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Willbanks A, Leary M, Greenshields M, Tyminski C, Heerboth S, Lapinska K, Haskins K, Sarkar S. The Evolution of Epigenetics: From Prokaryotes to Humans and Its Biological Consequences. GENETICS & EPIGENETICS 2016; 8:25-36. [PMID: 27512339 PMCID: PMC4973776 DOI: 10.4137/geg.s31863] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 07/03/2016] [Accepted: 07/06/2016] [Indexed: 12/11/2022]
Abstract
The evolution process includes genetic alterations that started with prokaryotes and now continues in humans. A distinct difference between prokaryotic chromosomes and eukaryotic chromosomes involves histones. As evolution progressed, genetic alterations accumulated and a mechanism for gene selection developed. It was as if nature was experimenting to optimally utilize the gene pool without changing individual gene sequences. This mechanism is called epigenetics, as it is above the genome. Curiously, the mechanism of epigenetic regulation in prokaryotes is strikingly different from that in eukaryotes, mainly higher eukaryotes, like mammals. In fact, epigenetics plays a significant role in the conserved process of embryogenesis and human development. Malfunction of epigenetic regulation results in many types of undesirable effects, including cardiovascular disease, metabolic disorders, autoimmune diseases, and cancer. This review provides a comparative analysis and new insights into these aspects.
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Affiliation(s)
- Amber Willbanks
- Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Meghan Leary
- Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Molly Greenshields
- Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Camila Tyminski
- Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Sarah Heerboth
- Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Karolina Lapinska
- Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Kathryn Haskins
- Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Sibaji Sarkar
- Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA.; Genome Science Institute, Boston University School of Medicine, Boston, MA, USA
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Roquis D, Rognon A, Chaparro C, Boissier J, Arancibia N, Cosseau C, Parrinello H, Grunau C. Frequency and mitotic heritability of epimutations inSchistosoma mansoni. Mol Ecol 2016; 25:1741-58. [DOI: 10.1111/mec.13555] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 01/22/2016] [Accepted: 01/23/2016] [Indexed: 12/28/2022]
Affiliation(s)
- David Roquis
- Université de Perpignan Via Domitia; Perpignan F-66860 France
- CNRS; UMR 5244; Interactions Hôtes-Pathogènes-Environnements (IHPE); Perpignan F-66860 France
| | - Anne Rognon
- Université de Perpignan Via Domitia; Perpignan F-66860 France
- CNRS; UMR 5244; Interactions Hôtes-Pathogènes-Environnements (IHPE); Perpignan F-66860 France
| | - Cristian Chaparro
- Université de Perpignan Via Domitia; Perpignan F-66860 France
- CNRS; UMR 5244; Interactions Hôtes-Pathogènes-Environnements (IHPE); Perpignan F-66860 France
| | - Jerome Boissier
- Université de Perpignan Via Domitia; Perpignan F-66860 France
- CNRS; UMR 5244; Interactions Hôtes-Pathogènes-Environnements (IHPE); Perpignan F-66860 France
| | - Nathalie Arancibia
- Université de Perpignan Via Domitia; Perpignan F-66860 France
- CNRS; UMR 5244; Interactions Hôtes-Pathogènes-Environnements (IHPE); Perpignan F-66860 France
| | - Celine Cosseau
- Université de Perpignan Via Domitia; Perpignan F-66860 France
- CNRS; UMR 5244; Interactions Hôtes-Pathogènes-Environnements (IHPE); Perpignan F-66860 France
| | - Hugues Parrinello
- MGX - Montpellier GenomiX IBiSA, Institut de Génomique Fonctionnelle; 141, rue de la Cardonille F-34094 Montpellier Cedex 05 France
| | - Christoph Grunau
- Université de Perpignan Via Domitia; Perpignan F-66860 France
- CNRS; UMR 5244; Interactions Hôtes-Pathogènes-Environnements (IHPE); Perpignan F-66860 France
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Ashapkin VV, Kutueva LI, Vanyushin BF. Dnmt2 is the most evolutionary conserved and enigmatic cytosine DNA methyltransferase in eukaryotes. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416030029] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Cai P, Gobert GN, You H, McManus DP. The Tao survivorship of schistosomes: implications for schistosomiasis control. Int J Parasitol 2016; 46:453-63. [PMID: 26873753 DOI: 10.1016/j.ijpara.2016.01.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 01/06/2016] [Accepted: 01/06/2016] [Indexed: 01/06/2023]
Abstract
Schistosomiasis, caused by blood flukes of the genus Schistosoma, is a major public health problem which contributes substantially to the economic and financial burdens of many nations in the developing world. An array of survival strategies, such as the unique structure of the tegument which acts as a major host-parasite interface, immune modulation mechanisms, gene regulation, and apoptosis and self-renewal have been adopted by schistosome parasites over the course of long-term evolution with their mammalian definitive hosts. Recent generation of complete schistosome genomes together with numerous biological, immunological, high-throughput "-omics" and gene function studies have revealed the Tao or strategies that schistosomes employ not only to promote long-term survival, but also to ensure effective life cycle transmission. New scenarios for the future control of this important neglected tropical disease will present themselves as our understanding of these Tao increases.
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Affiliation(s)
- Pengfei Cai
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Queensland, Australia.
| | - Geoffrey N Gobert
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Hong You
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Donald P McManus
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Queensland, Australia.
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55
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Epigenetic mechanisms of dietary restriction induced aging in Drosophila. Exp Gerontol 2015; 72:38-44. [DOI: 10.1016/j.exger.2015.08.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 08/04/2015] [Accepted: 08/25/2015] [Indexed: 01/07/2023]
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56
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Wasik K, Gurtowski J, Zhou X, Ramos OM, Delás MJ, Battistoni G, El Demerdash O, Falciatori I, Vizoso DB, Smith AD, Ladurner P, Schärer L, McCombie WR, Hannon GJ, Schatz M. Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano. Proc Natl Acad Sci U S A 2015; 112:12462-7. [PMID: 26392545 PMCID: PMC4603488 DOI: 10.1073/pnas.1516718112] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The free-living flatworm, Macrostomum lignano has an impressive regenerative capacity. Following injury, it can regenerate almost an entirely new organism because of the presence of an abundant somatic stem cell population, the neoblasts. This set of unique properties makes many flatworms attractive organisms for studying the evolution of pathways involved in tissue self-renewal, cell-fate specification, and regeneration. The use of these organisms as models, however, is hampered by the lack of a well-assembled and annotated genome sequences, fundamental to modern genetic and molecular studies. Here we report the genomic sequence of M. lignano and an accompanying characterization of its transcriptome. The genome structure of M. lignano is remarkably complex, with ∼75% of its sequence being comprised of simple repeats and transposon sequences. This has made high-quality assembly from Illumina reads alone impossible (N50=222 bp). We therefore generated 130× coverage by long sequencing reads from the Pacific Biosciences platform to create a substantially improved assembly with an N50 of 64 Kbp. We complemented the reference genome with an assembled and annotated transcriptome, and used both of these datasets in combination to probe gene-expression patterns during regeneration, examining pathways important to stem cell function.
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Affiliation(s)
- Kaja Wasik
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - James Gurtowski
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Xin Zhou
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Molecular and Cellular Biology Graduate Program, Stony Brook University, NY 11794
| | - Olivia Mendivil Ramos
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - M Joaquina Delás
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Giorgia Battistoni
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Osama El Demerdash
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Ilaria Falciatori
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Dita B Vizoso
- Department of Evolutionary Biology, Zoological Institute, University of Basel, 4051 Basel, Switzerland
| | - Andrew D Smith
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089
| | - Peter Ladurner
- Department of Evolutionary Biology, Institute of Zoology and Center for Molecular Biosciences Innsbruck, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Lukas Schärer
- Department of Evolutionary Biology, Zoological Institute, University of Basel, 4051 Basel, Switzerland
| | - W Richard McCombie
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Gregory J Hannon
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom;
| | - Michael Schatz
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724;
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Egg-specific expression of protein with DNA methyltransferase activity in the biocarcinogenic liver fluke Clonorchis sinensis. Parasitology 2015; 142:1228-38. [PMID: 26036304 DOI: 10.1017/s0031182015000566] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Despite recent reports regarding the biology of cytosine methylation in Schistosoma mansoni, the impact of the regulatory machinery remains unclear in diverse platyhelminthes. This ambiguity is reinforced by discoveries of DNA methyltransferase 2 (DNMT2)-only organisms and the substrate specificity of DNMT2 preferential to RNA molecules. Here, we characterized a novel DNA methyltransferase, named CsDNMT2, in a liver fluke Clonorchis sinensis. The protein exhibited structural properties conserved in other members of the DNMT2 family. The native and recombinant CsDNMT2 exhibited considerable enzymatic activity on DNA. The spatiotemporal expression of CsDNMT2 mirrored that of 5-methylcytosine (5 mC), both of which were elevated in the C. sinensis eggs. However, CsDNMT2 and 5 mC were marginally detected in other histological regions of C. sinensis adults including ovaries and seminal receptacle. The methylation site seemed not related to genomic loci occupied by progenies of an active long-terminal-repeat retrotransposon. Taken together, our data strongly suggest that C. sinensis has preserved the functional DNA methylation machinery and that DNMT2 acts as a genuine alternative to DNMT1/DNMT3 to methylate DNA in the DNMT2-only organism. The epigenetic regulation would target functional genes primarily involved in the formation and/or maturation of eggs, rather than retrotransposons.
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You H, Gobert GN, Cai P, Mou R, Nawaratna S, Fang G, Villinger F, McManus DP. Suppression of the Insulin Receptors in Adult Schistosoma japonicum Impacts on Parasite Growth and Development: Further Evidence of Vaccine Potential. PLoS Negl Trop Dis 2015; 9:e0003730. [PMID: 25961574 PMCID: PMC4427307 DOI: 10.1371/journal.pntd.0003730] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 03/30/2015] [Indexed: 12/19/2022] Open
Abstract
To further investigate the importance of insulin signaling in the growth, development, sexual maturation and egg production of adult schistosomes, we have focused attention on the insulin receptors (SjIRs) of Schistosoma japonicum, which we have previously cloned and partially characterised. We now show, by Biolayer Interferometry, that human insulin can bind the L1 subdomain (insulin binding domain) of recombinant (r)SjIR1 and rSjIR2 (designated SjLD1 and SjLD2) produced using the Drosophila S2 protein expression system. We have then used RNA interference (RNAi) to knock down the expression of the SjIRs in adult S. japonicum in vitro and show that, in addition to their reduced transcription, the transcript levels of other important downstream genes within the insulin pathway, associated with glucose metabolism and schistosome fecundity, were also impacted substantially. Further, a significant decrease in glucose uptake was observed in the SjIR-knockdown worms compared with luciferase controls. In vaccine/challenge experiments, we found that rSjLD1 and rSjLD2 depressed female growth, intestinal granuloma density and faecal egg production in S. japonicum in mice presented with a low dose challenge infection. These data re-emphasize the potential of the SjIRs as veterinary transmission blocking vaccine candidates against zoonotic schistosomiasis japonica in China and the Philippines. Schistosomiasis affects over 200 million people globally. An anti-schistosome vaccine is not currently available. Schistosome eggs play a critical role in host pathology and the transmission of schistosomiasis; thus a vaccine targeting parasite fecundity and/or egg viability represents a realistic strategy for blocking transmission, promoting disease control in endemic areas. Based on our previous studies on the insulin receptors (SjIRs) of Schistosoma japonicum, as potential vaccine candidates, we have now further investigated the impact of insulin signaling on the growth, development, sexual maturation and egg production of adult schistosomes. Protein binding assays and RNAi strongly support our hypothesis that the insulin pathway in schistosomes is activated by the binding between host insulin and the parasite IRs, regulating the transcription of downstream genes integrally involved in glucose uptake and fecundity in these parasites. This feature was reflected in the striking decreased glucose levels of worms when the SjIRs were knocked down. Furthermore, the importance of the SjIRs in the growth and fecundity of adult S. japonicum was further demonstrated in murine vaccine trials using a low dose cercarial challenge which resulted in depressed female growth and faecal egg production in mice vaccinated with the recombinant L1 subdomains of SjIR1 and SjIR2.
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Affiliation(s)
- Hong You
- Molecular Parasitology Laboratory, Infectious Diseases Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- * E-mail: (HY); (DPM)
| | - Geoffrey N. Gobert
- Molecular Parasitology Laboratory, Infectious Diseases Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Pengfei Cai
- Molecular Parasitology Laboratory, Infectious Diseases Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Rong Mou
- Department of Parasitology, Guiyang Medical University, Guiyang, China
| | - Sujeevi Nawaratna
- Molecular Parasitology Laboratory, Infectious Diseases Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Guofu Fang
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Francois Villinger
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Pathology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Donald P. McManus
- Molecular Parasitology Laboratory, Infectious Diseases Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- * E-mail: (HY); (DPM)
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Edwards J, Brown M, Peak E, Bartholomew B, Nash RJ, Hoffmann KF. The diterpenoid 7-keto-sempervirol, derived from Lycium chinense, displays anthelmintic activity against both Schistosoma mansoni and Fasciola hepatica. PLoS Negl Trop Dis 2015; 9:e0003604. [PMID: 25768432 PMCID: PMC4358835 DOI: 10.1371/journal.pntd.0003604] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 02/06/2015] [Indexed: 12/30/2022] Open
Abstract
Background Two platyhelminths of biomedical and commercial significance are Schistosoma mansoni (blood fluke) and Fasciola hepatica (liver fluke). These related trematodes are responsible for the chronic neglected tropical diseases schistosomiasis and fascioliasis, respectively. As no vaccine is currently available for anti-flukicidal immunoprophylaxis, current treatment is mediated by mono-chemical chemotherapy in the form of mass drug administration (MDA) (praziquantel for schistosomiasis) or drenching (triclabendazole for fascioliasis) programmes. This overreliance on single chemotherapeutic classes has dramatically limited the number of novel chemical entities entering anthelmintic drug discovery pipelines, raising significant concerns for the future of sustainable blood and liver fluke control. Methodology/ Principle Findings Here we demonstrate that 7-keto-sempervirol, a diterpenoid isolated from Lycium chinense, has dual anthelmintic activity against related S. mansoni and F. hepatica trematodes. Using a microtiter plate-based helminth fluorescent bioassay (HFB), this activity is specific (Therapeutic index = 4.2, when compared to HepG2 cell lines) and moderately potent (LD50 = 19.1 μM) against S. mansoni schistosomula cultured in vitro. This anti-schistosomula effect translates into activity against both adult male and female schistosomes cultured in vitro where 7-keto-sempervirol negatively affects motility/behaviour, surface architecture (inducing tegumental holes, tubercle swelling and spine loss/shortening), oviposition rates and egg morphology. As assessed by the HFB and microscopic phenotypic scoring matrices, 7-keto-sempervirol also effectively kills in vitro cultured F. hepatica newly excysted juveniles (NEJs, LD50 = 17.7 μM). Scanning electron microscopy (SEM) evaluation of adult F. hepatica liver flukes co-cultured in vitro with 7-keto-sempervirol additionally demonstrates phenotypic abnormalities including breaches in tegumental integrity and spine loss. Conclusions/ Significance 7-keto-sempervirol negatively affects the viability and phenotype of two related pathogenic trematodes responsible for significant human and animal infectious diseases. This plant-derived, natural product is also active against both larval and adult developmental forms. As such, the data collectively indicate that 7-keto-sempervirol is an important starting point for anthelmintic drug development. Medicinal chemistry optimisation of more potent 7-keto-sempervirol analogues could lead to the identification of novel chemical entities useful for future combinatorial or replacement anthelmintic control. Schistosomiasis and fascioliasis are caused by two related trematodes found within the phylum Platyhelminthes (flatworms), and are classified as neglected diseases of poverty due to their effects on people living in the most underprivileged areas of the world. With no vaccine currently near development, and the existing strategy for global control based on the over-reliance on single-class chemotherapies, there is an urgent requirement for the identification of next generation anthelmintics. Here we demonstrate that 7-keto-sempervirol, a natural product derived from Lycium chinense, displays dual anthelmintic activity towards both Schistosoma mansoni (causative agent of schistosomiasis) and Fasciola hepatica (causative agent of fascioliasis). Utilising objective and phenotypic matrices, we show this activity to be selective (compared to a human cell line) and moderately potent against S. mansoni and F. hepatica larvae. This anti-larval effect translates into additional activity against both S. mansoni and F. hepatica adults where 7-keto-sempervirol induces phenotypic abnormalities including tegumental damage, motility disruption and oviposition inhibition. Due to 7-keto-sempervirol’s anthelmintic activity against multiple life stages of two parasitic trematodes, we contend that this starting chemical scaffold could be used to develop more effective compounds useful in controlling important parasites of biomedical and commercial relevance.
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Affiliation(s)
- Jennifer Edwards
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Martha Brown
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Emily Peak
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | | | - Robert J. Nash
- Phytoquest Ltd, Plas Gogerddan, Aberystwyth, United Kingdom
| | - Karl F. Hoffmann
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
- * E-mail:
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The genomic proliferation of transposable elements in colonizing populations: Schistosoma mansoni in the new world. Genetica 2015; 143:287-98. [PMID: 25681233 DOI: 10.1007/s10709-015-9825-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Accepted: 02/02/2015] [Indexed: 10/24/2022]
Abstract
Transposable elements (TEs) are mobile genes with an inherent ability to move within and among genomes. Theory predicts that TEs proliferate extensively during physiological stress due to the breakdown of TE repression systems. We tested this hypothesis in Schistosoma mansoni, a widespread trematode parasite that causes the human disease schistosomiasis. According to phylogenetic analysis, S. mansoni invaded the new world during the last 500 years. We hypothesized that new world strains of S. mansoni would have more copies of TEs than old world strains due to the physiological stress associated with invasion of the new world. We quantified the copy number of six TEs (Saci-1, Saci-2 and Saci-3, Perere-1, Merlin-sm1, and SmTRC1) in the genome and the transcriptome of old world and new world strains of S. mansoni, using qPCR relative quantification. As predicted, the genomes of new world parasites contain significantly more copies of class I and class II TEs in both laboratory and field strains. However, such differences are not observed in the transcriptome suggesting that either TE silencing mechanisms have reactivated to control the expression of these elements or the presence of inactive truncated copies of TEs.
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Rodríguez López CM, Wilkinson MJ. Epi-fingerprinting and epi-interventions for improved crop production and food quality. FRONTIERS IN PLANT SCIENCE 2015; 6:397. [PMID: 26097484 PMCID: PMC4456566 DOI: 10.3389/fpls.2015.00397] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 05/18/2015] [Indexed: 05/05/2023]
Abstract
Increasing crop production at a time of rapid climate change represents the greatest challenge facing contemporary agricultural research. Our understanding of the genetic control of yield derives from controlled field experiments designed to minimize environmental variance. In spite of these efforts there is substantial residual variability among plants attributable to Genotype × Environment interactions. Recent advances in the field of epigenetics have revealed a plethora of gene control mechanisms that could account for much of this unassigned variation. These systems act as a regulatory interface between the perception of the environment and associated alterations in gene expression. Direct intervention of epigenetic control systems hold the enticing promise of creating new sources of variability that could enhance crop performance. Equally, understanding the relationship between various epigenetic states and responses of the crop to specific aspects of the growing environment (epigenetic fingerprinting) could allow for a more tailored approach to plant agronomy. In this review, we explore the many ways in which epigenetic interventions and epigenetic fingerprinting can be deployed for the improvement of crop production and quality.
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Affiliation(s)
- Carlos M. Rodríguez López
- *Correspondence: Carlos M. Rodríguez López, Plant Research Centre, School of Agriculture, Food and Wine, Faculty of Sciences, University of Adelaide, Waite Campus, PMB1, Glen Osmond, Adelaide, SA 5064, Australia
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Abstract
Anti-parasite responses of the snail Biomphalaria glabrata involve antigen-reactive plasma lectins termed fibrinogen-related proteins (FREPs) comprising a C-terminal fibrinogen (FBG) domain and one or two upstream immunoglobulin domains. FREPs are highly polymorphic; they derive from several gene families with multiple loci and alleles that are diversified by exon loss, alternative splicing, and random somatic mutation (gene conversion and point mutations). Individual B. glabrata snails have dynamically distinct FREP sequence repertoires. The immune relevance of B. glabrata FREPs is indicated by FREP binding to polymorphic antigens of (snail-specific) digenean parasites and altered resistance of B. glabrata to digeneans following RNAi knockdown of FREPs. The compatibility polymorphism hypothesis proposes that FREP mutation increases the range of germline-encoded immune recognition in B. glabrata to counter antigenically-varied parasites. Somatic mutation may result from sequence exchange among tandemly arranged FREP genes in the genome, and analysis of sequence variants also suggests involvement of cytidine deaminase-like activity or epigenetic regulation. Without current indications of selection or retention of effective sequence variants toward immunological memory, FREP diversification is thought to afford B. glabrata immunity that is anticipatory but not adaptive. More remains to be learned about this system; other mollusks elaborate diversified lectins consisting of single FBG domains, and bona fide FREPs were reported from additional gastropod species, but these may not be diversified. Future comparative immunological studies and gene discovery driven by next-generation sequencing will further clarify taxonomic distribution of FREP diversification and the underlying mutator mechanisms as a component of immune function in mollusks.
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Affiliation(s)
- Coen M Adema
- Biology Department, Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM, 87131, USA.
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Strongyloides stercoralis and relatives: recent advances in general and molecular biology. CURRENT TROPICAL MEDICINE REPORTS 2014; 1:194-206. [PMID: 29577012 DOI: 10.1007/s40475-014-0033-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Human strongyloidiasis is a threat to global health, presenting significant challenges in diagnosis and clinical management. The imperative to incorporate strongyoidiasis more fully into control programs for soil-transmitted helminths is increasingly recognized. The unique life cycles of S. stercoralis and congeneric species contain both free-living and parasitic generations, and transcriptomic methods have recently identified genes of potential importance to parasitism in these parasites. Proteomics recently revealed stage-specific secreted proteins that appear crucial to the host-parasite interaction. A comprehensive genome sequencing project for Strongyloides spp. is now nearing completion. Recent technical advances in transgenesis for S. stercoralis and S. ratti, including the first establishment of stable transgenic lines, promise to advance functional evaluations of genes expressed in conjunction with crucial life cycle events. Studies employing these methods recently bolstered the hypothesis that S. stercoralis uses cellular signaling pathways homologous to three that regulate dauer larval development in Caenorhabditis elegans to regulate morphogenesis and development of its infective third-stage larva. The free-living generation of Strongyloides makes classical genetics formally possible. Recent advances, such as a genetic map of S. ratti and a molecular genetic and karyotypic analysis of sex determination in S. papillosus, will greatly facilitate this approach. Advanced methods for study of chemosensation in C. elegans were recently applied to discover numerous host attractant molecules that mediate host finding and contact by infective third-stage larvae of Strongyloides spp. Finally, nucleic acid-based diagnostic methods have recently come to the fore as alternatives to parasitological and immunodiagnostic techniques.
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Arican-Goktas HD, Ittiprasert W, Bridger JM, Knight M. Differential spatial repositioning of activated genes in Biomphalaria glabrata snails infected with Schistosoma mansoni. PLoS Negl Trop Dis 2014; 8:e3013. [PMID: 25211244 PMCID: PMC4161332 DOI: 10.1371/journal.pntd.0003013] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 05/20/2014] [Indexed: 11/18/2022] Open
Abstract
Schistosomiasis is an infectious disease infecting mammals as the definitive host and fresh water snails as the intermediate host. Understanding the molecular and biochemical relationship between the causative schistosome parasite and its hosts will be key to understanding and ultimately treating and/or eradicating the disease. There is increasing evidence that pathogens that have co-evolved with their hosts can manipulate their hosts' behaviour at various levels to augment an infection. Bacteria, for example, can induce beneficial chromatin remodelling of the host genome. We have previously shown in vitro that Biomphalaria glabrata embryonic cells co-cultured with schistosome miracidia display genes changing their nuclear location and becoming up-regulated. This also happens in vivo in live intact snails, where early exposure to miracidia also elicits non-random repositioning of genes. We reveal differences in the nuclear repositioning between the response of parasite susceptible snails as compared to resistant snails and with normal or live, attenuated parasites. Interestingly, the stress response gene heat shock protein (Hsp) 70 is only repositioned and then up-regulated in susceptible snails with the normal parasite. This movement and change in gene expression seems to be controlled by the parasite. Other differences in the behaviour of genes support the view that some genes are responding to tissue damage, for example the ferritin genes move and are up-regulated whether the snails are either susceptible or resistant and upon exposure to either normal or attenuated parasite. This is the first time host genome reorganisation has been seen in a parasitic host and only the second time for any pathogen. We believe that the parasite elicits a spatio-epigenetic reorganisation of the host genome to induce favourable gene expression for itself and this might represent a fundamental mechanism present in the human host infected with schistosome cercariae as well as in other host-pathogen relationships. Bilharzia is a parasitic disease endemic in many parts of the world. The schistosoma parasite that causes Bilharzia infects humans but uses a fresh water snail as a secondary host. These two organisms have co-evolved together, and as such the parasite will have mechanisms to overcome the host defences. Understanding this delicately balanced relationship is fundamental to controlling or eradicating the disease. We have studied how this parasite can influence how the DNA within the snail behaves. We have shown snail genes have specific locations within the cell nuclei. Further, we have revealed that specific snail genes related to a schistosome infection change to a new non-random nuclear location as they are turned on or up-regulated. We have snail strains that are susceptible or resistant to the infection of parasites and we can also take live parasites and make them unable to complete an infection by irradiating them. In this unique study, we have shown a gene that is involved in stress pathways moves to a new nuclear location and becomes turned on, but only in susceptible snails, infected with fully functional parasite. Our data suggest that this gene is regulated by the parasite, which has control over the host's DNA, so that the gene is moved to an area where it can be actively expressed. We have uncovered a novel mechanism whereby the spatial organization of a host organism is interfered with by a pathogen. This type of control is probably found in other host-pathogen relationships.
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Affiliation(s)
- Halime D. Arican-Goktas
- Lab of Nuclear and Genomic Health, Centre for Cell and Chromosome Biology, Biosciences, School of Health Sciences and Social Care, Brunel University, London, United Kingdom
| | | | - Joanna M. Bridger
- Lab of Nuclear and Genomic Health, Centre for Cell and Chromosome Biology, Biosciences, School of Health Sciences and Social Care, Brunel University, London, United Kingdom
- * E-mail: (JMB); (MK)
| | - Matty Knight
- Department of Microbiology, Immunology and Tropical Medicine, School of Medicine and Health Science, George Washington University, Washington, D.C., United States of America
- * E-mail: (JMB); (MK)
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Cabezas-Cruz A, Lancelot J, Caby S, Oliveira G, Pierce RJ. Epigenetic control of gene function in schistosomes: a source of therapeutic targets? Front Genet 2014; 5:317. [PMID: 25309576 PMCID: PMC4159997 DOI: 10.3389/fgene.2014.00317] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 08/24/2014] [Indexed: 12/31/2022] Open
Abstract
The discovery of the epigenetic regulation of gene expression has revolutionized both our understanding of how genomes function and approaches to the therapy of numerous pathologies. Schistosomes are metazoan parasites and as such utilize most, if not all the epigenetic mechanisms in play in their vertebrate hosts: histone variants, histone tail modifications, non-coding RNA and, perhaps, DNA methylation. Moreover, we are acquiring an increasing understanding of the ways in which these mechanisms come into play during the complex schistosome developmental program. In turn, interest in the actors involved in epigenetic mechanisms, particularly the enzymes that carry out epigenetic modifications of histones or nucleic acid, as therapeutic targets has been stimulated by the finding that their inhibitors exert profound effects, not only on survival, but also on the reproductive function of Schistosoma mansoni. Here, we review our current knowledge, and what we can infer, about the role of epigenetic mechanisms in schistosome development, differentiation and survival. We will consider which epigenetic actors can be targeted for drug discovery and what strategies can be employed to develop potent, selective inhibitors as drugs to cure schistosomiasis.
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Affiliation(s)
- Alejandro Cabezas-Cruz
- Institut National de la Santé et de la Recherche Médicale U1019 – Centre National de la Recherche Scientifique UMR 8204, Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Université de LilleLille, France
| | - Julien Lancelot
- Institut National de la Santé et de la Recherche Médicale U1019 – Centre National de la Recherche Scientifique UMR 8204, Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Université de LilleLille, France
| | - Stéphanie Caby
- Institut National de la Santé et de la Recherche Médicale U1019 – Centre National de la Recherche Scientifique UMR 8204, Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Université de LilleLille, France
| | - Guilherme Oliveira
- Genomics and Computational Biology Group, Fundação Oswaldo Cruz, Center for Excellence in Bioinformatics, Centro de Pesquisas René Rachou, National Institute of Science and Technology in Tropical DiseasesBelo Horizonte, Brazil
| | - Raymond J. Pierce
- Institut National de la Santé et de la Recherche Médicale U1019 – Centre National de la Recherche Scientifique UMR 8204, Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Université de LilleLille, France
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66
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Roquis D, Lepesant JMJ, Villafan E, Boissier J, Vieira C, Cosseau C, Grunau C. Exposure to hycanthone alters chromatin structure around specific gene functions and specific repeats in Schistosoma mansoni. Front Genet 2014; 5:207. [PMID: 25076965 PMCID: PMC4099960 DOI: 10.3389/fgene.2014.00207] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 06/18/2014] [Indexed: 11/23/2022] Open
Abstract
Schistosoma mansoni is a parasitic plathyhelminth responsible for intestinal schistosomiasis (or bilharzia), a disease affecting 67 million people worldwide and causing an important economic burden. The schistosomicides hycanthone, and its later proxy oxamniquine, were widely used for treatments in endemic areas during the twentieth century. Recently, the mechanism of action, as well as the genetic origin of a stably and Mendelian inherited resistance for both drugs was elucidated in two strains. However, several observations suggested early on that alternative mechanisms might exist, by which resistance could be induced for these two drugs in sensitive lines of schistosomes. This induced resistance appeared rapidly, within the first generation, but was metastable (not stably inherited). Epigenetic inheritance could explain such a phenomenon and we therefore re-analyzed the historical data with our current knowledge of epigenetics. In addition, we performed new experiments such as ChIP-seq on hycanthone treated worms. We found distinct chromatin structure changes between sensitive worms and induced resistant worms from the same strain. No specific pathway was discovered, but genes in which chromatin structure modifications were observed are mostly associated with transport and catabolism, which makes sense in the context of the elimination of the drug. Specific differences were observed in the repetitive compartment of the genome. We finally describe what types of experiments are needed to understand the complexity of heritability that can be based on genetic and/or epigenetic mechanisms for drug resistance in schistosomes.
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Affiliation(s)
- David Roquis
- Département de Biologie, Université de Perpignan Via DomitiaPerpignan, France
- CNRS, UMR 5244, Écologie et Évolution des Interactions (2EI)Perpignan, France
| | - Julie M. J. Lepesant
- Département de Biologie, Université de Perpignan Via DomitiaPerpignan, France
- CNRS, UMR 5244, Écologie et Évolution des Interactions (2EI)Perpignan, France
| | - Emanuel Villafan
- CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Évolutive, Département de Biologie, Université Lyon 1Villeurbane, France
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C.Xalapa, México
| | - Jérôme Boissier
- Département de Biologie, Université de Perpignan Via DomitiaPerpignan, France
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C.Xalapa, México
| | - Cristina Vieira
- CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Évolutive, Département de Biologie, Université Lyon 1Villeurbane, France
- Département de Biologie, Institut Universitaire de FranceParis, France
| | - Céline Cosseau
- Département de Biologie, Université de Perpignan Via DomitiaPerpignan, France
- CNRS, UMR 5244, Écologie et Évolution des Interactions (2EI)Perpignan, France
| | - Christoph Grunau
- Département de Biologie, Université de Perpignan Via DomitiaPerpignan, France
- CNRS, UMR 5244, Écologie et Évolution des Interactions (2EI)Perpignan, France
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Yoshino TP, Brown M, Wu XJ, Jackson CJ, Ocadiz-Ruiz R, Chalmers IW, Kolb M, Hokke CH, Hoffmann KF. Excreted/secreted Schistosoma mansoni venom allergen-like 9 (SmVAL9) modulates host extracellular matrix remodelling gene expression. Int J Parasitol 2014; 44:551-63. [PMID: 24859313 PMCID: PMC4079936 DOI: 10.1016/j.ijpara.2014.04.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 04/15/2014] [Accepted: 04/16/2014] [Indexed: 12/31/2022]
Abstract
Schistosoma mansoni VAL9 (SmVAL9) is a secreted N-linked glycoprotein containing a unique, difucosyl modification. SmVAL9 is found throughout miracidia/sporocyst parenchymal cell inclusions/vesicles and germinal cells. SmVAL9 differentially regulates murine and snail matrix metalloproteinases.
The Schistosoma mansoni venom allergen-like (SmVAL) protein family consists of 29 members, each possessing a conserved α-β-α sandwich tertiary feature called the Sperm-coating protein/Tpx-1/Ag5/PR-1/Sc7 (SCP/TAPS) domain. While the SmVALs have been found in both excretory/secretory (E/S) products and in intra/sub-tegumental (non-E/S) fractions, the role(s) of this family in host/parasite relationships or schistosome developmental processes remains poorly resolved. In order to begin quantifying SmVAL functional diversity or redundancy, dissecting the specific activity (ies) of individual family members is necessary. Towards this end, we present the characterisation of SmVAL9; a protein previously found enriched in both miracidia/sporocyst larval transformation proteins and in egg secretions. While our study confirms that SmVAL9 is indeed found in soluble egg products and miracidia/sporocyst larval transformation proteins, we find it to be maximally transcribed/translated in miracidia and subsequently down-regulated during in vitro sporocyst development. SmVAL9 localisation within sporocysts appears concentrated in parenchymal cells/vesicles as well as associated with larval germinal cells. Furthermore, we demonstrate that egg-derived SmVAL9 carries an N-linked glycan containing a schistosome-specific difucosyl element and is an immunogenic target during chronic murine schistosomiasis. Finally, we demonstrate that recombinant SmVAL9 affects the expression of extracellular matrix, remodelling matrix metalloproteinase (MMP) and tissue inhibitors of metalloproteinase (TIMP) gene products in both Biomphalaria glabrata embryonic cell (BgMMP1) and Mus musculus bone marrow-derived macrophage (MmMMP2, MmMMP9, MmMMP12, MmMMP13, MmMMP14, MmMMP28, TIMP1 and TIMP2) in vitro cultures. These findings importantly suggest that excreted/secreted SmVAL9 participates in tissue reorganisation/extracellular matrix remodelling during intra-mammalian egg translocation, miracidia infection and intra-molluscan sporocyst development/migration.
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Affiliation(s)
- Timothy P Yoshino
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - Martha Brown
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Room 3.31, Edward Llwyd Building, Penglais Campus, Aberystwyth SY23 3DA, UK
| | - Xiao-Jun Wu
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - Colin J Jackson
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Room 3.31, Edward Llwyd Building, Penglais Campus, Aberystwyth SY23 3DA, UK
| | - Ramon Ocadiz-Ruiz
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - Iain W Chalmers
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Room 3.31, Edward Llwyd Building, Penglais Campus, Aberystwyth SY23 3DA, UK
| | - Marlen Kolb
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Room 3.31, Edward Llwyd Building, Penglais Campus, Aberystwyth SY23 3DA, UK
| | - Cornelis H Hokke
- Department of Parasitology, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Karl F Hoffmann
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Room 3.31, Edward Llwyd Building, Penglais Campus, Aberystwyth SY23 3DA, UK.
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Epigenetics in an ecotoxicological context. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2014; 764-765:36-45. [DOI: 10.1016/j.mrgentox.2013.08.008] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 08/22/2013] [Indexed: 11/23/2022]
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Capuano F, Mülleder M, Kok R, Blom HJ, Ralser M. Cytosine DNA methylation is found in Drosophila melanogaster but absent in Saccharomyces cerevisiae, Schizosaccharomyces pombe, and other yeast species. Anal Chem 2014; 86:3697-702. [PMID: 24640988 PMCID: PMC4006885 DOI: 10.1021/ac500447w] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
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The methylation of cytosine to 5-methylcytosine
(5-meC) is an important
epigenetic DNA modification in many bacteria, plants, and mammals,
but its relevance for important model organisms, including Caenorhabditis elegans and Drosophila
melanogaster, is still equivocal. By reporting the
presence of 5-meC in a broad variety of wild, laboratory, and industrial
yeasts, a recent study also challenged the dogma about the absence
of DNA methylation in yeast species. We would like to bring to attention
that the protocol used for gas chromatography/mass spectrometry involved
hydrolysis of the DNA preparations. As this process separates cytosine
and 5-meC from the sugar phosphate backbone, this method is unable
to distinguish DNA- from RNA-derived 5-meC. We employed an alternative
LC–MS/MS protocol where by targeting 5-methyldeoxycytidine
moieties after enzymatic digestion, only 5-meC specifically derived
from DNA is quantified. This technique unambiguously identified cytosine
DNA methylation in Arabidopsis thaliana (14.0% of cytosines methylated), Mus musculus (7.6%), and Escherichia coli (2.3%).
Despite achieving a detection limit at 250 attomoles (corresponding
to <0.00002 methylated cytosines per nonmethylated cytosine), we
could not confirm any cytosine DNA methylation in laboratory and industrial
strains of Saccharomyces cerevisiae, Schizosaccharomyces pombe, Saccharomyces boulardii, Saccharomyces
paradoxus, or Pichia pastoris. The protocol however unequivocally confirmed DNA methylation in
adult Drosophila melanogaster at a
value (0.034%) that is up to 2 orders of magnitude below the detection
limit of bisulphite sequencing. Thus, 5-meC is a rare DNA modification
in drosophila but absent in yeast.
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Affiliation(s)
- Floriana Capuano
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge , 80 Tennis Court Road, Cambridge CB2 1GA, U.K
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microRNAs of parasitic helminths - Identification, characterization and potential as drug targets. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2014; 4:85-94. [PMID: 25057458 PMCID: PMC4095049 DOI: 10.1016/j.ijpddr.2014.03.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Revised: 03/10/2014] [Accepted: 03/11/2014] [Indexed: 01/14/2023]
Abstract
Importance of microRNAs in helminth post-transcriptional gene regulation is reviewed. Increasing helminth miRNA data are available from deep sequencing. Some miRNAs are helminth-specific, many are novel to each species. miRNAs may regulate parasite and host gene expression. Uptake of miRNA inhibitors and mimics is feasible for functional analysis.
microRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional gene regulation. They were first identified in the free-living nematode Caenorhabditis elegans, where the miRNAs lin-4 and let-7 were shown to be essential for regulating correct developmental progression. The sequence of let-7 was subsequently found to be conserved in higher organisms and changes in expression of let-7, as well as other miRNAs, are associated with certain cancers, indicating important regulatory roles. Some miRNAs have been shown to have essential functions, but the roles of many are currently unknown. With the increasing availability of genome sequence data, miRNAs have now been identified from a number of parasitic helminths, by deep sequencing of small RNA libraries and bioinformatic approaches. While some miRNAs are widely conserved in a range of organisms, others are helminth-specific and many are novel to each species. Here we review the potential roles of miRNAs in regulating helminth development, in interacting with the host environment and in development of drug resistance. Use of fluorescently-labeled small RNAs demonstrates uptake by parasites, at least in vitro. Therefore delivery of miRNA inhibitors or mimics has potential to alter miRNA activity, providing a useful tool for probing the roles of miRNAs and suggesting novel routes to therapeutics for parasite control.
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Phenotypic plasticity of male Schistosoma mansoni from the peritoneal cavity and hepatic portal system of laboratory mice and hamsters. J Helminthol 2014; 89:294-301. [PMID: 24572281 DOI: 10.1017/s0022149x14000066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Morphometric analysis of Schistosoma mansoni male worms obtained from AKR/J and Swiss mice was carried out. Rodents infected by the intraperitoneal route with 80 cercariae of the schistosome (LE strain) were killed by cervical dislocation at 45 and 60 days post-infection and both peritoneal lavage and perfusion of the portal system were performed for the recovery of adult worms. Characteristics including total body length, the distance between oral and ventral suckers, extension of testicular mass and the number of testes were considered in the morphological analysis. Changes that occurred in S. mansoni recovered from the peritoneal cavity or from the portal system of AKR/J and Swiss mice included total body length and reproductive characteristics. Significant morphometric alterations were also observed when worms recovered from the portal system of both strains of mice were compared with the schistosomes obtained from hamsters (Mesocricetus auratus), the vertebrate host in which the LE strain had been adapted and maintained by successive passages for more than four decades. The present results reinforce the idea that S. mansoni has high plastic potential and adaptive capacity.
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Gao F, Wang R, Liu M. Trichinella spiralis, potential model nematode for epigenetics and its implication in metazoan parasitism. Front Physiol 2014; 4:410. [PMID: 24454291 PMCID: PMC3887316 DOI: 10.3389/fphys.2013.00410] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 12/26/2013] [Indexed: 01/02/2023] Open
Abstract
The recent discovery of DNA methylation in the nematode T.spiralis may raise the possibility of using it as a potential model organism for epigenetic studies instead of C. elegans, which is deficient in this important epigenetic modification. In contrast to the free-living nematode C. elegans, T. spiralis is a parasitic worm that possesses a complicated life cycle and undergoes a complex developmental regulation of genes. We emphasize that the differential methylomes in the different life-history stages of T. spiralis can provide insight on how DNA methylation is triggered and regulated. In particular, we have demonstrated that DNA methylation is involved in the regulation of its parasitism-related genes. Further computational analyses indicated that the regulatory machinery for DNA methylation can also be found in the T. spiralis genome. By a logical extension of this point, we speculate that comprehensively addressing the epigenetic machinery of T. spiralis may help to understand epigenetics in invertebrates. Furthermore, considering the implication of epigenetics in metazoan parasitism, using T. spiralis as an epigenetic model organism may further contribute to drug development against metazoan parasites.
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Affiliation(s)
- Fei Gao
- Science and Technology Department, BGI-Shenzhen, Beishan Industrial Zone Shenzhen, China
| | - Rui Wang
- Science and Technology Department, BGI-Shenzhen, Beishan Industrial Zone Shenzhen, China
| | - Mingyuan Liu
- Key Lab for Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University Changchun, China ; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses Yangzhou, China
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Jaber-Hijazi F, Lo PJKP, Mihaylova Y, Foster JM, Benner JS, Tejada Romero B, Chen C, Malla S, Solana J, Ruzov A, Aziz Aboobaker A. Planarian MBD2/3 is required for adult stem cell pluripotency independently of DNA methylation. Dev Biol 2013; 384:141-53. [PMID: 24063805 PMCID: PMC3824064 DOI: 10.1016/j.ydbio.2013.09.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 09/09/2013] [Accepted: 09/16/2013] [Indexed: 12/12/2022]
Abstract
Planarian adult stem cells (pASCs) or neoblasts represent an ideal system to study the evolution of stem cells and pluripotency as they underpin an unrivaled capacity for regeneration. We wish to understand the control of differentiation and pluripotency in pASCs and to understand how conserved, convergent or divergent these mechanisms are across the Bilateria. Here we show the planarian methyl-CpG Binding Domain 2/3 (mbd2/3) gene is required for pASC differentiation during regeneration and tissue homeostasis. The genome does not have detectable levels of 5-methylcytosine (5mC) and we find no role for a potential DNA methylase. We conclude that MBD proteins may have had an ancient role in broadly controlling animal stem cell pluripotency, but that DNA methylation is not involved in planarian stem cell differentiation. A single ancestral MBD2/3 protein is present in the planarian Schmidtea mediterranea. The genome of S. mediterranea does not have pervasive cytosine methylation. MBD2/3 is required for pluripotent stem cell differentiation down multiple but not all cell lineages. MBD2/3 may have had an ancestral role in regulating stem cell pluripotency.
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Affiliation(s)
- Farah Jaber-Hijazi
- Department of Zoology, Tinbergen Building, South Parks Road, University of Oxford, Oxford OX1 3PS, United Kingdom
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The genome of the hydatid tapeworm Echinococcus granulosus. Nat Genet 2013; 45:1168-75. [PMID: 24013640 DOI: 10.1038/ng.2757] [Citation(s) in RCA: 216] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 08/14/2013] [Indexed: 12/12/2022]
Abstract
Cystic echinococcosis (hydatid disease), caused by the tapeworm E. granulosus, is responsible for considerable human morbidity and mortality. This cosmopolitan disease is difficult to diagnose, treat and control. We present a draft genomic sequence for the worm comprising 151.6 Mb encoding 11,325 genes. Comparisons with the genome sequences from other taxa show that E. granulosus has acquired a spectrum of genes, including the EgAgB family, whose products are secreted by the parasite to interact and redirect host immune responses. We also find that genes in bile salt pathways may control the bidirectional development of E. granulosus, and sequence differences in the calcium channel subunit EgCavβ1 may be associated with praziquantel sensitivity. Our study offers insights into host interaction, nutrient acquisition, strobilization, reproduction, immune evasion and maturation in the parasite and provides a platform to facilitate the development of new, effective treatments and interventions for echinococcosis control.
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Perrin C, Lepesant JMJ, Roger E, Duval D, Fneich S, Thuillier V, Alliene JF, Mitta G, Grunau C, Cosseau C. Schistosoma mansoni mucin gene (SmPoMuc) expression: epigenetic control to shape adaptation to a new host. PLoS Pathog 2013; 9:e1003571. [PMID: 24009504 PMCID: PMC3757033 DOI: 10.1371/journal.ppat.1003571] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 06/27/2013] [Indexed: 11/28/2022] Open
Abstract
The digenetic trematode Schistosoma mansoni is a human parasite that uses the mollusc Biomphalaria glabrata as intermediate host. Specific S. mansoni strains can infect efficiently only certain B. glabrata strains (compatible strain) while others are incompatible. Strain-specific differences in transcription of a conserved family of polymorphic mucins (SmPoMucs) in S. mansoni are the principle determinants for this compatibility. In the present study, we investigated the bases of the control of SmPoMuc expression that evolved to evade B. glabrata diversified antigen recognition molecules. We compared the DNA sequences and chromatin structure of SmPoMuc promoters of two S. mansoni strains that are either compatible (C) or incompatible (IC) with a reference snail host. We reveal that although sequence differences are observed between active promoter regions of SmPoMuc genes, the sequences of the promoters are not diverse and are conserved between IC and C strains, suggesting that genetics alone cannot explain the evolution of compatibility polymorphism. In contrast, promoters carry epigenetic marks that are significantly different between the C and IC strains. Moreover, we show that modifications of the structure of the chromatin of the parasite modify transcription of SmPoMuc in the IC strain compared to the C strain and correlate with the presence of additional combinations of SmPoMuc transcripts only observed in the IC phenotype. Our results indicate that transcription polymorphism of a gene family that is responsible for an important adaptive trait of the parasite is epigenetically encoded. These strain-specific epigenetic marks are heritable, but can change while the underlying genetic information remains stable. This suggests that epigenetic changes may be important for the early steps in the adaptation of pathogens to new hosts, and might be an initial step in adaptive evolution in general. Schistosoma mansoni is a parasitic worm and agent of a disease that causes a considerable economic burden in African and South American countries. The propagation of the parasite requires passage through a freshwater snail of Biomphalaria genus. In the field, actually very few snails are infected. This is due to the fact that specific strains of the parasite can infect only specific strains of the snail. Comparative studies have shown that this so-called compatibility is based on the expression of a family of genes that are called SmPoMucs. We have shown previously that all parasites strains possess the repertoire of all SmPoMuc genes but every strain and even every individual parasite expresses only a subset. These differences could be due to DNA sequence differences in the regions that control gene expression, but here we show that these regions are nearly identical. Instead, the chromatin structure shows strain-specific characteristics. This means that the parasite can adapt to different snail strains simply by changing its chromatin structure and not necessarily the DNA sequence. If this holds true for other parasites, then we have to rethink the way parasite evolution is currently imagined but this also provides a new potential entry point to control the spread of diseases.
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Affiliation(s)
- Cecile Perrin
- Université de Perpignan Via Domitia, Perpignan, France
- CNRS, UMR 5244, Ecologie et Evolution des Interactions (2EI), Perpignan, France
| | - Julie M. J. Lepesant
- Université de Perpignan Via Domitia, Perpignan, France
- CNRS, UMR 5244, Ecologie et Evolution des Interactions (2EI), Perpignan, France
| | - Emmanuel Roger
- Center for Infection and Immunity of Lille, Inserm U1019, CNRS UMR 8204, Institut Pasteur de Lille, University Lille Nord de France, Lille, France
| | - David Duval
- Université de Perpignan Via Domitia, Perpignan, France
- CNRS, UMR 5244, Ecologie et Evolution des Interactions (2EI), Perpignan, France
| | - Sara Fneich
- Université de Perpignan Via Domitia, Perpignan, France
- CNRS, UMR 5244, Ecologie et Evolution des Interactions (2EI), Perpignan, France
| | - Virginie Thuillier
- Université de Perpignan Via Domitia, Perpignan, France
- CNRS, UMR 5244, Ecologie et Evolution des Interactions (2EI), Perpignan, France
| | - Jean-Francois Alliene
- Université de Perpignan Via Domitia, Perpignan, France
- CNRS, UMR 5244, Ecologie et Evolution des Interactions (2EI), Perpignan, France
| | - Guillaume Mitta
- Université de Perpignan Via Domitia, Perpignan, France
- CNRS, UMR 5244, Ecologie et Evolution des Interactions (2EI), Perpignan, France
| | - Christoph Grunau
- Université de Perpignan Via Domitia, Perpignan, France
- CNRS, UMR 5244, Ecologie et Evolution des Interactions (2EI), Perpignan, France
| | - Celine Cosseau
- Université de Perpignan Via Domitia, Perpignan, France
- CNRS, UMR 5244, Ecologie et Evolution des Interactions (2EI), Perpignan, France
- * E-mail:
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Cytosine methylation is a conserved epigenetic feature found throughout the phylum Platyhelminthes. BMC Genomics 2013; 14:462. [PMID: 23837670 PMCID: PMC3710501 DOI: 10.1186/1471-2164-14-462] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 07/03/2013] [Indexed: 12/22/2022] Open
Abstract
Background The phylum Platyhelminthes (flatworms) contains an important group of bilaterian organisms responsible for many debilitating and chronic infectious diseases of human and animal populations inhabiting the planet today. In addition to their biomedical and veterinary relevance, some platyhelminths are also frequently used models for understanding tissue regeneration and stem cell biology. Therefore, the molecular (genetic and epigenetic) characteristics that underlie trophic specialism, pathogenicity or developmental maturation are likely to be pivotal in our continued studies of this important metazoan group. Indeed, in contrast to earlier studies that failed to detect evidence of cytosine or adenine methylation in parasitic flatworm taxa, our laboratory has recently defined a critical role for cytosine methylation in Schistosoma mansoni oviposition, egg maturation and ovarian development. Thus, in order to identify whether this epigenetic modification features in other platyhelminth species or is a novelty of S. mansoni, we conducted a study simultaneously surveying for DNA methylation machinery components and DNA methylation marks throughout the phylum using both parasitic and non-parasitic representatives. Results Firstly, using both S. mansoni DNA methyltransferase 2 (SmDNMT2) and methyl-CpG binding domain protein (SmMBD) as query sequences, we illustrate that essential DNA methylation machinery components are well conserved throughout the phylum. Secondly, using both molecular (methylation specific amplification polymorphism, MSAP) and immunological (enzyme-linked immunoabsorbent assay, ELISA) methodologies, we demonstrate that representative species (Echinococcus multilocularis, Protopolystoma xenopodis, Schistosoma haematobium, Schistosoma japonicum, Fasciola hepatica and Polycelis nigra) within all four platyhelminth classes (Cestoda, Monogenea, Trematoda and ‘Turbellaria’) contain methylated cytosines within their genome compartments. Conclusions Collectively, these findings provide the first direct evidence for a functionally conserved and enzymatically active DNA methylation system throughout the Platyhelminthes. Defining how this epigenetic feature shapes phenotypic diversity and development within the phylum represents an exciting new area of metazoan biology.
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Fneich S, Dheilly N, Adema C, Rognon A, Reichelt M, Bulla J, Grunau C, Cosseau C. 5-methyl-cytosine and 5-hydroxy-methyl-cytosine in the genome of Biomphalaria glabrata, a snail intermediate host of Schistosoma mansoni. Parasit Vectors 2013; 6:167. [PMID: 23742053 PMCID: PMC3681652 DOI: 10.1186/1756-3305-6-167] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 05/27/2013] [Indexed: 11/29/2022] Open
Abstract
Background Biomphalaria glabrata is the mollusc intermediate host for Schistosoma mansoni, a digenean flatworm parasite that causes human intestinal schistosomiasis. An estimated 200 million people in 74 countries suffer from schistosomiasis, in terms of morbidity this is the most severe tropical disease after malaria. Epigenetic information informs on the status of gene activity that is heritable, for which changes are reversible and that is not based on the DNA sequence. Epigenetic mechanisms generate variability that provides a source for potentially heritable phenotypic variation and therefore could be involved in the adaptation to environmental constraint. Phenotypic variations are particularly important in host-parasite interactions in which both selective pressure and rate of evolution are high. In this context, epigenetic changes are expected to be major drivers of phenotypic plasticity and co-adaptation between host and parasite. Consequently, with characterization of the genomes of invertebrates that are parasite vectors or intermediate hosts, it is also essential to understand how the epigenetic machinery functions to better decipher the interplay between host and parasite. Methods The CpGo/e ratios were used as a proxy to investigate the occurrence of CpG methylation in B. glabrata coding regions. The presence of DNA methylation in B. glabrata was also confirmed by several experimental approaches: restriction enzymatic digestion with isoschizomers, bisulfite conversion based techniques and LC-MS/MS analysis. Results In this work, we report that DNA methylation, which is one of the carriers of epigenetic information, occurs in B. glabrata; approximately 2% of cytosine nucleotides are methylated. We describe the methylation machinery of B. glabrata. Methylation occurs predominantly at CpG sites, present at high ratios in coding regions of genes associated with housekeeping functions. We also demonstrate by bisulfite treatment that methylation occurs in multiple copies of Nimbus, a transposable element. Conclusions This study details DNA methylation for the first time, one of the carriers of epigenetic information in B. glabrata. The general characteristics of DNA methylation that we observed in the B. glabrata genome conform to what epigenetic studies have reported from other invertebrate species.
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Affiliation(s)
- Sara Fneich
- Université de Perpignan Via Domitia, Perpignan, France
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Abstract
Several organisms have retained methyltransferase 2 (Dnmt2) as their only candidate DNA methyltransferase gene. However, information about Dnmt2-dependent methylation patterns has been limited to a few isolated loci and the results have been discussed controversially. In addition, recent studies have shown that Dnmt2 functions as a tRNA methyltransferase, which raised the possibility that Dnmt2-only genomes might be unmethylated. We have now used whole-genome bisulfite sequencing to analyze the methylomes of Dnmt2-only organisms at single-base resolution. Our results show that the genomes of Schistosoma mansoni and Drosophila melanogaster lack detectable DNA methylation patterns. Residual unconverted cytosine residues shared many attributes with bisulfite deamination artifacts and were observed at comparable levels in Dnmt2-deficient flies. Furthermore, genetically modified Dnmt2-only mouse embryonic stem cells lost the DNA methylation patterns found in wild-type cells. Our results thus uncover fundamental differences among animal methylomes and suggest that DNA methylation is dispensable for a considerable number of eukaryotic organisms.
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Gómez-Díaz E, Jordà M, Peinado MA, Rivero A. Epigenetics of host-pathogen interactions: the road ahead and the road behind. PLoS Pathog 2012; 8:e1003007. [PMID: 23209403 PMCID: PMC3510240 DOI: 10.1371/journal.ppat.1003007] [Citation(s) in RCA: 169] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
A growing body of evidence points towards epigenetic mechanisms being responsible for a wide range of biological phenomena, from the plasticity of plant growth and development to the nutritional control of caste determination in honeybees and the etiology of human disease (e.g., cancer). With the (partial) elucidation of the molecular basis of epigenetic variation and the heritability of certain of these changes, the field of evolutionary epigenetics is flourishing. Despite this, the role of epigenetics in shaping host-pathogen interactions has received comparatively little attention. Yet there is plenty of evidence supporting the implication of epigenetic mechanisms in the modulation of the biological interaction between hosts and pathogens. The phenotypic plasticity of many key parasite life-history traits appears to be under epigenetic control. Moreover, pathogen-induced effects in host phenotype may have transgenerational consequences, and the bases of these changes and their heritability probably have an epigenetic component. The significance of epigenetic modifications may, however, go beyond providing a mechanistic basis for host and pathogen plasticity. Epigenetic epidemiology has recently emerged as a promising area for future research on infectious diseases. In addition, the incorporation of epigenetic inheritance and epigenetic plasticity mechanisms to evolutionary models and empirical studies of host-pathogen interactions will provide new insights into the evolution and coevolution of these associations. Here, we review the evidence available for the role epigenetics on host-pathogen interactions, and the utility and versatility of the epigenetic technologies available that can be cross-applied to host-pathogen studies. We conclude with recommendations and directions for future research on the burgeoning field of epigenetics as applied to host-pathogen interactions.
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Affiliation(s)
- Elena Gómez-Díaz
- Institut de Biologia Evolutiva (IBE, CSIC-UPF), Barcelona, Spain
| | - Mireia Jordà
- Institut de Medicina Predictiva i Personalitzada del Càncer (IMPPC), Badalona, Spain
| | - Miguel Angel Peinado
- Institut de Medicina Predictiva i Personalitzada del Càncer (IMPPC), Badalona, Spain
| | - Ana Rivero
- Maladies Infectieuses et Vecteurs: Écologie, Génétique, Évolution et Contrôle (MIVEGEC, UMR CNRS-UM2-UM1 5290, IRD 224), Centre IRD, Montpellier, France
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Rinaldi G, Eckert SE, Tsai IJ, Suttiprapa S, Kines KJ, Tort JF, Mann VH, Turner DJ, Berriman M, Brindley PJ. Germline transgenesis and insertional mutagenesis in Schistosoma mansoni mediated by murine leukemia virus. PLoS Pathog 2012; 8:e1002820. [PMID: 22911241 PMCID: PMC3406096 DOI: 10.1371/journal.ppat.1002820] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2012] [Accepted: 06/11/2012] [Indexed: 12/11/2022] Open
Abstract
Functional studies will facilitate characterization of role and essentiality of newly available genome sequences of the human schistosomes, Schistosoma mansoni, S. japonicum and S. haematobium. To develop transgenesis as a functional approach for these pathogens, we previously demonstrated that pseudotyped murine leukemia virus (MLV) can transduce schistosomes leading to chromosomal integration of reporter transgenes and short hairpin RNA cassettes. Here we investigated vertical transmission of transgenes through the developmental cycle of S. mansoni after introducing transgenes into eggs. Although MLV infection of schistosome eggs from mouse livers was efficient in terms of snail infectivity, >10-fold higher transgene copy numbers were detected in cercariae derived from in vitro laid eggs (IVLE). After infecting snails with miracidia from eggs transduced by MLV, sequencing of genomic DNA from cercariae released from the snails also revealed the presence of transgenes, demonstrating that transgenes had been transmitted through the asexual developmental cycle, and thereby confirming germline transgenesis. High-throughput sequencing of genomic DNA from schistosome populations exposed to MLV mapped widespread and random insertion of transgenes throughout the genome, along each of the autosomes and sex chromosomes, validating the utility of this approach for insertional mutagenesis. In addition, the germline-transmitted transgene encoding neomycin phosphotransferase rescued cultured schistosomules from toxicity of the antibiotic G418, and PCR analysis of eggs resulting from sexual reproduction of the transgenic worms in mice confirmed that retroviral transgenes were transmitted to the next (F1) generation. These findings provide the first description of wide-scale, random insertional mutagenesis of chromosomes and of germline transmission of a transgene in schistosomes. Transgenic lines of schistosomes expressing antibiotic resistance could advance functional genomics for these significant human pathogens. DATABASE ACCESSION: Sequence data from this study have been submitted to the European Nucleotide Archive (http://www.ebi.ac.uk/embl) under accession number ERP000379.
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Affiliation(s)
- Gabriel Rinaldi
- Department of Microbiology, Immunology & Tropical Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, DC, United States of America
- Departamento de Genética, Facultad de Medicina, Universidad de la República, (UDELAR), Montevideo, Uruguay
| | - Sabine E. Eckert
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Oxford Nanopore Technologies, Oxford, United Kingdom
| | - Isheng J. Tsai
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Sutas Suttiprapa
- Department of Microbiology, Immunology & Tropical Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, DC, United States of America
- Department of Pathobiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Kristine J. Kines
- Department of Microbiology, Immunology & Tropical Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, DC, United States of America
- Tulane Cancer Center, Tulane University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - José F. Tort
- Departamento de Genética, Facultad de Medicina, Universidad de la República, (UDELAR), Montevideo, Uruguay
| | - Victoria H. Mann
- Department of Microbiology, Immunology & Tropical Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, DC, United States of America
| | - Daniel J. Turner
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Oxford Nanopore Technologies, Oxford, United Kingdom
| | - Matthew Berriman
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Paul J. Brindley
- Department of Microbiology, Immunology & Tropical Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, DC, United States of America
- Research Center for Neglected Diseases of Poverty, The George Washington University, Washington, DC, United States of America
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Mourão MM, Grunau C, LoVerde PT, Jones MK, Oliveira G. Recent advances in Schistosoma genomics. Parasite Immunol 2012; 34:151-62. [PMID: 22145587 DOI: 10.1111/j.1365-3024.2011.01349.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Schistosome research has entered the genomic era with the publications reporting the Schistosoma mansoni and Schistosoma japonicum genomes. Schistosome genomics is motivated by the need for new control tools. However, much can also be learned about the biology of Schistosoma, which is a tractable experimental model. In this article, we review the recent achievements in the field of schistosome research and discuss future perspectives on genomics and how it can be integrated in a usable format, on the genetic mapping and how it has improved the genome assembly and provided new research approaches, on how epigenetics provides interesting insights into the biology of the species and on new functional genomics tools that will contribute to the understanding of the function of genes, many of which are parasite- or taxon specific.
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Affiliation(s)
- M M Mourão
- Genomics and Computational Biology Group, Instituto Nacional de Ciência e Tecnologia em Doenças Tropicais, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz - FIOCRUZ, Belo Horizonte, MG, Brazil
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Duffy MF, Selvarajah SA, Josling GA, Petter M. The role of chromatin in Plasmodium gene expression. Cell Microbiol 2012; 14:819-28. [DOI: 10.1111/j.1462-5822.2012.01777.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Geyer KK, Hoffmann KF. Epigenetics: a key regulator of platyhelminth developmental biology? Int J Parasitol 2012; 42:221-4. [PMID: 22366548 DOI: 10.1016/j.ijpara.2012.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 02/07/2012] [Accepted: 02/09/2012] [Indexed: 11/18/2022]
Abstract
The Platyhelminthes (flukes/flatworms) are a large group of derived metazoans beautifully adapted for existence in diversely challenging ecosystems. As tractable examples of development and self-regeneration or as causative agents of aquacultural, veterinary and biomedically-relevant parasitic diseases, the platyhelminths are subject to intensive inter-disciplinary research. Given the complex lifestyles exhibited by individuals within this phylum, we postulate that epigenetic processes feature in many aspects of platyhelminth lifecycle diversity, development and environmentally-driven adaptations.
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Affiliation(s)
- Kathrin K Geyer
- Institute of Biological, Environmental and Rural Sciences (IBERS), Edward Llwyd Building, Aberystwyth University, Aberystwyth, UK
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84
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Whole-genome sequence of Schistosoma haematobium. Nat Genet 2012; 44:221-5. [PMID: 22246508 DOI: 10.1038/ng.1065] [Citation(s) in RCA: 332] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 12/07/2011] [Indexed: 12/14/2022]
Abstract
Schistosomiasis is a neglected tropical disease caused by blood flukes (genus Schistosoma; schistosomes) and affecting 200 million people worldwide. No vaccines are available, and treatment relies on one drug, praziquantel. Schistosoma haematobium has come into the spotlight as a major cause of urogenital disease, as an agent linked to bladder cancer and as a predisposing factor for HIV/AIDS. The parasite is transmitted to humans from freshwater snails. Worms dwell in blood vessels and release eggs that become embedded in the bladder wall to elicit chronic immune-mediated disease and induce squamous cell carcinoma. Here we sequenced the 385-Mb genome of S. haematobium using Illumina-based technology at 74-fold coverage and compared it to sequences from related parasites. We included genome annotation based on function, gene ontology, networking and pathway mapping. This genome now provides an unprecedented resource for many fundamental research areas and shows great promise for the design of new disease interventions.
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Abstract
SUMMARYAlmost a decade has passed since the first report of RNA interference (RNAi) in a parasitic helminth. Whilst much progress has been made with RNAi informing gene function studies in disparate nematode and flatworm parasites, substantial and seemingly prohibitive difficulties have been encountered in some species, hindering progress. An appraisal of current practices, trends and ideals of RNAi experimental design in parasitic helminths is both timely and necessary for a number of reasons: firstly, the increasing availability of parasitic helminth genome/transcriptome resources means there is a growing need for gene function tools such as RNAi; secondly, fundamental differences and unique challenges exist for parasite species which do not apply to model organisms; thirdly, the inherent variation in experimental design, and reported difficulties with reproducibility undermine confidence. Ideally, RNAi studies of gene function should adopt standardised experimental design to aid reproducibility, interpretation and comparative analyses. Although the huge variations in parasite biology and experimental endpoints make RNAi experimental design standardization difficult or impractical, we must strive to validate RNAi experimentation in helminth parasites. To aid this process we identify multiple approaches to RNAi experimental validation and highlight those which we deem to be critical for gene function studies in helminth parasites.
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Roberts SB, Gavery MR. Is There a Relationship between DNA Methylation and Phenotypic Plasticity in Invertebrates? Front Physiol 2012; 2:116. [PMID: 22232607 PMCID: PMC3249382 DOI: 10.3389/fphys.2011.00116] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 12/14/2011] [Indexed: 11/13/2022] Open
Abstract
There is a significant amount of variation in DNA methylation characteristics across organisms. Likewise, the biological role of DNA methylation varies across taxonomic lineages. The complexity of DNA methylation patterns in invertebrates has only recently begun to be characterized in-depth. In some invertebrate species that have been examined to date, methylated DNA is found primarily within coding regions and patterning is closely associated with gene function. Here we provide a perspective on the potential role of DNA methylation in these invertebrates with a focus on how limited methylation may contribute to increased phenotypic plasticity in highly fluctuating environments. Specifically, limited methylation could facilitate a variety of transcriptional opportunities including access to alternative transcription start sites, increasing sequence mutations, exon skipping, and transient methylation.
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Affiliation(s)
- Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
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Swain MT, Larkin DM, Caffrey CR, Davies SJ, Loukas A, Skelly PJ, Hoffmann KF. Schistosoma comparative genomics: integrating genome structure, parasite biology and anthelmintic discovery. Trends Parasitol 2011; 27:555-64. [PMID: 22024648 PMCID: PMC3223292 DOI: 10.1016/j.pt.2011.09.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 09/09/2011] [Accepted: 09/20/2011] [Indexed: 12/11/2022]
Abstract
Schistosoma genomes provide a comprehensive resource for identifying the molecular processes that shape parasite evolution and for discovering novel chemotherapeutic or immunoprophylactic targets. Here, we demonstrate how intragenus and intergenus comparative genomics can be used to drive these investigations forward, illustrate the advantages and limitations of these approaches and review how post-genomic technologies offer complementary strategies for genome characterisation. Although sequencing and functional characterisation of other schistosome/platyhelminth genomes continues to expedite anthelmintic discovery, we contend that future priorities should equally focus on improving assembly quality, and chromosomal assignment, of existing schistosome/platyhelminth genomes.
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Affiliation(s)
- Martin T Swain
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
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