1
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The Transcriptome and Methylome of the Developing and Aging Brain and Their Relations to Gliomas and Psychological Disorders. Cells 2022; 11:cells11030362. [PMID: 35159171 PMCID: PMC8834030 DOI: 10.3390/cells11030362] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/15/2022] [Accepted: 01/18/2022] [Indexed: 02/01/2023] Open
Abstract
Mutually linked expression and methylation dynamics in the brain govern genome regulation over the whole lifetime with an impact on cognition, psychological disorders, and cancer. We performed a joint study of gene expression and DNA methylation of brain tissue originating from the human prefrontal cortex of individuals across the lifespan to describe changes in cellular programs and their regulation by epigenetic mechanisms. The analysis considers previous knowledge in terms of functional gene signatures and chromatin states derived from independent studies, aging profiles of a battery of chromatin modifying enzymes, and data of gliomas and neuropsychological disorders for a holistic view on the development and aging of the brain. Expression and methylation changes from babies to elderly adults decompose into different modes associated with the serial activation of (brain) developmental, learning, metabolic and inflammatory functions, where methylation in gene promoters mostly represses transcription. Expression of genes encoding methylome modifying enzymes is very diverse reflecting complex regulations during lifetime which also associates with the marked remodeling of chromatin between permissive and restrictive states. Data of brain cancer and psychotic disorders reveal footprints of pathophysiologies related to brain development and aging. Comparison of aging brains with gliomas supports the view that glioblastoma-like and astrocytoma-like tumors exhibit higher cellular plasticity activated in the developing healthy brain while oligodendrogliomas have a more stable differentiation hierarchy more resembling the aged brain. The balance and specific shifts between volatile and stable and between more irreversible and more plastic epigenomic networks govern the development and aging of healthy and diseased brain.
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2
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Understanding the interplay between CpG island-associated gene promoters and H3K4 methylation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194567. [PMID: 32360393 PMCID: PMC7294231 DOI: 10.1016/j.bbagrm.2020.194567] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/24/2020] [Accepted: 04/22/2020] [Indexed: 02/07/2023]
Abstract
The precise regulation of gene transcription is required to establish and maintain cell type-specific gene expression programs during multicellular development. In addition to transcription factors, chromatin, and its chemical modification, play a central role in regulating gene expression. In vertebrates, DNA is pervasively methylated at CG dinucleotides, a modification that is repressive to transcription. However, approximately 70% of vertebrate gene promoters are associated with DNA elements called CpG islands (CGIs) that are refractory to DNA methylation. CGIs integrate the activity of a range of chromatin-regulating factors that can post-translationally modify histones and modulate gene expression. This is exemplified by the trimethylation of histone H3 at lysine 4 (H3K4me3), which is enriched at CGI-associated gene promoters and correlates with transcriptional activity. Through studying H3K4me3 at CGIs it has become clear that CGIs shape the distribution of H3K4me3 and, in turn, H3K4me3 influences the chromatin landscape at CGIs. Here we will discuss our understanding of the emerging relationship between CGIs, H3K4me3, and gene expression.
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3
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Himeoka Y, Kaneko K. Epigenetic Ratchet: Spontaneous Adaptation via Stochastic Gene Expression. Sci Rep 2020; 10:459. [PMID: 31949247 PMCID: PMC6965613 DOI: 10.1038/s41598-019-57372-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 12/30/2019] [Indexed: 11/09/2022] Open
Abstract
Adaptation to unforeseen environmental changes is one of the most prominent features that characterize the living system. Although signal transduction and gene regulation networks evolved to adapt specific environmental conditions that they frequently experience, it is also reported that bacteria can modify their gene expression patterns to survive a huge variety of environmental conditions even without such pre-designed networks to adapt specically to each environment. Here we propose a general mechanism of cells for such "spontaneous" adaptation, on the basis of stochastic gene expression and epigenetic modication. First, a variety of gene expression states that are marginally stable states are generated by epigenetic modication. Then by taking advantage of stochastic gene expression and dilution by cellular growth, it is shown that, a gene expression pattern that achieves greater cell growth is generically selected, as conrmed by simulations and analysis of several models. The mechanism does not require any design of gene regulation networks. General relevance of the mechanism to cell biology is also discussed.
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Affiliation(s)
- Yusuke Himeoka
- Department of Basic Science, University of Tokyo, Komaba, Meguro-ku, Tokyo, 153-8902, Japan.,Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Kunihiko Kaneko
- Research Center for Complex Systems Biology, Universal Biology Institute, University of Tokyo, 3-8-1, Komaba, Tokyo, 153-8902, Japan.
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4
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Monitoring of switches in heterochromatin-induced silencing shows incomplete establishment and developmental instabilities. Proc Natl Acad Sci U S A 2019; 116:20043-20053. [PMID: 31527269 DOI: 10.1073/pnas.1909724116] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Position effect variegation (PEV) in Drosophila results from new juxtapositions of euchromatic and heterochromatic chromosomal regions, and manifests as striking bimodal patterns of gene expression. The semirandom patterns of PEV, reflecting clonal relationships between cells, have been interpreted as gene-expression states that are set in development and thereafter maintained without change through subsequent cell divisions. The rate of instability of PEV is almost entirely unexplored beyond the final expression of the modified gene; thus the origin of the expressivity and patterns of PEV remain unexplained. Many properties of PEV are not predicted from currently accepted biochemical and theoretical models. In this work we investigate the time at which expressivity of silencing is set, and find that it is determined before heterochromatin exists. We employ a mathematical simulation and a corroborating experimental approach to monitor switching (i.e., gains and losses of silencing) through development. In contrast to current views, we find that gene silencing is incompletely set early in embryogenesis, but nevertheless is repeatedly lost and gained in individual cells throughout development. Our data support an alternative to locus-specific "epigenetic" silencing at variegating gene promoters that more fully accounts for the final patterns of PEV.
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5
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Cortez MJV, Rabajante JF, Tubay JM, Babierra AL. From epigenetic landscape to phenotypic fitness landscape: Evolutionary effect of pathogens on host traits. INFECTION GENETICS AND EVOLUTION 2017; 51:245-254. [PMID: 28408285 DOI: 10.1016/j.meegid.2017.04.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 04/03/2017] [Accepted: 04/06/2017] [Indexed: 02/07/2023]
Abstract
The epigenetic landscape illustrates how cells differentiate through the control of gene regulatory networks. Numerous studies have investigated epigenetic gene regulation but there are limited studies on how the epigenetic landscape and the presence of pathogens influence the evolution of host traits. Here, we formulate a multistable decision-switch model involving several phenotypes with the antagonistic influence of parasitism. As expected, pathogens can drive dominant (common) phenotypes to become inferior through negative frequency-dependent selection. Furthermore, novel predictions of our model show that parasitism can steer the dynamics of phenotype specification from multistable equilibrium convergence to oscillations. This oscillatory behavior could explain pathogen-mediated epimutations and excessive phenotypic plasticity. The Red Queen dynamics also occur in certain parameter space of the model, which demonstrates winnerless cyclic phenotype-switching in hosts and in pathogens. The results of our simulations elucidate the association between the epigenetic and phenotypic fitness landscapes and how parasitism facilitates non-genetic phenotypic diversity.
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Affiliation(s)
- Mark Jayson V Cortez
- Institute of Mathematical Sciences and Physics, University of the Philippines Los Baños, College, Laguna 4031, Philippines
| | - Jomar F Rabajante
- Institute of Mathematical Sciences and Physics, University of the Philippines Los Baños, College, Laguna 4031, Philippines.
| | - Jerrold M Tubay
- Institute of Mathematical Sciences and Physics, University of the Philippines Los Baños, College, Laguna 4031, Philippines
| | - Ariel L Babierra
- Institute of Mathematical Sciences and Physics, University of the Philippines Los Baños, College, Laguna 4031, Philippines
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6
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El Taghdouini A, van Grunsven LA. Epigenetic regulation of hepatic stellate cell activation and liver fibrosis. Expert Rev Gastroenterol Hepatol 2016; 10:1397-1408. [PMID: 27762150 DOI: 10.1080/17474124.2016.1251309] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chronic liver injury to hepatocytes or cholangiocytes, when left unmanaged, leads to the development of liver fibrosis, a condition characterized by the excessive intrahepatic deposition of extracellular matrix proteins. Activated hepatic stellate cells constitute the predominant source of extracellular matrix in fibrotic livers and their transition from a quiescent state during fibrogenesis is associated with important alterations in their transcriptional and epigenetic landscape. Areas covered: We briefly describe the processes involved in hepatic stellate cell activation and discuss our current understanding of alterations in the epigenetic landscape, i.e DNA methylation, histone modifications and the functional role of non-coding RNAs that accompany this key event in the development of chronic liver disease. Expert commentary: Although great progress has been made, our understanding of the epigenetic regulation of hepatic stellate cell activation is limited and, thus far, insufficient to allow the development of epigenetic drugs that can selectively interrupt liver fibrosis.
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Affiliation(s)
- Adil El Taghdouini
- a Institut de Recherche Expérimentale et Clinique (IREC), Laboratory of Pediatric Hepatology and Cell Therapy , Université Catholique de Louvain , Brussels , Belgium.,b Liver Cell Biology Laboratory , Vrije Universiteit Brussel (VUB) , Brussels , Belgium
| | - Leo A van Grunsven
- b Liver Cell Biology Laboratory , Vrije Universiteit Brussel (VUB) , Brussels , Belgium
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7
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Minarovits J, Banati F, Szenthe K, Niller HH. Epigenetic Regulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 879:1-25. [DOI: 10.1007/978-3-319-24738-0_1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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8
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Nagaraj VH, Mukhopadhyay S, Dayarian A, Sengupta AM. Breaking an epigenetic chromatin switch: curious features of hysteresis in Saccharomyces cerevisiae telomeric silencing. PLoS One 2014; 9:e113516. [PMID: 25536038 PMCID: PMC4275178 DOI: 10.1371/journal.pone.0113516] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 10/29/2014] [Indexed: 11/18/2022] Open
Abstract
In addition to gene network switches, local epigenetic modifications to DNA and histones play an important role in all-or-none cellular decision-making. Here, we study the dynamical design of a well-characterized epigenetic chromatin switch: the yeast SIR system, in order to understand the origin of the stability of epigenetic states. We study hysteresis in this system by perturbing it with a histone deacetylase inhibitor. We find that SIR silencing has many characteristics of a non-linear bistable system, as observed in conventional genetic switches, which are based on activities of a few promoters affecting each other through the abundance of their gene products. Quite remarkably, our experiments in yeast telomeric silencing show a very distinctive pattern when it comes to the transition from bistability to monostability. In particular, the loss of the stable silenced state, upon increasing the inhibitor concentration, does not seem to show the expected saddle node behavior, instead looking like a supercritical pitchfork bifurcation. In other words, the 'off' state merges with the 'on' state at a threshold concentration leading to a single state, as opposed to the two states remaining distinct up to the threshold and exhibiting a discontinuous jump from the 'off' to the 'on' state. We argue that this is an inevitable consequence of silenced and active regions coexisting with dynamic domain boundaries. The experimental observations in our study therefore have broad implications for the understanding of chromatin silencing in yeast and beyond.
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Affiliation(s)
| | | | - Adel Dayarian
- Kavli Institute for Theoretical Physics, University of California Santa Barbara, Santa Barbara, CA, United States of America
| | - Anirvan M. Sengupta
- BioMaPS Institute, Rutgers University, Piscataway, NJ, United States of America
- Department of Physics and Astronomy, Rutgers University, Piscataway, NJ, United States of America
- * E-mail:
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9
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Dekker J. Two ways to fold the genome during the cell cycle: insights obtained with chromosome conformation capture. Epigenetics Chromatin 2014; 7:25. [PMID: 25435919 PMCID: PMC4247682 DOI: 10.1186/1756-8935-7-25] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 10/15/2014] [Indexed: 01/19/2023] Open
Abstract
Genetic and epigenetic inheritance through mitosis is critical for dividing cells to maintain their state. This process occurs in the context of large-scale re-organization of chromosome conformation during prophase leading to the formation of mitotic chromosomes, and during the reformation of the interphase nucleus during telophase and early G1. This review highlights how recent studies over the last 5 years employing chromosome conformation capture combined with classical models of chromosome organization based on decades of microscopic observations, are providing new insights into the three-dimensional organization of chromatin inside the interphase nucleus and within mitotic chromosomes. One striking observation is that interphase genome organization displays cell type-specific features that are related to cell type-specific gene expression, whereas mitotic chromosome folding appears universal and tissue invariant. This raises the question of whether or not there is a need for an epigenetic memory for genome folding. Herein, the two different folding states of mammalian genomes are reviewed and then models are discussed wherein instructions for cell type-specific genome folding are locally encoded in the linear genome and transmitted through mitosis, e.g., as open chromatin sites with or without continuous binding of transcription factors. In the next cell cycle these instructions are used to re-assemble protein complexes on regulatory elements which then drive three-dimensional folding of the genome from the bottom up through local action and self-assembly into higher order levels of cell type-specific organization. In this model, no explicit epigenetic memory for cell type-specific chromosome folding is required.
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Affiliation(s)
- Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605-0103 USA
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10
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Andreoli F, Del Rio A. Physicochemical modifications of histones and their impact on epigenomics. Drug Discov Today 2014; 19:1372-9. [PMID: 24853949 DOI: 10.1016/j.drudis.2014.05.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 03/28/2014] [Accepted: 05/12/2014] [Indexed: 01/06/2023]
Abstract
The study of histone post-translational modifications (PTMs) has made extraordinary progress over the past few years and many epigenetic modifications have been identified and found to be associated with fundamental biological processes and pathological conditions. Most histone-modifying enzymes produce specific covalent modifications on histone tails that, taken together, elicit complex and concerted processes. An even higher level of complexity is generated by the action of small molecules that are able to modulate pharmacologically epigenetic enzymes and interfere with these biochemical mechanisms. In this article, we provide an overview of histone PTMs by reviewing and discussing them in terms of their physicochemical properties, emphasizing these concepts in view of recent research efforts to elucidate epigenetic mechanisms and devise future epigenetic drugs.
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Affiliation(s)
- Federico Andreoli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum, University of Bologna, Via S. Giacomo 14, Bologna 40126, Italy
| | - Alberto Del Rio
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum, University of Bologna, Via S. Giacomo 14, Bologna 40126, Italy; Institute of Organic Synthesis and Photoreactivity, National Research Council, Via P. Gobetti, 101, Bologna 40129, Italy.
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11
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Klose RJ, Cooper S, Farcas AM, Blackledge NP, Brockdorff N. Chromatin sampling--an emerging perspective on targeting polycomb repressor proteins. PLoS Genet 2013; 9:e1003717. [PMID: 23990804 PMCID: PMC3749931 DOI: 10.1371/journal.pgen.1003717] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Robert J. Klose
- Laboratory of Chromatin Biology and Transcription, Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- * E-mail: (RJK); (NB)
| | - Sarah Cooper
- Laboratory of Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Anca M. Farcas
- Laboratory of Chromatin Biology and Transcription, Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Neil P. Blackledge
- Laboratory of Chromatin Biology and Transcription, Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Neil Brockdorff
- Laboratory of Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- * E-mail: (RJK); (NB)
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12
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Arnold C, Stadler PF, Prohaska SJ. Chromatin computation: epigenetic inheritance as a pattern reconstruction problem. J Theor Biol 2013; 336:61-74. [PMID: 23880640 DOI: 10.1016/j.jtbi.2013.07.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 07/02/2013] [Accepted: 07/15/2013] [Indexed: 01/19/2023]
Abstract
Eukaryotic histones carry a diverse set of specific chemical modifications that accumulate over the life-time of a cell and have a crucial impact on the cell state in general and the transcriptional program in particular. Replication constitutes a dramatic disruption of the chromatin states that effectively amounts to partial erasure of stored information. To preserve its epigenetic state the cell reconstructs (at least part of) the histone modifications by means of processes that are still very poorly understood. A plausible hypothesis is that the different combinations of reader and writer domains in histone-modifying enzymes implement local rewriting rules that are capable of "recomputing" the desired parental modification patterns on the basis of the partial information contained in that half of the nucleosomes that predate replication. To test whether such a mechanism is theoretically feasible, we have developed a flexible stochastic simulation system (available at http://www.bioinf.uni-leipzig.de/Software/StoChDyn) for studying the dynamics of histone modification states. The implementation is based on Gillespie's approach, i.e., it models the master equation of a detailed chemical model. It is efficient enough to use an evolutionary algorithm to find patterns across multiple cell divisions with high accuracy. We found that it is easy to evolve a system of enzymes that can maintain a particular chromatin state roughly stable, even without explicit boundary elements separating differentially modified chromatin domains. However, the success of this task depends on several previously unanticipated factors, such as the length of the initial state, the specific pattern that should be maintained, the time between replications, and chemical parameters such as enzymatic binding and dissociation rates. All these factors also influence the accumulation of errors in the wake of cell divisions.
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Affiliation(s)
- Christian Arnold
- Computational EvoDevo Group, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany; Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany; Harvard University, Department of Human Evolutionary Biology, 11 Divinity Avenue, Cambridge, MA 02138, USA.
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13
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Przybilla J, Buske P, Binder H, Galle J. Histone modifications control DNA methylation profiles during ageing and tumour expansion. FRONTIERS IN LIFE SCIENCE 2013. [DOI: 10.1080/21553769.2013.854279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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14
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Furusawa C, Kaneko K. Epigenetic feedback regulation accelerates adaptation and evolution. PLoS One 2013; 8:e61251. [PMID: 23667436 PMCID: PMC3648564 DOI: 10.1371/journal.pone.0061251] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 03/07/2013] [Indexed: 01/09/2023] Open
Abstract
A simple cell model consisting of a gene regulatory network with epigenetic feedback regulation is studied to evaluate the effect of epigenetic dynamics on adaptation and evolution. We find that, the type of epigenetic dynamics considered enables a cell to adapt to unfamiliar environmental changes, for which no regulatory program has been prepared, through noise-driven selection of a cellular state with a high growth rate. Furthermore, we demonstrate that the inclusion of epigenetic regulation promotes evolutionary development of a regulatory network that can respond to environmental changes in a fast and precise manner. These results strongly suggest that epigenetic feedback regulation in gene expression dynamics provides a significant increase in fitness by engendering an increase in cellular plasticity during adaptation and evolution.
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15
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Binder H, Steiner L, Przybilla J, Rohlf T, Prohaska S, Galle J. Transcriptional regulation by histone modifications: towards a theory of chromatin re-organization during stem cell differentiation. Phys Biol 2013; 10:026006. [PMID: 23481318 DOI: 10.1088/1478-3975/10/2/026006] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Chromatin-related mechanisms, as e.g. histone modifications, are known to be involved in regulatory switches within the transcriptome. Only recently, mathematical models of these mechanisms have been established. So far they have not been applied to genome-wide data. We here introduce a mathematical model of transcriptional regulation by histone modifications and apply it to data of trimethylation of histone 3 at lysine 4 (H3K4me3) and 27 (H3K27me3) in mouse pluripotent and lineage-committed cells. The model describes binding of protein complexes to chromatin which are capable of reading and writing histone marks. Molecular interactions of the complexes with DNA and modified histones create a regulatory switch of transcriptional activity. The regulatory states of the switch depend on the activity of histone (de-) methylases, the strength of complex-DNA-binding and the number of nucleosomes capable of cooperatively contributing to complex-binding. Our model explains experimentally measured length distributions of modified chromatin regions. It suggests (i) that high CpG-density facilitates recruitment of the modifying complexes in embryonic stem cells and (ii) that re-organization of extended chromatin regions during lineage specification into neuronal progenitor cells requires targeted de-modification. Our approach represents a basic step towards multi-scale models of transcriptional control during development and lineage specification.
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Affiliation(s)
- Hans Binder
- Interdisciplinary Centre for Bioinformatics, University of Leipzig, D-04107 Leipzig, Härtelstr. 16-18, Germany.
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16
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Steiner L, Hopp L, Wirth H, Galle J, Binder H, Prohaska SJ, Rohlf T. A global genome segmentation method for exploration of epigenetic patterns. PLoS One 2012; 7:e46811. [PMID: 23077526 PMCID: PMC3470578 DOI: 10.1371/journal.pone.0046811] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 09/05/2012] [Indexed: 11/18/2022] Open
Abstract
Current genome-wide ChIP-seq experiments on different epigenetic marks aim at unraveling the interplay between their regulation mechanisms. Published evaluation tools, however, allow testing for predefined hypotheses only. Here, we present a novel method for annotation-independent exploration of epigenetic data and their inter-correlation with other genome-wide features. Our method is based on a combinatorial genome segmentation solely using information on combinations of epigenetic marks. It does not require prior knowledge about the data (e.g. gene positions), but allows integrating the data in a straightforward manner. Thereby, it combines compression, clustering and visualization of the data in a single tool. Our method provides intuitive maps of epigenetic patterns across multiple levels of organization, e.g. of the co-occurrence of different epigenetic marks in different cell types. Thus, it facilitates the formulation of new hypotheses on the principles of epigenetic regulation. We apply our method to histone modification data on trimethylation of histone H3 at lysine 4, 9 and 27 in multi-potent and lineage-primed mouse cells, analyzing their combinatorial modification pattern as well as differentiation-related changes of single modifications. We demonstrate that our method is capable of reproducing recent findings of gene centered approaches, e.g. correlations between CpG-density and the analyzed histone modifications. Moreover, combining the clustered epigenetic data with information on the expression status of associated genes we classify differences in epigenetic status of e.g. house-keeping genes versus differentiation-related genes. Visualizing the distribution of modification states on the chromosomes, we discover strong patterns for chromosome X. For example, exclusively H3K9me3 marked segments are enriched, while poised and active states are rare. Hence, our method also provides new insights into chromosome-specific epigenetic patterns, opening up new questions how "epigenetic computation" is distributed over the genome in space and time.
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Affiliation(s)
- Lydia Steiner
- Junior Professorship for Computational EvoDevo, Institute of Computer Science, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
| | - Lydia Hopp
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Henry Wirth
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Jörg Galle
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
| | - Hans Binder
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
| | - Sonja J. Prohaska
- Junior Professorship for Computational EvoDevo, Institute of Computer Science, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
| | - Thimo Rohlf
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Max-Planck-Institute for Mathematics in the Sciences, Leipzig, Germany
- * E-mail:
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17
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Sampey GC, Guendel I, Das R, Jaworski E, Klase Z, Narayanan A, Kehn-Hall K, Kashanchi F. Transcriptional Gene Silencing (TGS) via the RNAi Machinery in HIV-1 Infections. BIOLOGY 2012; 1:339-69. [PMID: 24832229 PMCID: PMC4009781 DOI: 10.3390/biology1020339] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 08/03/2012] [Accepted: 08/13/2012] [Indexed: 12/21/2022]
Abstract
Gene silencing via non-coding RNA, such as siRNA and miRNA, can occur at the transcriptional, post-transcriptional, and translational stages of expression. Transcriptional gene silencing (TGS) involving the RNAi machinery generally occurs through DNA methylation, as well as histone post-translational modifications, and corresponding remodeling of chromatin around the target gene into a heterochromatic state. The mechanism by which mammalian TGS occurs includes the recruitment of RNA-induced initiation of transcriptional gene silencing (RITS) complexes, DNA methyltransferases (DNMTs), and other chromatin remodelers. Additionally, virally infected cells encoding miRNAs have also been shown to manipulate the host cell RNAi machinery to induce TGS at the viral genome, thereby establishing latency. Furthermore, the introduction of exogenous siRNA and shRNA into infected cells that target integrated viral promoters can greatly suppress viral transcription via TGS. Here we examine the latest findings regarding mammalian TGS, specifically focusing on HIV-1 infected cells, and discuss future avenues of exploration in this field.
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Affiliation(s)
- Gavin C Sampey
- National Center for Biodefense and Infectious Disease, School of Systems Biology, George Mason University, 10900 University Blvd, Manassas, VA 20108, USA.
| | - Irene Guendel
- National Center for Biodefense and Infectious Disease, School of Systems Biology, George Mason University, 10900 University Blvd, Manassas, VA 20108, USA.
| | - Ravi Das
- National Center for Biodefense and Infectious Disease, School of Systems Biology, George Mason University, 10900 University Blvd, Manassas, VA 20108, USA.
| | - Elizabeth Jaworski
- National Center for Biodefense and Infectious Disease, School of Systems Biology, George Mason University, 10900 University Blvd, Manassas, VA 20108, USA.
| | - Zachary Klase
- Molecular Virology Section, Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, 9000 Rockville Pike, Bethesda, MD 20810, USA.
| | - Aarthi Narayanan
- National Center for Biodefense and Infectious Disease, School of Systems Biology, George Mason University, 10900 University Blvd, Manassas, VA 20108, USA.
| | - Kylene Kehn-Hall
- National Center for Biodefense and Infectious Disease, School of Systems Biology, George Mason University, 10900 University Blvd, Manassas, VA 20108, USA.
| | - Fatah Kashanchi
- National Center for Biodefense and Infectious Disease, School of Systems Biology, George Mason University, 10900 University Blvd, Manassas, VA 20108, USA.
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Steffen PA, Fonseca JP, Ringrose L. Epigenetics meets mathematics: towards a quantitative understanding of chromatin biology. Bioessays 2012; 34:901-13. [PMID: 22911103 DOI: 10.1002/bies.201200076] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
How fast? How strong? How many? So what? Why do numbers matter in biology? Chromatin binding proteins are forever in motion, exchanging rapidly between bound and free pools. How do regulatory systems whose components are in constant flux ensure stability and flexibility? This review explores the application of quantitative and mathematical approaches to mechanisms of epigenetic regulation. We discuss methods for measuring kinetic parameters and protein quantities in living cells, and explore the insights that have been gained by quantifying and modelling dynamics of chromatin binding proteins.
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Przybilla J, Galle J, Rohlf T. Is adult stem cell aging driven by conflicting modes of chromatin remodeling? Bioessays 2012; 34:841-8. [PMID: 22821708 DOI: 10.1002/bies.201100190] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Epigenetic control of gene expression by chromatin remodeling is critical for adult stem cell function. A decline in stem cell function is observed during aging, which is accompanied by changes in the chromatin structure that are currently unexplained. Here, we hypothesize that these epigenetic changes originate from the limited cellular capability to inherit epigenetic information. We suggest that spontaneous loss of histone modification, due to fluctuations over short time scales, gives rise to long-term changes in DNA methylation and, accordingly, in gene expression. These changes are assumed to impair stem cell function and, thus, to contribute to aging. We discuss cell replication as a major source of fluctuations in histone modification patterns. Gene silencing by our proposed mechanism can be interpreted as a manifestation of the conflict between the stem cell plasticity required for tissue regeneration and the permanent silencing of potentially deleterious genomic sequences.
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Affiliation(s)
- Jens Przybilla
- Interdisciplinary Center for Bioinformatics, University Leipzig, Leipzig, Germany
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