1
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Fukushima HS, Ikeda T, Ikeda S, Takeda H. Cell cycle length governs heterochromatin reprogramming during early development in non-mammalian vertebrates. EMBO Rep 2024; 25:3300-3323. [PMID: 38943003 PMCID: PMC11315934 DOI: 10.1038/s44319-024-00188-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 06/06/2024] [Accepted: 06/12/2024] [Indexed: 06/30/2024] Open
Abstract
Heterochromatin marks such as H3K9me3 undergo global erasure and re-establishment after fertilization, and the proper reprogramming of H3K9me3 is essential for early development. Despite the widely conserved dynamics of heterochromatin reprogramming in invertebrates and non-mammalian vertebrates, previous studies have shown that the underlying mechanisms may differ between species. Here, we investigate the molecular mechanism of H3K9me3 dynamics in medaka (Japanese killifish, Oryzias latipes) as a non-mammalian vertebrate model, and show that rapid cell cycle during cleavage stages causes DNA replication-dependent passive erasure of H3K9me3. We also find that cell cycle slowing, toward the mid-blastula transition, permits increasing nuclear accumulation of H3K9me3 histone methyltransferase Setdb1, leading to the onset of H3K9me3 re-accumulation. We further demonstrate that cell cycle length in early development also governs H3K9me3 reprogramming in zebrafish and Xenopus laevis. Together with the previous studies in invertebrates, we propose that a cell cycle length-dependent mechanism for both global erasure and re-accumulation of H3K9me3 is conserved among rapid-cleavage species of non-mammalian vertebrates and invertebrates such as Drosophila, C. elegans, Xenopus and teleost fish.
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Affiliation(s)
- Hiroto S Fukushima
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
- Center for Integrative Medical Sciences, RIKEN, Yokohama, 230-0045, Japan.
| | - Takafumi Ikeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
- Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, 603-8555, Japan
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, 603-8555, Japan
| | - Shinra Ikeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, 603-8555, Japan.
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2
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Pérez-Maldonado MA, González-González XA, Chimal-Monroy J, Marín-Llera JC. Influence of DNA-methylation at multiple stages of limb chondrogenesis. Dev Biol 2024; 512:1-10. [PMID: 38657748 DOI: 10.1016/j.ydbio.2024.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 04/05/2024] [Accepted: 04/18/2024] [Indexed: 04/26/2024]
Abstract
Precise regulation of gene expression is of utmost importance during cell fate specification. DNA methylation is a key epigenetic mechanism that plays a significant role in the regulation of cell fate by recruiting repression proteins or inhibiting the binding of transcription factors to DNA to regulate gene expression. Limb development is a well-established model for understanding cell fate decisions, and the formation of skeletal elements is coordinated through a sequence of events that control chondrogenesis spatiotemporally. It has been established that epigenetic control participates in cartilage maturation. However, further investigation is required to determine its role in the earliest stages of chondrocyte differentiation. This study investigates how the DNA methylation environment affects cell fate divergence during the early chondrogenic events. Our research has shown for the first time that inhibiting DNA methylation in interdigital tissue with 5-azacytidine results in the formation of an ectopic digit. This discovery suggested that DNA methylation dynamics could regulate the fate of cells between chondrogenesis and cell death during autopod development. Our in vitro findings indicate that DNA methylation at the early stages of chondrogenesis is integral in regulating condensation by controlling cell adhesion and proapoptotic genes. As a result, the dynamics of methylation and demethylation are crucial in governing chondrogenesis and cell death during different stages of limb chondrogenesis.
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Affiliation(s)
- Mario Alberto Pérez-Maldonado
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70228, Ciudad de México, 04510, México
| | - Ximena Alexandra González-González
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70228, Ciudad de México, 04510, México
| | - Jesús Chimal-Monroy
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70228, Ciudad de México, 04510, México.
| | - Jessica Cristina Marín-Llera
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70228, Ciudad de México, 04510, México.
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3
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Ross SE, Vázquez-Marín J, Gert KRB, González-Rajal Á, Dinger ME, Pauli A, Martínez-Morales JR, Bogdanovic O. Evolutionary conservation of embryonic DNA methylome remodelling in distantly related teleost species. Nucleic Acids Res 2023; 51:9658-9671. [PMID: 37615576 PMCID: PMC10570028 DOI: 10.1093/nar/gkad695] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/28/2023] [Accepted: 08/09/2023] [Indexed: 08/25/2023] Open
Abstract
Methylation of cytosines in the CG context (mCG) is the most abundant DNA modification in vertebrates that plays crucial roles in cellular differentiation and identity. After fertilization, DNA methylation patterns inherited from parental gametes are remodelled into a state compatible with embryogenesis. In mammals, this is achieved through the global erasure and re-establishment of DNA methylation patterns. However, in non-mammalian vertebrates like zebrafish, no global erasure has been observed. To investigate the evolutionary conservation and divergence of DNA methylation remodelling in teleosts, we generated base resolution DNA methylome datasets of developing medaka and medaka-zebrafish hybrid embryos. In contrast to previous reports, we show that medaka display comparable DNA methylome dynamics to zebrafish with high gametic mCG levels (sperm: ∼90%; egg: ∼75%), and adoption of a paternal-like methylome during early embryogenesis, with no signs of prior DNA methylation erasure. We also demonstrate that non-canonical DNA methylation (mCH) reprogramming at TGCT tandem repeats is a conserved feature of teleost embryogenesis. Lastly, we find remarkable evolutionary conservation of DNA methylation remodelling patterns in medaka-zebrafish hybrids, indicative of compatible DNA methylation maintenance machinery in far-related teleost species. Overall, these results suggest strong evolutionary conservation of DNA methylation remodelling pathways in teleosts, which is distinct from the global DNA methylome erasure and reestablishment observed in mammals.
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Affiliation(s)
- Samuel E Ross
- Garvan Institute of Medical Research, Sydney, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Javier Vázquez-Marín
- Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Krista R B Gert
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, A-1030, Vienna, Austria
| | - Álvaro González-Rajal
- Garvan Institute of Medical Research, Sydney, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Marcel E Dinger
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Andrea Pauli
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Juan Ramon Martínez-Morales
- Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Ozren Bogdanovic
- Garvan Institute of Medical Research, Sydney, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
- Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
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4
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Inoue Y, Takeda H. Teratorn and its relatives - a cross-point of distinct mobile elements, transposons and viruses. Front Vet Sci 2023; 10:1158023. [PMID: 37187934 PMCID: PMC10175614 DOI: 10.3389/fvets.2023.1158023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/10/2023] [Indexed: 05/17/2023] Open
Abstract
Mobile genetic elements (e.g., transposable elements and plasmids) and viruses display significant diversity with various life cycles, but how this diversity emerges remains obscure. We previously reported a novel and giant (180 kb long) mobile element, Teratorn, originally identified in the genome of medaka, Oryzias latipes. Teratorn is a composite DNA transposon created by a fusion of a piggyBac-like DNA transposon (piggyBac) and a novel herpesvirus of the Alloherpesviridae family. Genomic survey revealed that Teratorn-like herpesviruses are widely distributed among teleost genomes, the majority of which are also fused with piggyBac, suggesting that fusion with piggyBac is a trigger for the life-cycle shift of authentic herpesviruses to an intragenomic parasite. Thus, Teratorn-like herpesvirus provides a clear example of how novel mobile elements emerge, that is to say, the creation of diversity. In this review, we discuss the unique sequence and life-cycle characteristics of Teratorn, followed by the evolutionary process of piggyBac-herpesvirus fusion based on the distribution of Teratorn-like herpesviruses (relatives) among teleosts. Finally, we provide other examples of evolutionary associations between different classes of elements and propose that recombination could be a driving force generating novel mobile elements.
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Affiliation(s)
- Yusuke Inoue
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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5
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Fukushima HS, Takeda H, Nakamura R. Incomplete erasure of histone marks during epigenetic reprogramming in medaka early development. Genome Res 2023; 33:572-586. [PMID: 37117034 PMCID: PMC10234297 DOI: 10.1101/gr.277577.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/29/2023] [Indexed: 04/30/2023]
Abstract
Epigenetic modifications undergo drastic erasure and reestablishment after fertilization. This reprogramming is required for proper embryonic development and cell differentiation. In mammals, some histone modifications are not completely reprogrammed and play critical roles in later development. In contrast, in nonmammalian vertebrates, most histone modifications are thought to be more intensively erased and reestablished by the stage of zygotic genome activation (ZGA). However, histone modifications that escape reprogramming in nonmammalian vertebrates and their potential functional roles remain unknown. Here, we quantitatively and comprehensively analyzed histone modification dynamics during epigenetic reprogramming in Japanese killifish, medaka (Oryzias latipes) embryos. Our data revealed that H3K27ac, H3K27me3, and H3K9me3 escape complete reprogramming, whereas H3K4 methylation is completely erased during cleavage stage. Furthermore, we experimentally showed the functional roles of such retained modifications at early stages: (i) H3K27ac premarks promoters during the cleavage stage, and inhibition of histone acetyltransferases disrupts proper patterning of H3K4 and H3K27 methylation at CpG-dense promoters, but does not affect chromatin accessibility after ZGA; (ii) H3K9me3 is globally erased but specifically retained at telomeric regions, which is required for maintenance of genomic stability during the cleavage stage. These results expand the understanding of diversity and conservation of reprogramming in vertebrates, and unveil previously uncharacterized functions of histone modifications retained during epigenetic reprogramming.
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Affiliation(s)
- Hiroto S Fukushima
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Ryohei Nakamura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
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6
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Fukushima HS, Takeda H, Nakamura R. Targeted Manipulation of Histone Modification in Medaka Embryos. Methods Mol Biol 2023; 2577:279-293. [PMID: 36173581 DOI: 10.1007/978-1-0716-2724-2_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Recent development of targeted manipulation of histone modification enables us to experimentally and directly test the functional relevance of histone modifications accumulated at specific genomic regions. In particular, dCas9 epigenome editing has been widely used for site-specific manipulation of epigenetic modification. Here, we describe how to apply dCas9 epigenome editing in fish (medaka, Oryzias latipes) embryos and how to analyze induced changes in histone modification.
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Affiliation(s)
- Hiroto S Fukushima
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Ryohei Nakamura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
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7
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Liu S, Tengstedt ANB, Jacobsen MW, Pujolar JM, Jónsson B, Lobón-Cervià J, Bernatchez L, Hansen MM. Genome-wide methylation in the panmictic European eel (Anguilla anguilla). Mol Ecol 2022; 31:4286-4306. [PMID: 35767387 DOI: 10.1111/mec.16586] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/21/2022] [Accepted: 06/27/2022] [Indexed: 11/30/2022]
Abstract
The role of methylation in adaptive, developmental and speciation processes has attracted considerable interest, but interpretation of results is complicated by diffuse boundaries between genetic and non-genetic variation. We studied whole genome genetic and methylation variation in the European eel, distributed from subarctic to subtropical environments, but with panmixia precluding genetically based local adaptation beyond single-generation responses. Overall methylation was 70.9%, with hypomethylation predominantly found in promoters and first exons. Redundancy analyses involving juvenile glass eels showed 0.06% and 0.03% of the variance at SNPs to be explained by localities and environmental variables, respectively, with GO terms of genes associated with outliers primarily involving neural system functioning. For CpGs 2.98% and 1.36% of variance was explained by localities and environmental variables. Differentially methylated regions particularly included genes involved in developmental processes, with hox clusters featuring prominently. Life stage (adult versus glass eels) was the most important source of inter-individual variation in methylation, likely reflecting both ageing and developmental processes. Demethylation of transposable elements relative to pure European eel was observed in European X American eel hybrids, possibly representing postzygotic barriers in this system characterized by prolonged speciation and ongoing gene flow. Whereas the genetic data are consistent with a role of single-generation selective responses, the methylation results underpin the importance of epigenetics in the life cycle of eels and suggests interactions between local environments, development and phenotypic variation mediated by methylation variation. Eels are remarkable by having retained eight hox clusters, and the results suggest important roles of methylation at hox genes for adaptive processes.
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Affiliation(s)
- Shenglin Liu
- Department of Biology, Aarhus University, Aarhus, Denmark
| | | | - Magnus W Jacobsen
- Section for Marine Living Resources, National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Jose Martin Pujolar
- Centre for Gelatinous Plankton Ecology and Evolution, National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Bjarni Jónsson
- North West Iceland Nature Center, Iceland.,The Icelandic Parliament, Reykjavík, Iceland
| | | | - Louis Bernatchez
- IBIS (Institut de Biologie Intégrative et des Systèmes), Université Laval, Québec, Canada
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8
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Heilig AK, Nakamura R, Shimada A, Hashimoto Y, Nakamura Y, Wittbrodt J, Takeda H, Kawanishi T. Wnt11 acts on dermomyotome cells to guide epaxial myotome morphogenesis. eLife 2022; 11:71845. [PMID: 35522214 PMCID: PMC9075960 DOI: 10.7554/elife.71845] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 04/19/2022] [Indexed: 12/30/2022] Open
Abstract
The dorsal axial muscles, or epaxial muscles, are a fundamental structure covering the spinal cord and vertebrae, as well as mobilizing the vertebrate trunk. To date, mechanisms underlying the morphogenetic process shaping the epaxial myotome are largely unknown. To address this, we used the medaka zic1/zic4-enhancer mutant Double anal fin (Da), which exhibits ventralized dorsal trunk structures resulting in impaired epaxial myotome morphology and incomplete coverage over the neural tube. In wild type, dorsal dermomyotome (DM) cells reduce their proliferative activity after somitogenesis. Subsequently, a subset of DM cells, which does not differentiate into the myotome population, begins to form unique large protrusions extending dorsally to guide the epaxial myotome dorsally. In Da, by contrast, DM cells maintain the high proliferative activity and mainly form small protrusions. By combining RNA- and ChIP-sequencing analyses, we revealed direct targets of Zic1, which are specifically expressed in dorsal somites and involved in various aspects of development, such as cell migration, extracellular matrix organization, and cell-cell communication. Among these, we identified wnt11 as a crucial factor regulating both cell proliferation and protrusive activity of DM cells. We propose that dorsal extension of the epaxial myotome is guided by a non-myogenic subpopulation of DM cells and that wnt11 empowers the DM cells to drive the coverage of the neural tube by the epaxial myotome.
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Affiliation(s)
- Ann Kathrin Heilig
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan.,Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany.,Heidelberg Biosciences International Graduate School, Heidelberg, Germany
| | - Ryohei Nakamura
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Atsuko Shimada
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Yuka Hashimoto
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Yuta Nakamura
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Toru Kawanishi
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
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9
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Chowdhury K, Lin S, Lai SL. Comparative Study in Zebrafish and Medaka Unravels the Mechanisms of Tissue Regeneration. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.783818] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Tissue regeneration has been in the spotlight of research for its fascinating nature and potential applications in human diseases. The trait of regenerative capacity occurs diversely across species and tissue contexts, while it seems to decline over evolution. Organisms with variable regenerative capacity are usually distinct in phylogeny, anatomy, and physiology. This phenomenon hinders the feasibility of studying tissue regeneration by directly comparing regenerative with non-regenerative animals, such as zebrafish (Danio rerio) and mice (Mus musculus). Medaka (Oryzias latipes) is a fish model with a complete reference genome and shares a common ancestor with zebrafish approximately 110–200 million years ago (compared to 650 million years with mice). Medaka shares similar features with zebrafish, including size, diet, organ system, gross anatomy, and living environment. However, while zebrafish regenerate almost every organ upon experimental injury, medaka shows uneven regenerative capacity. Their common and distinct biological features make them a unique platform for reciprocal analyses to understand the mechanisms of tissue regeneration. Here we summarize current knowledge about tissue regeneration in these fish models in terms of injured tissues, repairing mechanisms, available materials, and established technologies. We further highlight the concept of inter-species and inter-organ comparisons, which may reveal mechanistic insights and hint at therapeutic strategies for human diseases.
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10
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Nakamura R, Motai Y, Kumagai M, Wike CL, Nishiyama H, Nakatani Y, Durand NC, Kondo K, Kondo T, Tsukahara T, Shimada A, Cairns BR, Aiden EL, Morishita S, Takeda H. CTCF looping is established during gastrulation in medaka embryos. Genome Res 2021; 31:968-980. [PMID: 34006570 PMCID: PMC8168583 DOI: 10.1101/gr.269951.120] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 03/30/2021] [Indexed: 12/23/2022]
Abstract
Chromatin looping plays an important role in genome regulation. However, because ChIP-seq and loop-resolution Hi-C (DNA-DNA proximity ligation) are extremely challenging in mammalian early embryos, the developmental stage at which cohesin-mediated loops form remains unknown. Here, we study early development in medaka (the Japanese killifish, Oryzias latipes) at 12 time points before, during, and after gastrulation (the onset of cell differentiation) and characterize transcription, protein binding, and genome architecture. We find that gastrulation is associated with drastic changes in genome architecture, including the formation of the first loops between sites bound by the insulator protein CTCF and a large increase in the size of contact domains. In contrast, the binding of the CTCF is fixed throughout embryogenesis. Loops form long after genome-wide transcriptional activation, and long after domain formation seen in mouse embryos. These results suggest that, although loops may play a role in differentiation, they are not required for zygotic transcription. When we repeated our experiments in zebrafish, loops did not emerge until gastrulation, that is, well after zygotic genome activation. We observe that loop positions are highly conserved in synteny blocks of medaka and zebrafish, indicating that the 3D genome architecture has been maintained for >110–200 million years of evolution.
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Affiliation(s)
- Ryohei Nakamura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033 Japan
| | - Yuichi Motai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
| | - Masahiko Kumagai
- Advanced Analysis Center, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8602, Japan
| | - Candice L Wike
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Haruyo Nishiyama
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033 Japan
| | - Yoichiro Nakatani
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Neva C Durand
- The Center for Genome Architecture, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, Texas 77005, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139 USA.,Center for Theoretical Biological Physics, Rice University, Houston, Texas 77030, USA
| | - Kaori Kondo
- RIKEN-IMS, Laboratory for Developmental Genetics, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Takashi Kondo
- RIKEN-IMS, Laboratory for Developmental Genetics, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Tatsuya Tsukahara
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Atsuko Shimada
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033 Japan
| | - Bradley R Cairns
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, Texas 77005, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139 USA.,Center for Theoretical Biological Physics, Rice University, Houston, Texas 77030, USA
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033 Japan
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11
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Shim WJ, Sinniah E, Xu J, Vitrinel B, Alexanian M, Andreoletti G, Shen S, Sun Y, Balderson B, Boix C, Peng G, Jing N, Wang Y, Kellis M, Tam PPL, Smith A, Piper M, Christiaen L, Nguyen Q, Bodén M, Palpant NJ. Conserved Epigenetic Regulatory Logic Infers Genes Governing Cell Identity. Cell Syst 2020; 11:625-639.e13. [PMID: 33278344 PMCID: PMC7781436 DOI: 10.1016/j.cels.2020.11.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 08/31/2020] [Accepted: 11/09/2020] [Indexed: 01/06/2023]
Abstract
Determining genes that orchestrate cell differentiation in development and disease remains a fundamental goal of cell biology. This study establishes a genome-wide metric based on the gene-repressive trimethylation of histone H3 at lysine 27 (H3K27me3) across hundreds of diverse cell types to identify genetic regulators of cell differentiation. We introduce a computational method, TRIAGE, which uses discordance between gene-repressive tendency and expression to identify genetic drivers of cell identity. We apply TRIAGE to millions of genome-wide single-cell transcriptomes, diverse omics platforms, and eukaryotic cells and tissue types. Using a wide range of data, we validate the performance of TRIAGE in identifying cell-type-specific regulatory factors across diverse species including human, mouse, boar, bird, fish, and tunicate. Using CRISPR gene editing, we use TRIAGE to experimentally validate RNF220 as a regulator of Ciona cardiopharyngeal development and SIX3 as required for differentiation of endoderm in human pluripotent stem cells. A record of this paper’s transparent peer review process is included in the Supplemental Information. Perturbing genes controlling cell decisions have major implications in development or disease. However, identifying key regulatory genes from the thousands expressed in a cell is challenging. TRIAGE is a computational method that distills patterns of epigenetic repression across diverse cell types to infer regulatory genes using input gene expression data from any cell type. Demonstrating its utility, we combine single-cell RNA-seq and TRIAGE to identify and experimentally confirm novel regulators of heart development in evolutionarily distant species.
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Affiliation(s)
- Woo Jun Shim
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Enakshi Sinniah
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Jun Xu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Burcu Vitrinel
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY, USA
| | - Michael Alexanian
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA, USA
| | - Gaia Andreoletti
- Institute for Computational Health Sciences, University of California, San Francisco, CA 94158, USA
| | - Sophie Shen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Yuliangzi Sun
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Brad Balderson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Carles Boix
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Guangdun Peng
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences and Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China; State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Naihe Jing
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences and Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China; State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yuliang Wang
- Paul G. Allen School of Computer Science and Engineering and Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA, USA
| | | | - Patrick P L Tam
- The University of Sydney, Children's Medical Research Institute, and School of Medical Sciences, Faculty of Medicine and Health, Westmead, NSW 2145, Australia
| | - Aaron Smith
- Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia; Translational Research Institute, Woolloongabba, Brisbane, Australia
| | - Michael Piper
- School of Biomedical Sciences, The University of Queensland, Brisbane, Australia; Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Lionel Christiaen
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY, USA
| | - Quan Nguyen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Mikael Bodén
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.
| | - Nathan J Palpant
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia.
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12
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Li Y, Liu Y, Yang H, Zhang T, Naruse K, Tu Q. Dynamic transcriptional and chromatin accessibility landscape of medaka embryogenesis. Genome Res 2020; 30:924-937. [PMID: 32591361 PMCID: PMC7370878 DOI: 10.1101/gr.258871.119] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 06/17/2020] [Indexed: 12/13/2022]
Abstract
Medaka (Oryzias latipes) has become an important vertebrate model widely used in genetics, developmental biology, environmental sciences, and many other fields. A high-quality genome sequence and a variety of genetic tools are available for this model organism. However, existing genome annotation is still rudimentary, as it was mainly based on computational prediction and short-read RNA-seq data. Here we report a dynamic transcriptome landscape of medaka embryogenesis profiled by long-read RNA-seq, short-read RNA-seq, and ATAC-seq. By integrating these data sets, we constructed a much-improved gene model set including about 17,000 novel isoforms and identified 1600 transcription factors, 1100 long noncoding RNAs, and 150,000 potential cis-regulatory elements as well. Time-series data sets provided another dimension of information. With the expression dynamics of genes and accessibility dynamics of cis-regulatory elements, we investigated isoform switching, as well as regulatory logic between accessible elements and genes, during embryogenesis. We built a user-friendly medaka omics data portal to present these data sets. This resource provides the first comprehensive omics data sets of medaka embryogenesis. Ultimately, we term these three assays as the minimum ENCODE toolbox and propose the use of it as the initial and essential profiling genomic assays for model organisms that have limited data available. This work will be of great value for the research community using medaka as the model organism and many others as well.
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Affiliation(s)
- Yingshu Li
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.,Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongjie Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.,Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hang Yang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.,Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ting Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.,Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Kiyoshi Naruse
- Laboratory of Bioresources, National Institute for Basic Biology, Okazaki 444-8585, Aichi, Japan
| | - Qiang Tu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.,Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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13
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Fukushima HS, Takeda H, Nakamura R. Targeted in vivo epigenome editing of H3K27me3. Epigenetics Chromatin 2019; 12:17. [PMID: 30871638 PMCID: PMC6419334 DOI: 10.1186/s13072-019-0263-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 03/07/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Epigenetic modifications have a central role in transcriptional regulation. While several studies using next-generation sequencing have revealed genome-wide associations between epigenetic modifications and transcriptional states, a direct causal relationship at specific genomic loci has not been fully demonstrated, due to a lack of technology for targeted manipulation of epigenetic modifications. Recently, epigenome editing techniques based on the CRISPR-Cas9 system have been reported to directly manipulate specific modifications at precise genomic regions. However, the number of editable modifications as well as studies applying these techniques in vivo is still limited. RESULTS Here, we report direct modification of the epigenome in medaka (Japanese killifish, Oryzias latipes) embryos. Specifically, we developed a method to ectopically induce the repressive histone modification, H3K27me3 in a locus-specific manner, using a fusion construct of Oryzias latipes H3K27 methyltransferase Ezh2 (olEzh2) and dCas9 (dCas9-olEzh2). Co-injection of dCas9-olEzh2 mRNA with single guide RNAs (sgRNAs) into one-cell-stage embryos induced specific H3K27me3 accumulation at the targeted loci and induced downregulation of gene expression. CONCLUSION In this study, we established the in vivo epigenome editing of H3K27me3 using medaka embryos. The locus-specific manipulation of the epigenome in living organisms will lead to a previously inaccessible understanding of the role of epigenetic modifications in development and disease.
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Affiliation(s)
- Hiroto S. Fukushima
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 Japan
| | - Ryohei Nakamura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 Japan
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14
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In Vivo Analysis of Embryo Development and Behavioral Response of Medaka Fish under Static Magnetic Field Exposures. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16050844. [PMID: 30857154 PMCID: PMC6427164 DOI: 10.3390/ijerph16050844] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/22/2019] [Accepted: 03/05/2019] [Indexed: 11/17/2022]
Abstract
The static magnetic field (SMF) in human exposure has become a health risk concern, especially with respect to prolonged exposure. The International Commission on Non-Ionizing Radiation Protection (ICNIRP) has been considering cell or animal models to be adopted to estimate the possible human health impacts after such exposure. The medaka fish is a good animal model for human-related health assessment studies; this paper examines both the embryo development and behavioral responses in medaka fish in vivo to long-term SMF exposure at the mT level. SMF exposure was examined for the complete developmental period of embryos until hatched; the embryos were monitored and recorded every 24 h for different morphological abnormalities in their developmental stages. The behavioral response of adult fish was also examined by analyzing their swimming velocities and positioning as compared with that of the control group. It was observed that there were no impacts on embryo development under prolonged exposure up to about 100 mT while the swimming behavior of the adult fish under exposure was different to the control group-the swimming movement of the treated group was more static, with an average velocity of 24.6% less as observed over a 24-h duration.
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15
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Novel components of germline sex determination acting downstream of foxl3 in medaka. Dev Biol 2019; 445:80-89. [DOI: 10.1016/j.ydbio.2018.10.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 10/08/2018] [Accepted: 10/23/2018] [Indexed: 12/20/2022]
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16
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Metzger DCH, Schulte PM. The DNA Methylation Landscape of Stickleback Reveals Patterns of Sex Chromosome Evolution and Effects of Environmental Salinity. Genome Biol Evol 2018; 10:775-785. [PMID: 29420714 PMCID: PMC5841383 DOI: 10.1093/gbe/evy034] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2018] [Indexed: 12/12/2022] Open
Abstract
Epigenetic mechanisms such as DNA methylation are a key component of dosage compensation on sex chromosomes and have been proposed as an important source of phenotypic variation influencing plasticity and adaptive evolutionary processes, yet little is known about the role of DNA methylation in an ecological or evolutionary context in vertebrates. The threespine stickleback (Gasterosteus aculeatus) is an ecological and evolutionary model system that has been used to study mechanisms involved in the evolution of adaptive phenotypes in novel environments as well as the evolution heteromorphic sex chromosomes and dosage compensation in vertebrates. Using whole genome bisulfite sequencing, we compared genome-wide DNA methylation patterns between threespine stickleback males and females and between stickleback reared at different environmental salinities. Apparent hypermethylation of the younger evolutionary stratum of the stickleback X chromosome in females relative to males suggests a potential role of DNA methylation in the evolution of heteromorphic sex chromosomes. We also demonstrate that rearing salinity has genome-wide effects on DNA methylation levels, which has the potential to lead to the accumulation of epigenetic variation between natural populations in different environments.
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Affiliation(s)
- David C H Metzger
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Patricia M Schulte
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
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17
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Motta-Neto CC, Marques A, Costa GW, Cioffi MB, Bertollo LA, Soares RX, Scortecci KC, Artoni RF, Molina WF. Differential hypomethylation of the repetitive Tol2/Alu-rich sequences in the genome of Bodianus species (Labriformes, Labridae). COMPARATIVE CYTOGENETICS 2018; 12:145-162. [PMID: 29675141 PMCID: PMC5904366 DOI: 10.3897/compcytogen.v12i2.21830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 02/28/2018] [Indexed: 06/08/2023]
Abstract
Representatives of the order Labriformes show karyotypes of extreme conservatism together with others with high chromosomal diversification. However, the cytological characterization of epigenetic modifications remains unknown for the majority of the species. In the family Labridae, the most abundant fishes on tropical reefs, the genomes of the genus Bodianus Bloch, 1790 have been characterized by the occurrence of a peculiar chromosomal region, here denominated BOD. This region is exceptionally decondensed, heterochromatic, argentophilic, GC-neutral and, in contrast to classical secondary constrictions, shows no signals of hybridization with 18S rDNA probes. In order to characterize the BOD region, the methylation pattern, the distribution of Alu and Tol2 retrotransposons and of 18S and 5S rDNA sites, respectively, were analyzed by Fluorescence In Situ Hybridization (FISH) on metaphase chromosomes of two Bodianus species, B. insularis Gomon & Lubbock, 1980 and B. pulchellus (Poey, 1860). Immunolocalization of the 5-methylcytosine revealed hypermethylated chromosomal regions, dispersed along the entire length of the chromosomes of both species, while the BOD regions exhibited a hypomethylated pattern. Hypomethylation of the BOD region is associated with the precise co-location of Tol2 and Alu elements, suggesting their active participation in the regulatory epigenetic process. This evidence underscores a probable differential methylation action during the cell cycle, as well as the role of Tol2/Alu elements in functional processes of fish genomes.
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Affiliation(s)
- Clóvis C. Motta-Neto
- Center of Biosciences, Department of Cellular Biology and Genetics, Federal University of Rio Grande do Norte, Natal, Brazil
| | - André Marques
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Gideão W.W.F. Costa
- Center of Biosciences, Department of Cellular Biology and Genetics, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Marcelo B. Cioffi
- Department of Genetics and Evolution, Federal University of São Carlos, São Paulo, Brazil
| | - Luiz A.C. Bertollo
- Department of Genetics and Evolution, Federal University of São Carlos, São Paulo, Brazil
| | - Rodrigo X. Soares
- Center of Biosciences, Department of Cellular Biology and Genetics, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Kátia C. Scortecci
- Center of Biosciences, Department of Cellular Biology and Genetics, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Roberto F. Artoni
- Department of Structural and Molecular Biology and Genetics, State University of Ponta Grossa, Ponta Grossa, Brazil
| | - Wagner F. Molina
- Center of Biosciences, Department of Cellular Biology and Genetics, Federal University of Rio Grande do Norte, Natal, Brazil
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18
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Abe K, Kawanishi T, Takeda H. Zic Genes in Teleosts: Their Roles in Dorsoventral Patterning in the Somite. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1046:141-156. [DOI: 10.1007/978-981-10-7311-3_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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19
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Cheung NKM, Nakamura R, Uno A, Kumagai M, Fukushima HS, Morishita S, Takeda H. Unlinking the methylome pattern from nucleotide sequence, revealed by large-scale in vivo genome engineering and methylome editing in medaka fish. PLoS Genet 2017; 13:e1007123. [PMID: 29267279 PMCID: PMC5755920 DOI: 10.1371/journal.pgen.1007123] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 01/05/2018] [Accepted: 11/23/2017] [Indexed: 11/17/2022] Open
Abstract
The heavily methylated vertebrate genomes are punctuated by stretches of poorly methylated DNA sequences that usually mark gene regulatory regions. It is known that the methylation state of these regions confers transcriptional control over their associated genes. Given its governance on the transcriptome, cellular functions and identity, genome-wide DNA methylation pattern is tightly regulated and evidently predefined. However, how is the methylation pattern determined in vivo remains enigmatic. Based on in silico and in vitro evidence, recent studies proposed that the regional hypomethylated state is primarily determined by local DNA sequence, e.g., high CpG density and presence of specific transcription factor binding sites. Nonetheless, the dependency of DNA methylation on nucleotide sequence has not been carefully validated in vertebrates in vivo. Herein, with the use of medaka (Oryzias latipes) as a model, the sequence dependency of DNA methylation was intensively tested in vivo. Our statistical modeling confirmed the strong statistical association between nucleotide sequence pattern and methylation state in the medaka genome. However, by manipulating the methylation state of a number of genomic sequences and reintegrating them into medaka embryos, we demonstrated that artificially conferred DNA methylation states were predominantly and robustly maintained in vivo, regardless of their sequences and endogenous states. This feature was also observed in the medaka transgene that had passed across generations. Thus, despite the observed statistical association, nucleotide sequence was unable to autonomously determine its own methylation state in medaka in vivo. Our results apparently argue against the notion of the governance on the DNA methylation by nucleotide sequence, but instead suggest the involvement of other epigenetic factors in defining and maintaining the DNA methylation landscape. Further investigation in other vertebrate models in vivo will be needed for the generalization of our observations made in medaka. The genomes of vertebrate animals are naturally and extensively modified by methylation. The DNA methylation is essential to normal functions of cells, hence the whole animal, since it governs gene expression. Defects in the establishment and maintenance of proper methylation pattern are commonly associated with various developmental abnormalities and diseases. How exactly is the normal pattern defined in vertebrate animals is not fully understood, but recent researches with computational analyses and cultured cells suggested that DNA sequence is a primary determinant of the methylation pattern. This study encompasses the first experiments that rigorously test this notion in whole animal (medaka fish). In statistical sense, we observed the very strong correlation between DNA sequence and methylation state. However, by introducing unmethylated and artificially methylated native genomic DNA sequences into the genome, we demonstrated that the artificially conferred methylation states were robustly maintained in the animal, independent of the sequence and native state. Our results thus demonstrate that genome-wide DNA methylation pattern is not autonomously determined by the DNA sequence, which underpins the vital role of DNA methylation pattern as a core epigenetic element.
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Affiliation(s)
- Napo K M Cheung
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Ryohei Nakamura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Ayako Uno
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Masahiko Kumagai
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hiroto S Fukushima
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.,CREST, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,CREST, Japan Science and Technology Agency, Kawaguchi, Japan
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20
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Ichikawa K, Tomioka S, Suzuki Y, Nakamura R, Doi K, Yoshimura J, Kumagai M, Inoue Y, Uchida Y, Irie N, Takeda H, Morishita S. Centromere evolution and CpG methylation during vertebrate speciation. Nat Commun 2017. [PMID: 29184138 DOI: 10.1038/s41467-017-01982-7.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Centromeres and large-scale structural variants evolve and contribute to genome diversity during vertebrate speciation. Here, we perform de novo long-read genome assembly of three inbred medaka strains that are derived from geographically isolated subpopulations and undergo speciation. Using single-molecule real-time (SMRT) sequencing, we obtain three chromosome-mapped genomes of length ~734, ~678, and ~744Mbp with a resource of twenty-two centromeric regions of length 20-345kbp. Centromeres are positionally conserved among the three strains and even between four pairs of chromosomes that were duplicated by the teleost-specific whole-genome duplication 320-350 million years ago. The centromeres do not all evolve at a similar pace; rather, centromeric monomers in non-acrocentric chromosomes evolve significantly faster than those in acrocentric chromosomes. Using methylation sensitive SMRT reads, we uncover centromeres are mostly hypermethylated but have hypomethylated sub-regions that acquire unique sequence compositions independently. These findings reveal the potential of non-acrocentric centromere evolution to contribute to speciation.
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Affiliation(s)
- Kazuki Ichikawa
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8583, Japan
| | - Shingo Tomioka
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8583, Japan
| | - Yuta Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8583, Japan
| | - Ryohei Nakamura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Koichiro Doi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8583, Japan
| | - Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8583, Japan
| | - Masahiko Kumagai
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yusuke Inoue
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yui Uchida
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Naoki Irie
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Shinich Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8583, Japan.
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21
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Centromere evolution and CpG methylation during vertebrate speciation. Nat Commun 2017; 8:1833. [PMID: 29184138 PMCID: PMC5705604 DOI: 10.1038/s41467-017-01982-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 10/31/2017] [Indexed: 11/10/2022] Open
Abstract
Centromeres and large-scale structural variants evolve and contribute to genome diversity during vertebrate speciation. Here, we perform de novo long-read genome assembly of three inbred medaka strains that are derived from geographically isolated subpopulations and undergo speciation. Using single-molecule real-time (SMRT) sequencing, we obtain three chromosome-mapped genomes of length ~734, ~678, and ~744Mbp with a resource of twenty-two centromeric regions of length 20–345kbp. Centromeres are positionally conserved among the three strains and even between four pairs of chromosomes that were duplicated by the teleost-specific whole-genome duplication 320–350 million years ago. The centromeres do not all evolve at a similar pace; rather, centromeric monomers in non-acrocentric chromosomes evolve significantly faster than those in acrocentric chromosomes. Using methylation sensitive SMRT reads, we uncover centromeres are mostly hypermethylated but have hypomethylated sub-regions that acquire unique sequence compositions independently. These findings reveal the potential of non-acrocentric centromere evolution to contribute to speciation. Centromeres and large-scale structural variants evolve and contribute to genome diversity during vertebrate speciation. Here Ichikawa et al perform de novo long-read genome assembly of three inbred medaka strains, and report long-range structure of centromeres and their methylation as well as correlation of structural variants with differential gene expression.
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22
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Hypomethylated domain-enriched DNA motifs prepattern the accessible nucleosome organization in teleosts. Epigenetics Chromatin 2017; 10:44. [PMID: 28931432 PMCID: PMC5607494 DOI: 10.1186/s13072-017-0152-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 09/13/2017] [Indexed: 12/22/2022] Open
Abstract
Background Gene promoters in vertebrate genomes show distinct chromatin features such as stably positioned nucleosome array and DNA hypomethylation. The nucleosomes are known to have certain sequence preferences, and the prediction of nucleosome positioning from DNA sequence has been successful in some organisms such as yeast. However, at gene promoters where nucleosomes are much more stably positioned than in other regions, the sequence-based model has failed to work well, and sequence-independent mechanisms have been proposed. Results Using DNase I-seq in medaka embryos, we demonstrated that hypomethylated domains (HMDs) specifically possess accessible nucleosome organization with longer linkers, and we reassessed the DNA sequence preference for nucleosome positioning in these specific regions. Remarkably, we found with a supervised machine learning algorithm, k-mer SVM, that nucleosome positioning in HMDs is accurately predictable from DNA sequence alone. Specific short sequences (6-mers) that contribute to the prediction are specifically enriched in HMDs and distribute periodically with approximately 200-bp intervals which prepattern the position of accessible linkers. Surprisingly, the sequence preference of the nucleosome and linker in HMDs is opposite from that reported previously. Furthermore, the periodicity of specific motifs at hypomethylated promoters was conserved in zebrafish. Conclusion This study reveals strong link between nucleosome positioning and DNA sequence at vertebrate promoters, and we propose hypomethylated DNA-specific regulation of nucleosome positioning. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0152-2) contains supplementary material, which is available to authorized users.
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23
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Complete fusion of a transposon and herpesvirus created the Teratorn mobile element in medaka fish. Nat Commun 2017; 8:551. [PMID: 28916771 PMCID: PMC5601938 DOI: 10.1038/s41467-017-00527-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 07/05/2017] [Indexed: 01/02/2023] Open
Abstract
Mobile genetic elements (e.g., transposable elements and viruses) display significant diversity with various life cycles, but how novel elements emerge remains obscure. Here, we report a giant (180-kb long) transposon, Teratorn, originally identified in the genome of medaka, Oryzias latipes. Teratorn belongs to the piggyBac superfamily and retains the transposition activity. Remarkably, Teratorn is largely derived from a herpesvirus of the Alloherpesviridae family that could infect fish and amphibians. Genomic survey of Teratorn-like elements reveals that some of them exist as a fused form between piggyBac transposon and herpesvirus genome in teleosts, implying the generality of transposon-herpesvirus fusion. We propose that Teratorn was created by a unique fusion of DNA transposon and herpesvirus, leading to life cycle shift. Our study supports the idea that recombination is the key event in generation of novel mobile genetic elements. Teratorn is a large mobile genetic element originally identified in the small teleost fish medaka. Here, the authors show that Teratorn is derived from the fusion of a piggyBac superfamily DNA transposon and an alloherpesvirus and that it is widely found across teleost fish.
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24
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Wang MY, Takeuchi H. Individual recognition and the 'face inversion effect' in medaka fish ( Oryzias latipes). eLife 2017; 6:e24728. [PMID: 28693720 PMCID: PMC5505697 DOI: 10.7554/elife.24728] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 06/09/2017] [Indexed: 11/24/2022] Open
Abstract
Individual recognition (IR) is essential for maintaining various social interactions in a group, and face recognition is one of the most specialised cognitive abilities in IR. We used both a mating preference system and an electric shock conditioning experiment to test IR ability in medaka, and found that signals near the face are important. Medaka required more time to discriminate vertically inverted faces, but not horizontally shifted faces or inverted non-face objects. The ability may be comparable to the classic 'face inversion effect' in humans and some other mammals. Extra patterns added to the face also did not influence the IR. These findings suggest the possibility that the process of face recognition may differ from that used for other objects. The complex form of recognition may promote specific processing adaptations, although the mechanisms and neurological bases might differ in mammals and medaka. The ability to recognise other individuals is important for shaping animal societies.
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Affiliation(s)
- Mu-Yun Wang
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- The Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Hideaki Takeuchi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- The Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
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Fukuda K, Inoguchi Y, Ichiyanagi K, Ichiyanagi T, Go Y, Nagano M, Yanagawa Y, Takaesu N, Ohkawa Y, Imai H, Sasaki H. Evolution of the sperm methylome of primates is associated with retrotransposon insertions and genome instability. Hum Mol Genet 2017. [DOI: 10.1093/hmg/ddx236] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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Dynamics of DNA methylomes underlie oyster development. PLoS Genet 2017; 13:e1006807. [PMID: 28594821 PMCID: PMC5481141 DOI: 10.1371/journal.pgen.1006807] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 06/22/2017] [Accepted: 05/08/2017] [Indexed: 12/26/2022] Open
Abstract
DNA methylation is a critical epigenetic regulator of development in mammals and social insects, but its significance in development outside these groups is not understood. Here we investigated the genome-wide dynamics of DNA methylation in a mollusc model, the oyster Crassostrea gigas, from the egg to the completion of organogenesis. Large-scale methylation maps reveal that the oyster genome displays a succession of methylated and non methylated regions, which persist throughout development. Differentially methylated regions (DMRs) are strongly regulated during cleavage and metamorphosis. The distribution and levels of methylated DNA within genomic features (exons, introns, promoters, repeats and transposons) show different developmental lansdscapes marked by a strong increase in the methylation of exons against introns after metamorphosis. Kinetics of methylation in gene-bodies correlate to their transcription regulation and to distinct functional gene clusters, and DMRs at cleavage and metamorphosis bear the genes functionally related to these steps, respectively. This study shows that DNA methylome dynamics underlie development through transcription regulation in the oyster, a lophotrochozoan species. To our knowledge, this is the first demonstration of such epigenetic regulation outside vertebrates and ecdysozoan models, bringing new insights into the evolution and the epigenetic regulation of developmental processes. Elucidating the mechanisms which govern the development of multicellular animals and their evolution is a fundamental task. Epigenetic mechanisms like DNA methylation have recently emerged as critical regulators of mammalian development through the control of genes that determine the identity of cells and the transmission of parental imprints. In invertebrates however, DNA is mostly unmethylated and does not play a role in development except in the peculiar case of social insects. Therefore the significance of DNA methylation in development is thought to be restricted to vertebrates, and thereby considered a recent evolutionary acquisition, and the situation in more distant organisms is unknown. Here we investigated the dynamics of genome-wide DNA methylation patterns in a mollusc, the oyster C. gigas, throughout its development. We found that the dynamics of DNA methylation correspond to the expression dynamics of distinct functional gene clusters that control two critical development steps, cleavage and metamorphosis, and we provide insights into the underlying molecular mechanisms in a non-vertebrate species. These findings challenge the present considerations on the evolution of developmental processes and their epigenetic regulation, and open a new area of research in molecular and developmental biology in invertebrates.
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Uno A, Nakamura R, Tsukahara T, Qu W, Sugano S, Suzuki Y, Morishita S, Takeda H. Comparative Analysis of Genome and Epigenome in Closely Related Medaka Species Identifies Conserved Sequence Preferences for DNA Hypomethylated Domains. Zoolog Sci 2017; 33:358-65. [PMID: 27498795 DOI: 10.2108/zs160030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The genomes of vertebrates are globally methylated, but a small portion of genomic regions are known to be hypomethylated. Although hypomethylated domains (HMDs) have been implicated in transcriptional regulation in various ways, how a HMD is determined in a particular genomic region remains elusive. To search for DNA motifs essential for the formation of HMDs, we performed the genome-wide comparative analysis of genome and DNA methylation patterns of the two medaka inbred lines, Hd-rRII1 and HNI-II, which are derived from northern and southern subpopulations of Japan and exhibit high levels of genetic variations (SNP, ∼ 3%). We successfully mapped > 70% of HMDs in both genomes and found that the majority of those mapped HMDs are conserved between the two lines (common HMDs). Unexpectedly, the average genetic variations are similar in the common HMD and other genome regions. However, we identified short well-conserved motifs that are specifically enriched in HMDs, suggesting that they may play roles in the establishment of HMDs in the medaka genome.
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Affiliation(s)
- Ayako Uno
- 1 Department of Biological Sciences, Graduate School of Science,The University of Tokyo, Tokyo 113-0033, Japan
| | - Ryohei Nakamura
- 1 Department of Biological Sciences, Graduate School of Science,The University of Tokyo, Tokyo 113-0033, Japan
| | - Tatsuya Tsukahara
- 1 Department of Biological Sciences, Graduate School of Science,The University of Tokyo, Tokyo 113-0033, Japan.,2 Department of Neurobiology, Harvard Medical School, 220 Longwood Ave,Boston, Massachusetts 02115, USA
| | - Wei Qu
- 3 Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences,The University of Tokyo, Kashiwa 277-8562, Japan
| | - Sumio Sugano
- 3 Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences,The University of Tokyo, Kashiwa 277-8562, Japan
| | - Yutaka Suzuki
- 3 Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences,The University of Tokyo, Kashiwa 277-8562, Japan
| | - Shinichi Morishita
- 3 Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences,The University of Tokyo, Kashiwa 277-8562, Japan
| | - Hiroyuki Takeda
- 1 Department of Biological Sciences, Graduate School of Science,The University of Tokyo, Tokyo 113-0033, Japan.,4 CREST, Japan Science and Technology Agency
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Rehimi R, Nikolic M, Cruz-Molina S, Tebartz C, Frommolt P, Mahabir E, Clément-Ziza M, Rada-Iglesias A. Epigenomics-Based Identification of Major Cell Identity Regulators within Heterogeneous Cell Populations. Cell Rep 2016; 17:3062-3076. [DOI: 10.1016/j.celrep.2016.11.046] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 10/05/2016] [Accepted: 11/14/2016] [Indexed: 12/21/2022] Open
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Morozova I, Flegontov P, Mikheyev AS, Bruskin S, Asgharian H, Ponomarenko P, Klyuchnikov V, ArunKumar G, Prokhortchouk E, Gankin Y, Rogaev E, Nikolsky Y, Baranova A, Elhaik E, Tatarinova TV. Toward high-resolution population genomics using archaeological samples. DNA Res 2016; 23:295-310. [PMID: 27436340 PMCID: PMC4991838 DOI: 10.1093/dnares/dsw029] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 05/22/2016] [Indexed: 12/30/2022] Open
Abstract
The term ‘ancient DNA’ (aDNA) is coming of age, with over 1,200 hits in the PubMed database, beginning in the early 1980s with the studies of ‘molecular paleontology’. Rooted in cloning and limited sequencing of DNA from ancient remains during the pre-PCR era, the field has made incredible progress since the introduction of PCR and next-generation sequencing. Over the last decade, aDNA analysis ushered in a new era in genomics and became the method of choice for reconstructing the history of organisms, their biogeography, and migration routes, with applications in evolutionary biology, population genetics, archaeogenetics, paleo-epidemiology, and many other areas. This change was brought by development of new strategies for coping with the challenges in studying aDNA due to damage and fragmentation, scarce samples, significant historical gaps, and limited applicability of population genetics methods. In this review, we describe the state-of-the-art achievements in aDNA studies, with particular focus on human evolution and demographic history. We present the current experimental and theoretical procedures for handling and analysing highly degraded aDNA. We also review the challenges in the rapidly growing field of ancient epigenomics. Advancement of aDNA tools and methods signifies a new era in population genetics and evolutionary medicine research.
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Affiliation(s)
- Irina Morozova
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic Bioinformatics Center, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Sergey Bruskin
- Vavilov Institute of General Genetics RAS, Moscow, Russia
| | - Hosseinali Asgharian
- Department of Computational and Molecular Biology, University of Southern California, Los Angeles, CA, USA
| | - Petr Ponomarenko
- Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA
| | | | | | - Egor Prokhortchouk
- Research Center of Biotechnology RAS, Moscow, Russia Department of Biology, Lomonosov Moscow State University, Russia
| | | | - Evgeny Rogaev
- Vavilov Institute of General Genetics RAS, Moscow, Russia University of Massachusetts Medical School, Worcester, MA, USA
| | - Yuri Nikolsky
- Vavilov Institute of General Genetics RAS, Moscow, Russia F1 Genomics, San Diego, CA, USA School of Systems Biology, George Mason University, VA, USA
| | - Ancha Baranova
- School of Systems Biology, George Mason University, VA, USA Research Centre for Medical Genetics, Moscow, Russia Atlas Biomed Group, Moscow, Russia
| | - Eran Elhaik
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield, South Yorkshire, UK
| | - Tatiana V Tatarinova
- Bioinformatics Center, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA
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Bhandari RK. Medaka as a model for studying environmentally induced epigenetic transgenerational inheritance of phenotypes. ENVIRONMENTAL EPIGENETICS 2016; 2:dvv010. [PMID: 29492282 PMCID: PMC5804509 DOI: 10.1093/eep/dvv010] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 11/24/2015] [Accepted: 12/08/2015] [Indexed: 05/29/2023]
Abstract
Ability of environmental stressors to induce transgenerational diseases has been experimentally demonstrated in plants, worms, fish, and mammals, indicating that exposures affect not only human health but also fish and ecosystem health. Small aquarium fish have been reliable model to study genetic and epigenetic basis of development and disease. Additionally, fish can also provide better, economic opportunity to study transgenerational inheritance of adverse health and epigenetic mechanisms. Molecular mechanisms underlying germ cell development in fish are comparable to those in mammals and humans. This review will provide a short overview of long-term effects of environmental chemical contaminant exposure in various models, associated epigenetic mechanisms, and a perspective on fish as model to study environmentally induced transgenerational inheritance of altered phenotypes.
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Affiliation(s)
- Ramji K Bhandari
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, MO 65211, USA
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Tet1 and Tet2 Protect DNA Methylation Canyons against Hypermethylation. Mol Cell Biol 2015; 36:452-61. [PMID: 26598602 PMCID: PMC4719427 DOI: 10.1128/mcb.00587-15] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 11/12/2015] [Indexed: 12/20/2022] Open
Abstract
DNA methylation is a dynamic epigenetic modification with an important role in cell fate specification and reprogramming. The Ten eleven translocation (Tet) family of enzymes converts 5-methylcytosine to 5-hydroxymethylcytosine, which promotes passive DNA demethylation and functions as an intermediate in an active DNA demethylation process. Tet1/Tet2 double-knockout mice are characterized by developmental defects and epigenetic instability, suggesting a requirement for Tet-mediated DNA demethylation for the proper regulation of gene expression during differentiation. Here, we used whole-genome bisulfite and transcriptome sequencing to characterize the underlying mechanisms. Our results uncover the hypermethylation of DNA methylation canyons as the genomic key feature of Tet1/Tet2 double-knockout mouse embryonic fibroblasts. Canyon hypermethylation coincided with disturbed regulation of associated genes, suggesting a mechanistic explanation for the observed Tet-dependent differentiation defects. Based on these results, we propose an important regulatory role of Tet-dependent DNA demethylation for the maintenance of DNA methylation canyons, which prevents invasive DNA methylation and allows functional regulation of canyon-associated genes.
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LSD1/KDM1A promotes hematopoietic commitment of hemangioblasts through downregulation of Etv2. Proc Natl Acad Sci U S A 2015; 112:13922-7. [PMID: 26512114 DOI: 10.1073/pnas.1517326112] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The hemangioblast is a progenitor cell with the capacity to give rise to both hematopoietic and endothelial progenitors. Currently, the regulatory mechanisms underlying hemangioblast formation are being elucidated, whereas those controllers for the selection of hematopoietic or endothelial fates still remain a mystery. To answer these questions, we screened for zebrafish mutants that have defects in the hemangioblast expression of Gata1, which is never expressed in endothelial progenitors. One of the isolated mutants, it627, showed not only down-regulation of hematopoietic genes but also up-regulation of endothelial genes. We identified the gene responsible for the it627 mutant as the zebrafish homolog of Lys-specific demethylase 1 (LSD1/KDM1A). Surprisingly, the hematopoietic defects in lsd1(it627) embryos were rescued by the gene knockdown of the Ets variant 2 gene (etv2), an essential regulator for vasculogenesis. Our results suggest that the LSD1-dependent shutdown of Etv2 gene expression may be a significant event required for hemangioblasts to initiate hematopoietic differentiation.
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Genome-wide epigenetic cross-talk between DNA methylation and H3K27me3 in zebrafish embryos. GENOMICS DATA 2015; 6:7-9. [PMID: 26697317 PMCID: PMC4664660 DOI: 10.1016/j.gdata.2015.07.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 07/17/2015] [Indexed: 01/08/2023]
Abstract
DNA methylation and histone modifications are epigenetic marks implicated in the complex regulation of vertebrate embryogenesis. The cross-talk between DNA methylation and Polycomb-dependent H3K27me3 histone mark has been reported in a number of organisms [1], [2], [3], [4], [5], [6], [7] and both marks are known to be required for proper developmental progression. Here we provide genome-wide DNA methylation (MethylCap-seq) and H3K27me3 (ChIP-seq) maps for three stages (dome, 24 hpf and 48 hpf) of zebrafish (Danio rerio) embryogenesis, as well as all analytical and methodological details associated with the generation of this dataset. We observe a strong antagonism between the two epigenetic marks present in CpG islands and their compatibility throughout the bulk of the genome, as previously reported in mammalian ESC lines (Brinkman et al., 2012). Next generation sequencing data linked to this project have been deposited in the Gene Expression Omnibus (GEO) database under accession numbers GSE35050 and GSE70847.
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Ichikawa K, Morishita S. A linear time algorithm for detecting long genomic regions enriched with a specific combination of epigenetic states. BMC Genomics 2015; 16 Suppl 2:S8. [PMID: 25708947 PMCID: PMC4331722 DOI: 10.1186/1471-2164-16-s2-s8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Background Epigenetic modifications are essential for controlling gene expression. Recent studies have shown that not only single epigenetic modifications but also combinations of multiple epigenetic modifications play vital roles in gene regulation. A striking example is the long hypomethylated regions enriched with modified H3K27me3 (called, "K27HMD" regions), which are exposed to suppress the expression of key developmental genes relevant to cellular development and differentiation during embryonic stages in vertebrates. It is thus a biologically important issue to develop an effective optimization algorithm for detecting long DNA regions (e.g., >4 kbp in size) that harbor a specific combination of epigenetic modifications (e.g., K27HMD regions). However, to date, optimization algorithms for these purposes have received little attention, and available methods are still heuristic and ad hoc. Results In this paper, we propose a linear time algorithm for calculating a set of non-overlapping regions that maximizes the sum of similarities between the vector of focal epigenetic states and the vectors of raw epigenetic states at DNA positions in the set of regions. The average elapsed time to process the epigenetic data of any of human chromosomes was less than 2 seconds on an Intel Xeon CPU. To demonstrate the effectiveness of the algorithm, we estimated large K27HMD regions in the medaka and human genomes using our method, ChromHMM, and a heuristic method. Conclusions We confirmed that the advantages of our method over those of the two other methods. Our method is flexible enough to handle other types of epigenetic combinations. The program that implements the method is called "CSMinfinder" and is made available at: http://mlab.cb.k.u-tokyo.ac.jp/~ichikawa/Segmentation/
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