1
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Karanwal S, Pal A, Chera JS, Batra V, Kumaresan A, Datta TK, Kumar R. Identification of protein candidates in spermatozoa of water buffalo ( Bubalus bubalis) bulls helps in predicting their fertility status. Front Cell Dev Biol 2023; 11:1119220. [PMID: 36891514 PMCID: PMC9986327 DOI: 10.3389/fcell.2023.1119220] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/07/2023] [Indexed: 02/22/2023] Open
Abstract
The water buffalo (Bubalus bubalis) is an indispensable part of the Indian dairy sector and in several instances, the farmers incur economic losses due to failed pregnancy after artificial insemination (AI). One of the key factors for the failure of conception is the use of semen from the bulls of low fertilizing potential and hence, it becomes important to predict the fertility status before performing AI. In this study, the global proteomic profile of high fertile (HF) and low fertile (LF) buffalo bull spermatozoa was established using a high-throughput LC-MS/MS technique. A total of 1,385 proteins (≥1 high-quality PSM/s, ≥1 unique peptides, p < 0.05, FDR < 0.01) were identified out of which, 1,002 were common between both the HF and LF groups while 288 and 95 proteins were unique to HF and LF groups respectively. We observed 211 and 342 proteins were significantly high (log Fc ≥ 2) and low abundant (log Fc ≤ 0.5) in HF spermatozoa (p < 0.05). Gene ontology analysis revealed that the fertility associated high abundant proteins in HF were involved in spermatogenesis, sperm motility, acrosome integrity, zona pellucida binding and other associated sperm functions. Besides this, the low abundant proteins in HF were involved in glycolysis, fatty acid degradation and inflammation. Furthermore, fertility related differentially abundant proteins (DAPs) on sperm viz., AKAP3, Sp17, and DLD were validated through Western blotting and immunocytochemistry which was in coherence with the LC-MS/MS data. The DAPs identified in this study may be used as potential protein candidates for predicting fertility in buffaloes. Our findings provide an opportunity in mitigating the economic losses that farmers incur due to male infertility.
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Affiliation(s)
- Seema Karanwal
- Animal Genomics Laboratory, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, India
| | - Ankit Pal
- Animal Genomics Laboratory, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, India
| | - Jatinder Singh Chera
- Animal Genomics Laboratory, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, India
| | - Vipul Batra
- Animal Genomics Laboratory, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, India
| | - Arumugam Kumaresan
- Theriogenelogy Laboratory, SRS of National Dairy Research Institute, Bengaluru, India
| | - Tirtha K Datta
- Animal Genomics Laboratory, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, India
| | - Rakesh Kumar
- Animal Genomics Laboratory, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, India
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2
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Zhao C, Biondic S, Vandal K, Björklund ÅK, Hagemann-Jensen M, Sommer TM, Canizo J, Clark S, Raymond P, Zenklusen DR, Rivron N, Reik W, Petropoulos S. Single-cell multi-omics of human preimplantation embryos shows susceptibility to glucocorticoids. Genome Res 2022; 32:gr.276665.122. [PMID: 35948369 PMCID: PMC9528977 DOI: 10.1101/gr.276665.122] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 08/04/2022] [Indexed: 11/25/2022]
Abstract
The preconceptual, intrauterine, and early life environments can have a profound and long-lasting impact on the developmental trajectories and health outcomes of the offspring. Given the relatively low success rates of assisted reproductive technologies (ART; ∼25%), additives and adjuvants, such as glucocorticoids, are used to improve the success rate. Considering the dynamic developmental events that occur during this window, these exposures may alter blastocyst formation at a molecular level, and as such, affect not only the viability of the embryo and the ability of the blastocyst to implant, but also the developmental trajectory of the first three cell lineages, ultimately influencing the physiology of the embryo. In this study, we present a comprehensive single-cell transcriptome, methylome, and small RNA atlas in the day 7 human embryo. We show that, despite no change in morphology and developmental features, preimplantation glucocorticoid exposure reprograms the molecular profile of the TE lineage, and these changes are associated with an altered metabolic and inflammatory response. Our data also suggest that glucocorticoids can precociously mature the TE sublineages, supported by the presence of extravillous trophoblast markers in the polar sublineage and presence of X Chromosome dosage compensation. Further, we have elucidated that epigenetic regulation-DNA methylation and microRNAs (miRNAs)-likely underlies the transcriptional changes observed. This study suggests that exposures to exogenous compounds during preimplantation may unintentionally reprogram the human embryo, possibly leading to suboptimal development and longer-term health outcomes.
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Affiliation(s)
- Cheng Zhao
- Department of Clinical Science, Intervention and Technology, Division of Obstetrics and Gynecology, Karolinska Institutet, 14186 Stockholm, Sweden
| | - Savana Biondic
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Axe Immunopathologie, H2X 0A9 Montréal, Canada
- Département de Médecine, Université de Montréal, H3T 1J4 Montréal, Canada
| | - Katherine Vandal
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Axe Immunopathologie, H2X 0A9 Montréal, Canada
- Département de Médecine, Université de Montréal, H3T 1J4 Montréal, Canada
| | - Åsa K Björklund
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, SE-752 37 Uppsala, Sweden
| | | | - Theresa Maria Sommer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Jesica Canizo
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Axe Immunopathologie, H2X 0A9 Montréal, Canada
- Département de Médecine, Université de Montréal, H3T 1J4 Montréal, Canada
| | - Stephen Clark
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Pascal Raymond
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, H3T 1J4 Montréal, Canada
| | - Daniel R Zenklusen
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, H3T 1J4 Montréal, Canada
| | - Nicolas Rivron
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Wolf Reik
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom
- Wellcome Sanger Institute, Cambridge CB10 1RQ, United Kingdom
- Center for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
| | - Sophie Petropoulos
- Department of Clinical Science, Intervention and Technology, Division of Obstetrics and Gynecology, Karolinska Institutet, 14186 Stockholm, Sweden
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Axe Immunopathologie, H2X 0A9 Montréal, Canada
- Département de Médecine, Université de Montréal, H3T 1J4 Montréal, Canada
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3
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Dijkwel Y, Tremethick DJ. The Role of the Histone Variant H2A.Z in Metazoan Development. J Dev Biol 2022; 10:jdb10030028. [PMID: 35893123 PMCID: PMC9326617 DOI: 10.3390/jdb10030028] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/12/2022] [Accepted: 06/23/2022] [Indexed: 12/10/2022] Open
Abstract
During the emergence and radiation of complex multicellular eukaryotes from unicellular ancestors, transcriptional systems evolved by becoming more complex to provide the basis for this morphological diversity. The way eukaryotic genomes are packaged into a highly complex structure, known as chromatin, underpins this evolution of transcriptional regulation. Chromatin structure is controlled by a variety of different epigenetic mechanisms, including the major mechanism for altering the biochemical makeup of the nucleosome by replacing core histones with their variant forms. The histone H2A variant H2A.Z is particularly important in early metazoan development because, without it, embryos cease to develop and die. However, H2A.Z is also required for many differentiation steps beyond the stage that H2A.Z-knockout embryos die. H2A.Z can facilitate the activation and repression of genes that are important for pluripotency and differentiation, and acts through a variety of different molecular mechanisms that depend upon its modification status, its interaction with histone and nonhistone partners, and where it is deposited within the genome. In this review, we discuss the current knowledge about the different mechanisms by which H2A.Z regulates chromatin function at various developmental stages and the chromatin remodeling complexes that determine when and where H2A.Z is deposited.
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4
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Izquierdo-Torres E, Hernández-Oliveras A, Lozano-Arriaga D, Zarain-Herzberg Á. Obesity, the other pandemic: linking diet and carcinogenesis by epigenetic mechanisms. J Nutr Biochem 2022; 108:109092. [PMID: 35718098 DOI: 10.1016/j.jnutbio.2022.109092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 03/19/2022] [Accepted: 05/30/2022] [Indexed: 11/25/2022]
Abstract
Both obesity and cancer are complex medical conditions that are considered public health problems. The influence of obesity on the predisposition to develop various types of cancer has been observed in a wide variety of studies. Due to their importance as public health problems, and the close relationship between both conditions, it is important to be able to understand and associate them mechanistically. In this review article, we intend to go a little further, by finding relationships between lifestyle, which can lead a person to develop obesity, and how it influences at the cellular and molecular level, affecting gene expression to favor signaling pathways or transcriptional programs involved in cancer. We describe how products of metabolism and intermediate metabolism can affect chromatin structure, participating in the regulation (or dysregulation) of gene expression, and we show an analysis of genes that are responsive to diets high in sugar and fat, and how their epigenetic landscape is altered.
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Affiliation(s)
- Eduardo Izquierdo-Torres
- Departamento de Bioquímica, Facultad de Medicina. Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Andrés Hernández-Oliveras
- Departamento de Bioquímica, Facultad de Medicina. Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Dalia Lozano-Arriaga
- Departamento de Bioquímica, Facultad de Medicina. Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Ángel Zarain-Herzberg
- Departamento de Bioquímica, Facultad de Medicina. Universidad Nacional Autónoma de México, Ciudad de México, México.
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5
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Rajam SM, Varghese PC, Dutta D. Histone Chaperones as Cardinal Players in Development. Front Cell Dev Biol 2022; 10:767773. [PMID: 35445016 PMCID: PMC9014011 DOI: 10.3389/fcell.2022.767773] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 03/03/2022] [Indexed: 11/25/2022] Open
Abstract
Dynamicity and flexibility of the chromatin landscape are critical for most of the DNA-dependent processes to occur. This higher-order packaging of the eukaryotic genome into the chromatin is mediated by histones and associated non-histone proteins that determine the states of chromatin. Histone chaperones- “the guardian of genome stability and epigenetic information” controls the chromatin accessibility by escorting the nucleosomal and non-nucleosomal histones as well as their variants. This distinct group of molecules is involved in all facets of histone metabolism. The selectivity and specificity of histone chaperones to the histones determine the maintenance of the chromatin in an open or closed state. This review highlights the functional implication of the network of histone chaperones in shaping the chromatin function in the development of an organism. Seminal studies have reported embryonic lethality at different stages of embryogenesis upon perturbation of some of the chaperones, suggesting their essentiality in development. We hereby epitomize facts and functions that emphasize the relevance of histone chaperones in orchestrating different embryonic developmental stages starting from gametogenesis to organogenesis in multicellular organisms.
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Affiliation(s)
- Sruthy Manuraj Rajam
- Regenerative Biology Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, India.,Manipal Academy of Higher Education, Manipal, India
| | - Pallavi Chinnu Varghese
- Regenerative Biology Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, India.,Manipal Academy of Higher Education, Manipal, India
| | - Debasree Dutta
- Regenerative Biology Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, India
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6
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Zhang C, Macchi F, Magnani E, Sadler KC. Chromatin states shaped by an epigenetic code confer regenerative potential to the mouse liver. Nat Commun 2021; 12:4110. [PMID: 34226551 PMCID: PMC8257577 DOI: 10.1038/s41467-021-24466-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 06/10/2021] [Indexed: 02/06/2023] Open
Abstract
We hypothesized that the highly controlled pattern of gene expression that is essential for liver regeneration is encoded by an epigenetic code set in quiescent hepatocytes. Here we report that epigenetic and transcriptomic profiling of quiescent and regenerating mouse livers define chromatin states that dictate gene expression and transposon repression. We integrate ATACseq and DNA methylation profiling with ChIPseq for the histone marks H3K4me3, H3K27me3 and H3K9me3 and the histone variant H2AZ to identify 6 chromatin states with distinct functional characteristics. We show that genes involved in proliferation reside in active states, but are marked with H3K27me3 and silenced in quiescent livers. We find that during regeneration, H3K27me3 is depleted from their promoters, facilitating their dynamic expression. These findings demonstrate that hepatic chromatin states in quiescent livers predict gene expression and that pro-regenerative genes are maintained in active chromatin states, but are restrained by H3K27me3, permitting a rapid and synchronized response during regeneration.
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Affiliation(s)
- Chi Zhang
- grid.440573.1Biology Program, NYU Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Filippo Macchi
- grid.440573.1Biology Program, NYU Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Elena Magnani
- grid.440573.1Biology Program, NYU Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Kirsten C. Sadler
- grid.440573.1Biology Program, NYU Abu Dhabi, Abu Dhabi, United Arab Emirates
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7
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Marchione AD, Thompson Z, Kathrein KL. DNA methylation and histone modifications are essential for regulation of stem cell formation and differentiation in zebrafish development. Brief Funct Genomics 2021:elab022. [PMID: 33782688 DOI: 10.1093/bfgp/elab022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/05/2021] [Accepted: 03/09/2021] [Indexed: 01/21/2023] Open
Abstract
The complex processes necessary for embryogenesis require a gene regulatory network that is complex and systematic. Gene expression regulates development and organogenesis, but this process is altered and fine-tuned by epigenetic regulators that facilitate changes in the chromatin landscape. Epigenetic regulation of embryogenesis adjusts the chromatin structure by modifying both DNA through methylation and nucleosomes through posttranslational modifications of histone tails. The zebrafish is a well-characterized model organism that is a quintessential tool for studying developmental biology. With external fertilization, low cost and high fecundity, the zebrafish are an efficient tool for studying early developmental stages. Genetic manipulation can be performed in vivo resulting in quick identification of gene function. Large-scale genome analyses including RNA sequencing, chromatin immunoprecipitation and chromatin structure all are feasible in the zebrafish. In this review, we highlight the key events in zebrafish development where epigenetic regulation plays a critical role from the early stem cell stages through differentiation and organogenesis.
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8
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Zhao BW, Sun SM, Xu K, Li YY, Lei WL, Li L, Liu SL, Ouyang YC, Sun QY, Wang ZB. FBXO34 Regulates the G2/M Transition and Anaphase Entry in Meiotic Oocytes. Front Cell Dev Biol 2021; 9:647103. [PMID: 33842473 PMCID: PMC8027338 DOI: 10.3389/fcell.2021.647103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/22/2021] [Indexed: 11/17/2022] Open
Abstract
There are two important events in oocyte meiotic maturation, the G2/M transition and metaphase I progression. Thousands of proteins participate in regulating oocyte maturation, which highlights the importance of the ubiquitin proteasome system (UPS) in regulating protein synthesis and degradation. Skp1–Cullin–F-box (SCF) complexes, as the best characterized ubiquitin E3 ligases in the UPS, specifically recognize their substrates. F-box proteins, as the variable adaptors of SCF, can bind substrates specifically. Little is known about the functions of the F-box proteins in oocyte maturation. In this study, we found that depletion of FBXO34, an F-box protein, led to failure of oocyte meiotic resumption due to a low activity of MPF, and this phenotype could be rescued by exogenous overexpression of CCNB1. Strikingly, overexpression of FBXO34 promoted germinal vesicle breakdown (GVBD), but caused continuous activation of spindle assembly checkpoint (SAC) and MI arrest of oocytes. Here, we demonstrated that FBXO34 regulated both the G2/M transition and anaphase entry in meiotic oocytes.
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Affiliation(s)
- Bing-Wang Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Si-Min Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Ke Xu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuan-Yuan Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Wen-Long Lei
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Li Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Sai-Li Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ying-Chun Ouyang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qing-Yuan Sun
- Fertility Preservation Lab, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Zhen-Bo Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
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9
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Creighton SD, Stefanelli G, Reda A, Zovkic IB. Epigenetic Mechanisms of Learning and Memory: Implications for Aging. Int J Mol Sci 2020; 21:E6918. [PMID: 32967185 PMCID: PMC7554829 DOI: 10.3390/ijms21186918] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/16/2020] [Accepted: 09/17/2020] [Indexed: 12/15/2022] Open
Abstract
The neuronal epigenome is highly sensitive to external events and its function is vital for producing stable behavioral outcomes, such as the formation of long-lasting memories. The importance of epigenetic regulation in memory is now well established and growing evidence points to altered epigenome function in the aging brain as a contributing factor to age-related memory decline. In this review, we first summarize the typical role of epigenetic factors in memory processing in a healthy young brain, then discuss the aspects of this system that are altered with aging. There is general agreement that many epigenetic marks are modified with aging, but there are still substantial inconsistencies in the precise nature of these changes and their link with memory decline. Here, we discuss the potential source of age-related changes in the epigenome and their implications for therapeutic intervention in age-related cognitive decline.
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Affiliation(s)
- Samantha D. Creighton
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada; (S.D.C.); (G.S.)
| | - Gilda Stefanelli
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada; (S.D.C.); (G.S.)
| | - Anas Reda
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S, Canada;
| | - Iva B. Zovkic
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada; (S.D.C.); (G.S.)
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S, Canada;
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10
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Abstract
Histone variants regulate chromatin accessibility and gene transcription. Given their distinct properties and functions, histone varint substitutions allow for profound alteration of nucleosomal architecture and local chromatin landscape. Skeletal myogenesis driven by the key transcription factor MyoD is characterized by precise temporal regulation of myogenic genes. Timed substitution of variants within the nucleosomes provides a powerful means to ensure sequential expression of myogenic genes. Indeed, growing evidence has shown H3.3, H2A.Z, macroH2A, and H1b to be critical for skeletal myogenesis. However, the relative importance of various histone variants and their associated chaperones in myogenesis is not fully appreciated. In this review, we summarize the role that histone variants play in altering chromatin landscape to ensure proper muscle differentiation. The temporal regulation and cross talk between histones variants and their chaperones in conjunction with other forms of epigenetic regulation could be critical to understanding myogenesis and their involvement in myopathies.
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Affiliation(s)
- Nandini Karthik
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore , Singapore
| | - Reshma Taneja
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore , Singapore
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11
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Cavalieri V. Histones, Their Variants and Post-translational Modifications in Zebrafish Development. Front Cell Dev Biol 2020; 8:456. [PMID: 32582716 PMCID: PMC7289917 DOI: 10.3389/fcell.2020.00456] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 05/15/2020] [Indexed: 01/01/2023] Open
Abstract
Complex multi-cellular organisms are shaped starting from a single-celled zygote, owing to elaborate developmental programs. These programs involve several layers of regulation to orchestrate the establishment of progressively diverging cell type-specific gene expression patterns. In this scenario, epigenetic modifications of chromatin are central in influencing spatiotemporal patterns of gene transcription. In fact, it is generally recognized that epigenetic changes of chromatin states impact on the accessibility of genomic DNA to regulatory proteins. Several lines of evidence highlighted that zebrafish is an excellent vertebrate model for research purposes in the field of developmental epigenetics. In this review, I focus on the dynamic roles recently emerged for histone post-translational modifications (PTMs), histone modifying enzymes, histone variants and histone themselves in the coordination between the precise execution of transcriptional programs and developmental progression in zebrafish. In particular, I first outline a synopsis of the current state of knowledge in this field during early embryogenesis. Then, I present a survey of histone-based epigenetic mechanisms occurring throughout morphogenesis, with a stronger emphasis on cardiac formation. Undoubtedly, the issues addressed in this review take on particular importance in the emerging field of comparative biology of epigenetics, as well as in translational research.
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Affiliation(s)
- Vincenzo Cavalieri
- Laboratory of Molecular Biology and Functional Genomics, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy.,Zebrafish Laboratory, Advanced Technologies Network (ATeN) Center, University of Palermo, Palermo, Italy
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12
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Wu F, Zhao J, Zhang E, Wu Q, Wu X, Zhang D, Liu Y, Wang R, Li W. Bisphenol A affects ovarian development in adolescent mice caused by genes expression change. Gene 2020; 740:144535. [DOI: 10.1016/j.gene.2020.144535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/24/2020] [Accepted: 03/05/2020] [Indexed: 12/26/2022]
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13
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Akdogan-Ozdilek B, Duval KL, Goll MG. Chromatin dynamics at the maternal to zygotic transition: recent advances from the zebrafish model. F1000Res 2020; 9. [PMID: 32528656 PMCID: PMC7262572 DOI: 10.12688/f1000research.21809.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/17/2020] [Indexed: 01/02/2023] Open
Abstract
Early animal development is characterized by intense reorganization of the embryonic genome, including large-scale changes in chromatin structure and in the DNA and histone modifications that help shape this structure. Particularly profound shifts in the chromatin landscape are associated with the maternal-to-zygotic transition, when the zygotic genome is first transcribed and maternally loaded transcripts are degraded. The accessibility of the early zebrafish embryo facilitates the interrogation of chromatin during this critical window of development, making it an important model for early chromatin regulation. Here, we review our current understanding of chromatin dynamics during early zebrafish development, highlighting new advances as well as similarities and differences between early chromatin regulation in zebrafish and other species.
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Affiliation(s)
| | | | - Mary G Goll
- Department of Genetics, University of Georgia, Athens, GA, USA
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14
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Raja DA, Subramaniam Y, Aggarwal A, Gotherwal V, Babu A, Tanwar J, Motiani RK, Sivasubbu S, Gokhale RS, Natarajan VT. Histone variant dictates fate biasing of neural crest cells to melanocyte lineage. Development 2020; 147:dev.182576. [PMID: 32098766 DOI: 10.1242/dev.182576] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 01/24/2020] [Indexed: 11/20/2022]
Abstract
In the neural crest lineage, progressive fate restriction and stem cell assignment are crucial for both development and regeneration. Whereas fate commitment events have distinct transcriptional footprints, fate biasing is often transitory and metastable, and is thought to be moulded by epigenetic programmes. Therefore, the molecular basis of specification is difficult to define. In this study, we established a role for a histone variant, H2a.z.2, in specification of the melanocyte lineage from multipotent neural crest cells. H2a.z.2 silencing reduces the number of melanocyte precursors in developing zebrafish embryos and from mouse embryonic stem cells in vitro We demonstrate that this histone variant occupies nucleosomes in the promoter of the key melanocyte determinant mitf, and enhances its induction. CRISPR/Cas9-based targeted mutagenesis of this gene in zebrafish drastically reduces adult melanocytes, as well as their regeneration. Thereby, our study establishes the role of a histone variant upstream of the core gene regulatory network in the neural crest lineage. This epigenetic mark is a key determinant of cell fate and facilitates gene activation by external instructive signals, thereby establishing melanocyte fate identity.
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Affiliation(s)
- Desingu Ayyappa Raja
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - Yogaspoorthi Subramaniam
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - Ayush Aggarwal
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - Vishvabandhu Gotherwal
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - Aswini Babu
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Jyoti Tanwar
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - Rajender K Motiani
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Sridhar Sivasubbu
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Rajesh S Gokhale
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Vivek T Natarajan
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India .,Academy of Scientific and Innovative Research, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
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15
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Jiang Y, Li J, Ren F, Ji C, Aniagu S, Chen T. PM2.5-induced extensive DNA methylation changes in the heart of zebrafish embryos and the protective effect of folic acid. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 255:113331. [PMID: 31614245 DOI: 10.1016/j.envpol.2019.113331] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 09/29/2019] [Accepted: 09/29/2019] [Indexed: 06/10/2023]
Abstract
We previously found that folic acid (FA) attenuated cardiac defects in zebrafish embryos exposed to extractable organic matter (EOM) from PM2.5, but the underlining mechanisms remain to be elucidated. Since DNA methylation is crucial to cardiac development, we hypothesized that EOM-induced aberrant DNA methylation changes could be diminished by FA supplementation. In this study, zebrafish embryos were exposed to EOM in the absence or presence of FA. Genomic-wide DNA methylation analysis identified both DNA hypo- and hyper-methylation changes in CCGG sites in zebrafish embryos exposed to EOM, which were attenuated by FA supplementation. We identified a total of 316 genes with extensive DNA methylation changes in EOM samples but little or no DNA methylation changes in EOM plus FA samples. The genes were involved in critical cellular processes and signaling pathways important for embryo development. In addition, the EOM-decreased SAM/SAH ratio was counteracted by FA supplementation. Furthermore, FA attenuated the EOM-induced changes in the expression of genes involved in the regulation of DNA methylation and in folate biosynthesis. In conclusion, our data suggest that FA supplementation protected zebrafish embryos from the cardiac developmental toxicity of PM2.5 by alleviating EOM-induced DNA methylation changes.
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Affiliation(s)
- Yan Jiang
- Medical College of Soochow University, Suzhou, China
| | - Jianxiang Li
- Medical College of Soochow University, Suzhou, China; Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, China
| | - Fei Ren
- Medical College of Soochow University, Suzhou, China; Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, China
| | - Cheng Ji
- Medical College of Soochow University, Suzhou, China
| | - Stanley Aniagu
- Toxicology, Risk Assessment and Research Division, Texas Commission on Environmental Quality, 12015 Park 35 Cir, Austin, TX, USA
| | - Tao Chen
- Medical College of Soochow University, Suzhou, China; Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, China.
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16
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Balasubramanian S, Raghunath A, Perumal E. Role of epigenetics in zebrafish development. Gene 2019; 718:144049. [DOI: 10.1016/j.gene.2019.144049] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/13/2019] [Accepted: 08/14/2019] [Indexed: 02/07/2023]
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17
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Packaging development: how chromatin controls transcription in zebrafish embryogenesis. Biochem Soc Trans 2019; 47:713-724. [DOI: 10.1042/bst20180617] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/15/2019] [Accepted: 03/19/2019] [Indexed: 12/12/2022]
Abstract
Abstract
How developmental gene expression is activated, co-ordinated and maintained is one of the biggest questions in developmental biology. While transcription factors lead the way in directing developmental gene expression, their accessibility to the correct repertoire of genes can depend on other factors such as DNA methylation, the presence of particular histone variants and post-translational modifications of histones. Collectively, factors that modify DNA or affect its packaging and accessibility contribute to a chromatin landscape that helps to control the timely expression of developmental genes. Zebrafish, perhaps better known for their strength as a model of embryology and organogenesis during development, are coming to the fore as a powerful model for interpreting the role played by chromatin in gene expression. Several recent advances have shown that zebrafish exhibit both similarities and differences to other models (and humans) in the way that they employ chromatin mechanisms of gene regulation. Here, I review how chromatin influences developmental transcriptional programmes during early zebrafish development, patterning and organogenesis. Lastly, I briefly highlight the importance of zebrafish chromatin research towards the understanding of human disease and transgenerational inheritance.
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18
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Barrachina F, Anastasiadi D, Jodar M, Castillo J, Estanyol JM, Piferrer F, Oliva R. Identification of a complex population of chromatin-associated proteins in the European sea bass (Dicentrarchus labrax) sperm. Syst Biol Reprod Med 2018; 64:502-517. [PMID: 29939100 DOI: 10.1080/19396368.2018.1482383] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A very common conception about the function of the spermatozoon is that its unique role is to transmit the paternal genome to the next generation. Most of the sperm genome is known to be condensed in many species by protamines, which are small and extremely positively charged proteins (50-70% arginine) with the functions of streamlining the sperm cell and protecting its DNA. However, more recently, it has been shown in mammals that 2-10% of its mature sperm chromatin is also associated to a complex population of histones and chromatin-associated proteins differentially distributed in the genome. These proteins are transferred to the oocyte upon fertilization and may be involved in the epigenetic marking of the paternal genome. However, little information is so far available on the additional potential sperm chromatin proteins present in other protamine-containing non-mammalian vertebrates detected through high-throughput mass spectrometry. Thus, we started the present work with the goal of characterizing the mature sperm proteome of the European sea bass, with a particular focus on the sperm chromatin, chosen as a representative of non-mammalian vertebrate protamine-containing species. Proteins were isolated by acidic extraction from purified sperm cells and from purified sperm nuclei, digested with trypsin, and subsequently the peptides were separated using liquid chromatography and identified through tandem mass spectrometry. A total of 296 proteins were identified. Of interest, the presence of 94 histones and other chromatin-associated proteins was detected, in addition to the protamines. These results provide phylogenetically strategic information, indicating that the coexistence of histones, additional chromatin proteins, and protamines in sperm is not exclusive of mammals, but is also present in other protamine-containing vertebrates. Thus, it indicates that the epigenetic marking of the sperm chromatin, first demonstrated in mammals, could be more fundamental and conserved than previously thought. Abbreviations: AU-PAGE: acetic acid-urea polyacrylamide gel electrophoresis; CPC: chromosomal passenger complex; DTT: dithiothreitol; EGA: embryonic genome activation; FDR: false discovery rate; GO: Gene Ontology; IAA: iodoacetamide; LC: liquid chromatography; LC-MS/MS: liquid chromatography coupled to tandem mass spectrometry; MS: mass spectrometry; MS/MS: tandem mass spectrometry; MW: molecular weight; PAGE: polyacrylamide gel electrophoresis; PBS: phosphate buffered saline; SDS: sodium dodecyl sulfate; SDS-PAGE: sodium dodecyl sulfate polyacrylamide gel electrophoresis; TCA: trichloroacetic acid.
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Affiliation(s)
- Ferran Barrachina
- a Molecular Biology of Reproduction and Development Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Faculty of Medicine and Health Sciences , University of Barcelona , Barcelona , Spain.,b Biochemistry and Molecular Genetics Service , Hospital Clínic , Barcelona , Spain
| | - Dafni Anastasiadi
- c Institut de Ciències del Mar , Consejo Superior de Investigaciones Científicas , Barcelona , Spain
| | - Meritxell Jodar
- a Molecular Biology of Reproduction and Development Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Faculty of Medicine and Health Sciences , University of Barcelona , Barcelona , Spain.,b Biochemistry and Molecular Genetics Service , Hospital Clínic , Barcelona , Spain
| | - Judit Castillo
- a Molecular Biology of Reproduction and Development Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Faculty of Medicine and Health Sciences , University of Barcelona , Barcelona , Spain.,b Biochemistry and Molecular Genetics Service , Hospital Clínic , Barcelona , Spain
| | - Josep Maria Estanyol
- d Proteomics Unit, Scientific and Technological Centers from the University of Barcelona , University of Barcelona , Barcelona , Spain
| | - Francesc Piferrer
- c Institut de Ciències del Mar , Consejo Superior de Investigaciones Científicas , Barcelona , Spain
| | - Rafael Oliva
- a Molecular Biology of Reproduction and Development Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Faculty of Medicine and Health Sciences , University of Barcelona , Barcelona , Spain.,b Biochemistry and Molecular Genetics Service , Hospital Clínic , Barcelona , Spain
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