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Ishihara A, Sapon MA, Yamauchi K. Seasonal acclimatization and thermal acclimation induce global histone epigenetic changes in liver of bullfrog (Lithobates catesbeianus) tadpole. Comp Biochem Physiol A Mol Integr Physiol 2019; 230:39-48. [DOI: 10.1016/j.cbpa.2018.12.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 12/19/2018] [Accepted: 12/19/2018] [Indexed: 01/08/2023]
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Abstract
Marine organisms' persistence hinges on the capacity for acclimatization and adaptation to the myriad of interacting environmental stressors associated with global climate change. In this context, epigenetics-mechanisms that facilitate phenotypic variation through genotype-environment interactions-are of great interest ecologically and evolutionarily. Our comprehensive review of marine environmental epigenetics guides our recommendations of four key areas for future research: the dynamics of wash-in and wash-out of epigenetic effects, the mechanistic understanding of the interplay of different epigenetic marks and the interaction with the microbiome, the capacity for and mechanisms of transgenerational epigenetic inheritance, and the evolutionary implications of the interaction of genetic and epigenetic features. Emerging insights in marine environmental epigenetics can be applied to critical issues such as aquaculture, biomonitoring, and biological invasions, thereby improving our ability to explain and predict the responses of marine taxa to global climate change.
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Affiliation(s)
- Jose M Eirin-Lopez
- Environmental Epigenetics Laboratory, Center for Coastal Oceans Research, Institute for Water and Environment, Florida International University, North Miami, Florida 33181, USA;
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island 02881, USA;
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3
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Beal A, Rodriguez-Casariego J, Rivera-Casas C, Suarez-Ulloa V, Eirin-Lopez JM. Environmental Epigenomics and Its Applications in Marine Organisms. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/13836_2018_28] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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4
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Rivera-Casas C, Gonzalez-Romero R, Garduño RA, Cheema MS, Ausio J, Eirin-Lopez JM. Molecular and Biochemical Methods Useful for the Epigenetic Characterization of Chromatin-Associated Proteins in Bivalve Molluscs. Front Physiol 2017; 8:490. [PMID: 28848447 PMCID: PMC5550673 DOI: 10.3389/fphys.2017.00490] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/26/2017] [Indexed: 12/11/2022] Open
Abstract
Bivalve molluscs constitute a ubiquitous taxonomic group playing key functions in virtually all ecosystems, and encompassing critical commercial relevance. Along with a sessile and filter-feeding lifestyle in most cases, these characteristics make bivalves model sentinel organisms routinely used for environmental monitoring studies in aquatic habitats. The study of epigenetic mechanisms linking environmental exposure and specific physiological responses (i.e., environmental epigenetics) stands out as a very innovative monitoring strategy, given the role of epigenetic modifications in acclimatization and adaptation. Furthermore, the heritable nature of many of those modifications constitutes a very promising avenue to explore the applicability of epigenetic conditioning and selection in management and restoration strategies. Chromatin provides a framework for the study of environmental epigenetic responses. Unfortunately, chromatin and epigenetic information are very limited in most non-traditional model organisms and even completely lacking in most environmentally and ecologically relevant organisms. The present work aims to provide a comprehensive and reproducible experimental workflow for the study of bivalve chromatin. First, a series of guidelines for the molecular isolation of genes encoding chromatin-associated proteins is provided, including information on primers suitable for conventional PCR, Rapid Amplification of cDNA Ends (RACE), genome walking and quantitative PCR (qPCR) experiments. This section is followed by the description of methods specifically developed for the analysis of histone and SNBP proteins in different bivalve tissues, including protein extraction, purification, separation and immunodetection. Lastly, information about available antibodies, their specificity and performance is also provided. The tools and protocols described here complement current epigenetic analyses (usually limited to DNA methylation) by incorporating the study of structural elements modulating chromatin dynamics.
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Affiliation(s)
- Ciro Rivera-Casas
- Environmental Epigenetics Group, Department of Biological Sciences, Florida International UniversityNorth Miami, FL, United States
| | - Rodrigo Gonzalez-Romero
- Environmental Epigenetics Group, Department of Biological Sciences, Florida International UniversityNorth Miami, FL, United States
| | - Rafael A Garduño
- Department of Microbiology and Immunology, Dalhousie UniversityHalifax, NS, Canada
| | - Manjinder S Cheema
- Department of Biochemistry and Microbiology, University of VictoriaVictoria, BC, Canada
| | - Juan Ausio
- Department of Biochemistry and Microbiology, University of VictoriaVictoria, BC, Canada
| | - Jose M Eirin-Lopez
- Environmental Epigenetics Group, Department of Biological Sciences, Florida International UniversityNorth Miami, FL, United States
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Nardocci G, Simonet NG, Navarro C, Längst G, Alvarez M. Differential enrichment of TTF-I and Tip5 in the T-like promoter structures of the rDNA contribute to the epigenetic response of Cyprinus carpio during environmental adaptation. Biochem Cell Biol 2016; 94:315-21. [PMID: 27458840 DOI: 10.1139/bcb-2016-0015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
To ensure homeostasis, ectothermic organisms adapt to environmental variations through molecular mechanisms. We previously reported that during the seasonal acclimatization of the common carp Cyprinus carpio, molecular and cellular functions are reprogrammed, resulting in distinctive traits. Importantly, the carp undergoes a drastic rearrangement of nucleolar components during adaptation. This ultrastructural feature reflects a fine modulation of rRNA gene transcription. Specifically, we identified the involvement of the transcription termination factor I (TTF-I) and Tip-5 (member of nucleolar remodeling complex, NoRC) in the control of rRNA transcription. Our results suggest that differential Tip5 enrichment is essential for silencing carp ribosomal genes and that the T0 element is key for regulating the ribosomal gene during the acclimatization process. Interestingly, the expression and content of Tip5 were significantly higher in winter than in summer. Since carp ribosomal gene expression is lower in the winter than in summer, and considering that expression concomitantly occurs with nucleolar ultrastructural changes of the acclimatization process, these results indicate that Tip5 importantly contributes to silencing the ribosomal genes. In conclusion, the current study provides novel evidence on the contributions of TTF-I and NoRC in the environmental reprogramming of ribosomal genes during the seasonal adaptation process in carp.
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Affiliation(s)
- Gino Nardocci
- a Laboratorio de Biología Celular y Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Quillota 980, Viña del Mar, Chile
| | - Nicolas G Simonet
- a Laboratorio de Biología Celular y Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Quillota 980, Viña del Mar, Chile
| | - Cristina Navarro
- b Laboratorio de Biotecnología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Avenida Republica 217, Santiago, Chile
| | - Gernot Längst
- c Institute for Biochemistry III, Biochemie-Zentrum Regensburg, University of Regensburg, Regensburg, Germany
| | - Marco Alvarez
- a Laboratorio de Biología Celular y Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Quillota 980, Viña del Mar, Chile.,d Interdisciplinary Center for Aquaculture Research (INCAR), Victor Lamas 1290, PO Box 160-C, Concepción, Chile
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Rivera-Casas C, Gonzalez-Romero R, Cheema MS, Ausió J, Eirín-López JM. The characterization of macroH2A beyond vertebrates supports an ancestral origin and conserved role for histone variants in chromatin. Epigenetics 2016; 11:415-25. [PMID: 27082816 DOI: 10.1080/15592294.2016.1172161] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Histone variants play a critical role in chromatin structure and epigenetic regulation. These "deviant" proteins have been historically considered as the evolutionary descendants of ancestral canonical histones, helping specialize the nucleosome structure during eukaryotic evolution. Such view is now challenged by 2 major observations: first, canonical histones present extremely unique features not shared with any other genes; second, histone variants are widespread across many eukaryotic groups. The present work further supports the ancestral nature of histone variants by providing the first in vivo characterization of a functional macroH2A histone (a variant long defined as a specific refinement of vertebrate chromatin) in a non-vertebrate organism (the mussel Mytilus) revealing its recruitment into heterochromatic fractions of actively proliferating tissues. Combined with in silico analyses of genomic data, these results provide evidence for the widespread presence of macroH2A in metazoan animals, as well as in the holozoan Capsaspora, supporting an evolutionary origin for this histone variant lineage before the radiation of Filozoans (including Filasterea, Choanoflagellata and Metazoa). Overall, the results presented in this work help configure a new evolutionary scenario in which histone variants, rather than modern "deviants" of canonical histones, would constitute ancient components of eukaryotic chromatin.
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Affiliation(s)
- Ciro Rivera-Casas
- a Department of Biological Sciences, Chromatin Structure and Evolution (Chromevol) Group , Florida International University , North Miami , FL , USA
| | - Rodrigo Gonzalez-Romero
- a Department of Biological Sciences, Chromatin Structure and Evolution (Chromevol) Group , Florida International University , North Miami , FL , USA
| | - Manjinder S Cheema
- b Department of Biochemistry and Microbiology , University of Victoria , Victoria , British Columbia , Canada
| | - Juan Ausió
- b Department of Biochemistry and Microbiology , University of Victoria , Victoria , British Columbia , Canada
| | - José M Eirín-López
- a Department of Biological Sciences, Chromatin Structure and Evolution (Chromevol) Group , Florida International University , North Miami , FL , USA
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7
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Hammond SA, Nelson CJ, Helbing CC. Environmental influences on the epigenomes of herpetofauna and fish. Biochem Cell Biol 2016; 94:95-100. [DOI: 10.1139/bcb-2015-0111] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Herpetofauna (amphibians and reptiles) and fish represent important sentinel and indicator species for environmental and ecosystem health. It is widely accepted that the epigenome plays an important role in gene expression regulation. Environmental stimuli, including temperature and pollutants, influence gene activity, and there is growing evidence demonstrating that an important mechanism is through modulation of the epigenome. This has been primarily studied in human and mammalian models; relatively little is known about the impact of environmental conditions or pollutants on herpetofauna or fish epigenomes and the regulatory consequences of these changes on gene expression. Herein we review recent studies that have begun to address this deficiency, which have mainly focused on limited specific epigenetic marks and individual genes or large-scale global changes in DNA methylation, owing to the comparative ease of measurement. Greater understanding of the epigenetic influences of these environmental factors will depend on increased availability of relevant species-specific genomic sequence information to facilitate chromatin immunoprecipitation and DNA methylation experiments.
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Affiliation(s)
- S. Austin Hammond
- Department of Biochemistry and Microbiology, University of Victoria, P.O. Box 1700, STN CSC, Victoria, BC V8W 2Y2, Canada
- Department of Biochemistry and Microbiology, University of Victoria, P.O. Box 1700, STN CSC, Victoria, BC V8W 2Y2, Canada
| | - Christopher J. Nelson
- Department of Biochemistry and Microbiology, University of Victoria, P.O. Box 1700, STN CSC, Victoria, BC V8W 2Y2, Canada
- Department of Biochemistry and Microbiology, University of Victoria, P.O. Box 1700, STN CSC, Victoria, BC V8W 2Y2, Canada
| | - Caren C. Helbing
- Department of Biochemistry and Microbiology, University of Victoria, P.O. Box 1700, STN CSC, Victoria, BC V8W 2Y2, Canada
- Department of Biochemistry and Microbiology, University of Victoria, P.O. Box 1700, STN CSC, Victoria, BC V8W 2Y2, Canada
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8
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Talbert PB, Henikoff S. Environmental responses mediated by histone variants. Trends Cell Biol 2014; 24:642-50. [PMID: 25150594 DOI: 10.1016/j.tcb.2014.07.006] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 07/22/2014] [Accepted: 07/24/2014] [Indexed: 01/19/2023]
Abstract
Fluctuations in the ambient environment can trigger chromatin disruptions, involving replacement of nucleosomes or exchange of their histone subunits. Unlike canonical histones, which are available only during S-phase, replication-independent histone variants are present throughout the cell cycle and are adapted for chromatin repair. The H2A.Z variant mediates responses to environmental perturbations including fluctuations in temperature and seasonal variation. Phosphorylation of histone H2A.X rapidly marks double-strand DNA breaks for chromatin repair, which is mediated by both H2A and H3 histone variants. Other histones are used as weapons in conflicts between parasites and their hosts, which suggests broad involvement of histone variants in environmental responses beyond chromatin repair.
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Affiliation(s)
- Paul B Talbert
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA.
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Skeletal muscle plasticity induced by seasonal acclimatization in carp involves differential expression of rRNA and molecules that epigenetically regulate its synthesis. Comp Biochem Physiol B Biochem Mol Biol 2014; 172-173:57-66. [DOI: 10.1016/j.cbpb.2014.04.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 03/28/2014] [Accepted: 04/16/2014] [Indexed: 01/10/2023]
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Cong R, Das S, Douet J, Wong J, Buschbeck M, Mongelard F, Bouvet P. macroH2A1 histone variant represses rDNA transcription. Nucleic Acids Res 2014; 42:181-92. [PMID: 24071584 PMCID: PMC3874179 DOI: 10.1093/nar/gkt863] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 08/30/2013] [Accepted: 09/04/2013] [Indexed: 01/21/2023] Open
Abstract
The regulation of ribosomal DNA transcription is an important step for the control of cell growth. Epigenetic marks such as DNA methylation and posttranslational modifications of canonical histones have been involved in this regulation, but much less is known about the role of histone variants. In this work, we show that the histone variant macroH2A1 is present on the promoter of methylated rDNA genes. The inhibition of the expression of macroH2A1 in human HeLa and HepG2 cells and in a mouse ES cell line resulted in an up to 5-fold increase of pre-rRNA levels. This increased accumulation of pre-rRNA is accompanied by an increase of the loading of RNA polymerase I and UBF on the rDNA without any changes in the number of active rDNA genes. The inhibition of RNA polymerase I transcription by actinomycin D or by knocking down nucleolin, induces the recruitment of macroH2A1 on the rDNA and the relocalization of macroH2A1 in the nucleolus. Interestingly, the inhibition of rDNA transcription induced by nucleolin depletion is alleviated by the inactivation of macroH2A1. These results demonstrate that macroH2A1 is a new factor involved in the regulation of rDNA transcription.
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Affiliation(s)
- Rong Cong
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Predictive and Personalized Medicine of Cancer (IMPPC), 08916 Badalona, Barcelona, Spain and The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Sadhan Das
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Predictive and Personalized Medicine of Cancer (IMPPC), 08916 Badalona, Barcelona, Spain and The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Julien Douet
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Predictive and Personalized Medicine of Cancer (IMPPC), 08916 Badalona, Barcelona, Spain and The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jiemin Wong
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Predictive and Personalized Medicine of Cancer (IMPPC), 08916 Badalona, Barcelona, Spain and The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Marcus Buschbeck
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Predictive and Personalized Medicine of Cancer (IMPPC), 08916 Badalona, Barcelona, Spain and The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Fabien Mongelard
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Predictive and Personalized Medicine of Cancer (IMPPC), 08916 Badalona, Barcelona, Spain and The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Philippe Bouvet
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Predictive and Personalized Medicine of Cancer (IMPPC), 08916 Badalona, Barcelona, Spain and The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
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11
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Fuentes EN, Safian D, Valdés JA, Molina A. Isolation and selection of suitable reference genes for real-time PCR analyses in the skeletal muscle of the fine flounder in response to nutritional status: assessment and normalization of gene expression of growth-related genes. FISH PHYSIOLOGY AND BIOCHEMISTRY 2013; 39:765-777. [PMID: 23086610 DOI: 10.1007/s10695-012-9739-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Accepted: 10/15/2012] [Indexed: 06/01/2023]
Abstract
In the present study, different reference genes were isolated, and their stability in the skeletal muscle of fine flounder subjected to different nutritional states was assessed using geNorm and NormFinder. The combinations between 18S and ActB; Fau and 18S; and Fau and Tubb were chosen as the most stable gene combinations in feeding, long-term fasting and refeeding, and short-term refeeding conditions, respectively. In all periods, ActB was identified as the single least stable gene. Subsequently, the expression of the myosin heavy chain (MYH) and the insulin-like growth factor-I receptor (IGF-IR) was assessed. A large variation in MYH and IGF-IR expression was found depending on the reference gene that was chosen for normalizing the expression of both genes. Using the most stable reference genes, mRNA levels of MYH decreased and IGF-IR increased during fasting, with both returning to basal levels during refeeding. However, the drop in mRNA levels for IGF-IR occurred during short-term refeeding, in contrast with the observed events in the expression of MYH, which occurred during long-term refeeding. The present study highlights the vast differences incurred when using unsuitable versus suitable reference genes for normalizing gene expression, pointing out that normalization without proper validation could result in a bias of gene expression.
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Affiliation(s)
- Eduardo N Fuentes
- Laboratorio de Biotecnologia Molecular, Departmento de Ciencias Biologicas, Facultad de Ciencias Biologicas, Universidad Andres Bello, Av. Republica 217, 8370146 Santiago, Chile
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Simonet NG, Reyes M, Nardocci G, Molina A, Alvarez M. Epigenetic regulation of the ribosomal cistron seasonally modulates enrichment of H2A.Z and H2A.Zub in response to different environmental inputs in carp (Cyprinus carpio). Epigenetics Chromatin 2013; 6:22. [PMID: 23866978 PMCID: PMC3726427 DOI: 10.1186/1756-8935-6-22] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 06/07/2013] [Indexed: 12/12/2022] Open
Abstract
Background The specific deposition of histone variants into chromatin is an important epigenetic mechanism that contributes to gene regulation through chromatin architectural changes. The histone variant H2A.Z is essential in higher eukaryotes, and its incorporation within chromatin is a relevant process for gene expression and genome stability. However, the dual positive and negative roles of H2A.Z in gene regulation still remain unclear. We previously reported that acclimatization in common carp fish (Cyprinus carpio) involves cyclical seasonal gene reprogramming as an adaptation response to its natural environment, when rRNA synthesis and processing are profoundly affected. Epigenetic mechanisms primarily contribute to the transcriptional modulation of ribosomal genes concomitant with the acclimatization process, thus significantly regulating this process. The aim of this study was to describe the presence of several H2A.Z subtypes in carp, and assess the role of H2A.Z on the ribosomal cistron in summer- and winter-acclimatized carp. Results This paper reports for the first time about the transcriptional expression of four different H2A.Z subtypes belonging to the same organism. Remarkably, a novel H2A.Z.7 was found, which corresponds to a tissue-specific histone subtype that contains seven amino acid residues longer than the canonical H2A.Z. Moreover, H2A.Z enrichment through the ribosomal cistron was significantly higher during summer, when rRNA transcription and processing are highly active, than it was in winter. Similar patterns of H2A.Z enrichment are found in two seasonally active promoters for genes transcribed by RNA polymerase II, the L41 and Δ9-desaturase genes. Interestingly, ubiquitylated-H2A.Z (H2A.Zub) was strongly enriched on regulatory regions of the ribosomal cistron in summer-acclimatized carp. Additionally, H2A.Z was present in both heterochromatin and euchromatin states on ribosomal cistron and RNA polymerase II promoters. Conclusions Our study revealed seasonally-dependent H2A.Z enrichment for active ribosomal cistron and RNA polymerase II promoters during the carp environmental adaptation. Moreover, seasonal H2A.Zub enrichment appears as a specific mechanism contributing to the regulation of chromatin architecture under natural conditions. The existence of several H2A.Z subtypes in carp suggests that the epigenetic regulation in this species constitutes a complex and finely tuned mechanism developed to cope with seasonal environmental changes that occur in its habitat.
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Affiliation(s)
- Nicolas Guillermo Simonet
- Interdisciplinary Center for Aquaculture Research (INCAR), Víctor Lamas 1290, PO Box 160-C, Concepción, Chile.
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Abstract
Histones are the protein components of chromatin and are important for its organization and compaction. Although core histones are exclusively expressed during S phase of the cell cycle, there exist variants of canonical histones that are expressed throughout the cell cycle. These histone variants are often deposited at defined regions of the genome and they play important roles in a variety of cellular processes, such as transcription regulation, heterochromatin formation and DNA repair. In this chapter, we will focus on several histone variants that have been linked to transcription regulation, and highlight their physical and functional features that facilitate their activities in this context.
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Affiliation(s)
- Cindy Law
- Ontario Cancer Institute, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
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14
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The macrodomain family: Rethinking an ancient domain from evolutionary perspectives. CHINESE SCIENCE BULLETIN = KEXUE TONGBAO 2013; 58:953-960. [PMID: 32214744 PMCID: PMC7088686 DOI: 10.1007/s11434-013-5674-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 09/28/2012] [Indexed: 11/18/2022]
Abstract
The reasons why certain domains evolve much slower than others is unclear. The notion that functionally more important genes evolve more slowly than less important genes is one of the few commonly believed principles of molecular evolution. The macro-domain (also known as the X domain) is an ancient, slowly evolving and highly conserved structural domain found in proteins throughout all of the kingdoms and was first discovered nearly two decades ago with the isolation and cloning of macroH2A1. Macrodomains, which are functionally promiscuous, have been studied intensively for the past decade due to their importance in the regulation of cellular responses to DNA damage, chromatin remodeling, transcription and tumorigenesis. Recent structural, phylogenetic and biological analyses, however, suggest the need for some reconsideration of the evolutionary advantage of concentrating such a plethora of diverse functions into the macrodomain and of how macrodomains could perform so many functions. In this article, we focus on macrodomains that are evolving slowly and broadly discuss the potential relationship between the biological evolution and functional diversity of macrodomains.
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15
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Cong R, Das S, Ugrinova I, Kumar S, Mongelard F, Wong J, Bouvet P. Interaction of nucleolin with ribosomal RNA genes and its role in RNA polymerase I transcription. Nucleic Acids Res 2012; 40:9441-54. [PMID: 22859736 PMCID: PMC3479187 DOI: 10.1093/nar/gks720] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 06/04/2012] [Accepted: 07/04/2012] [Indexed: 12/13/2022] Open
Abstract
Nucleolin is a multi-functional nucleolar protein that is required for ribosomal RNA gene (rRNA) transcription in vivo, but the mechanism by which nucleolin modulates RNA polymerase I (RNAPI) transcription is not well understood. Nucleolin depletion results in an increase in the heterochromatin mark H3K9me2 and a decrease in H4K12Ac and H3K4me3 euchromatin histone marks in rRNA genes. ChIP-seq experiments identified an enrichment of nucleolin in the ribosomal DNA (rDNA) coding and promoter region. Nucleolin is preferentially associated with unmethylated rRNA genes and its depletion leads to the accumulation of RNAPI at the beginning of the transcription unit and a decrease in UBF along the coding and promoter regions. Nucleolin is able to affect the binding of transcription termination factor-1 on the promoter-proximal terminator T0, thus inhibiting the recruitment of TIP5 and HDAC1 and the establishment of a repressive heterochromatin state. These results reveal the importance of nucleolin for the maintenance of the euchromatin state and transcription elongation of rDNA.
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Affiliation(s)
- Rong Cong
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China and BioCOS Life Sciences Private Limited, Biotech Park, Electronics City, Phase-1, Bangalore 560100, India
| | - Sadhan Das
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China and BioCOS Life Sciences Private Limited, Biotech Park, Electronics City, Phase-1, Bangalore 560100, India
| | - Iva Ugrinova
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China and BioCOS Life Sciences Private Limited, Biotech Park, Electronics City, Phase-1, Bangalore 560100, India
| | - Sanjeev Kumar
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China and BioCOS Life Sciences Private Limited, Biotech Park, Electronics City, Phase-1, Bangalore 560100, India
| | - Fabien Mongelard
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China and BioCOS Life Sciences Private Limited, Biotech Park, Electronics City, Phase-1, Bangalore 560100, India
| | - Jiemin Wong
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China and BioCOS Life Sciences Private Limited, Biotech Park, Electronics City, Phase-1, Bangalore 560100, India
| | - Philippe Bouvet
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China and BioCOS Life Sciences Private Limited, Biotech Park, Electronics City, Phase-1, Bangalore 560100, India
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Tanasijevic B, Rasmussen TP. X chromosome inactivation and differentiation occur readily in ES cells doubly-deficient for macroH2A1 and macroH2A2. PLoS One 2011; 6:e21512. [PMID: 21738686 PMCID: PMC3127949 DOI: 10.1371/journal.pone.0021512] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 05/31/2011] [Indexed: 12/29/2022] Open
Abstract
Macrohistones (mH2As) are unusual histone variants found exclusively in vertebrate chromatin. In mice, the H2afy gene encodes two splice variants, mH2A1.1 and mH2A1.2 and a second gene, H2afy2, encodes an additional mH2A2 protein. Both mH2A isoforms have been found enriched on the inactive X chromosome (Xi) in differentiated mammalian female cells, and are incorporated into the chromatin of developmentally-regulated genes. To investigate the functional significance of mH2A isoforms for X chromosome inactivation (XCI), we produced male and female embryonic stem cell (ESC) lines with stably-integrated shRNA constructs that simultaneously target both mH2A1 and mH2A2. Surprisingly, we find that female ESCs deficient for both mH2A1 and mH2A2 readily execute and maintain XCI upon differentiation. Furthermore, male and female mH2A-deficient ESCs proliferate normally under pluripotency culture conditions, and respond to several standard differentiation procedures efficiently. Our results show that XCI can readily proceed with substantially reduced total mH2A content.
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Affiliation(s)
- Borko Tanasijevic
- Center for Regenerative Biology, University of Connecticut, Storrs, Connecticut, United States of America
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Theodore P. Rasmussen
- Center for Regenerative Biology, University of Connecticut, Storrs, Connecticut, United States of America
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States of America
- * E-mail:
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