may be essential for insect survival. We further showed predominantly strong purifying selection on the SmydA gene family and a potential association between the regulation of gene expression and insect phenotypic plasticity by transcriptome analysis. Overall, these data suggest that the SmydA gene family retains essential functions that may possibly define novel regulatory pathways in insects. This work provides insights into the roles of lineage-specific domain duplication in insect evolution.
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Affiliation(s)
- Feng Jiang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Qing Liu
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yanli Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, China
| | - Jie Zhang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Huimin Wang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Tianqi Song
- Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, China
| | - Meiling Yang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xianhui Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Le Kang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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12
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Guo S, Guo L, Zhao W, Xu J, Li Y, Zhang X, Shen X, Wu M, Hou X. Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Paeonia ostii. Molecules 2018; 23:molecules23020246. [PMID: 29373520 PMCID: PMC6017096 DOI: 10.3390/molecules23020246] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 01/20/2018] [Accepted: 01/24/2018] [Indexed: 01/21/2023] Open
Abstract
Paeonia ostii, a common oil-tree peony, is important ornamentally and medicinally. However, there are few studies on the chloroplast genome of Paeonia ostii. We sequenced and analyzed the complete chloroplast genome of P. ostii. The size of the P. ostii chloroplast genome is 152,153 bp, including a large single-copy region (85,373 bp), a small single-copy region (17,054 bp), and a pair of inverted repeats regions (24,863 bp). The P. ostii chloroplast genome encodes 111 genes, including 77 protein-coding genes, four ribosomal RNA genes, and 30 transfer RNA genes. The genome contains forward repeats (22), palindromic repeats (28), and tandem repeats (24). The presence of rich simple-sequence repeat loci in the genome provides opportunities for future population genetics work for breeding new varieties. A phylogenetic analysis showed that P. ostii is more closely related to Paeonia delavayi and Paeonialudlowii than to Paeoniaobovata and Paeoniaveitchii. The results of this study provide an assembly of the whole chloroplast genome of P. ostii, which may be useful for future breeding and further biological discoveries. It will provide a theoretical basis for the improvement of peony yield and the determination of phylogenetic status.
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Affiliation(s)
- Shuai Guo
- College of Agricultural (College of Tree Peony), Henan University of Science and Technology, Luoyang 471023, Henan, China; (S.G.); (L.G.); (W.Z.); (Y.L.)
- Institute of Chinese Materia Medical, China Academy of Chinese Medical Sciences, Beijing 100700, China; (J.X.); (X.Z); (X.S.); (M.W.)
| | - Lili Guo
- College of Agricultural (College of Tree Peony), Henan University of Science and Technology, Luoyang 471023, Henan, China; (S.G.); (L.G.); (W.Z.); (Y.L.)
| | - Wei Zhao
- College of Agricultural (College of Tree Peony), Henan University of Science and Technology, Luoyang 471023, Henan, China; (S.G.); (L.G.); (W.Z.); (Y.L.)
| | - Jiang Xu
- Institute of Chinese Materia Medical, China Academy of Chinese Medical Sciences, Beijing 100700, China; (J.X.); (X.Z); (X.S.); (M.W.)
| | - Yuying Li
- College of Agricultural (College of Tree Peony), Henan University of Science and Technology, Luoyang 471023, Henan, China; (S.G.); (L.G.); (W.Z.); (Y.L.)
| | - Xiaoyan Zhang
- Institute of Chinese Materia Medical, China Academy of Chinese Medical Sciences, Beijing 100700, China; (J.X.); (X.Z); (X.S.); (M.W.)
- College of Life Science, Huaibei Normal University, Huaibei 235000, Anhui, China
| | - Xiaofeng Shen
- Institute of Chinese Materia Medical, China Academy of Chinese Medical Sciences, Beijing 100700, China; (J.X.); (X.Z); (X.S.); (M.W.)
| | - Mingli Wu
- Institute of Chinese Materia Medical, China Academy of Chinese Medical Sciences, Beijing 100700, China; (J.X.); (X.Z); (X.S.); (M.W.)
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, Hubei China
| | - Xiaogai Hou
- College of Agricultural (College of Tree Peony), Henan University of Science and Technology, Luoyang 471023, Henan, China; (S.G.); (L.G.); (W.Z.); (Y.L.)
- Correspondence: ; Tel: +86-0379-6998-0776
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