1551
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Abstract
Epigenetic mechanisms alter the structure of local chromosome domains to dynamically regulate gene expression by signalling and propagating transcriptional states. Nuclear receptors, a stimulus-inducible class of transcription factors, interact with chromatin to regulate transcription. To promote transcription, nuclear receptors interact with genomic regulatory elements that are epigenetically marked by modified histone tails, DNA methylation status, histone variants, chromatin accessibility and long-range interactions. Advances in throughput have allowed the profiling of regulatory factor activity on a genome-wide scale, with recent evidence from genomic analyses highlighting novel aspects of DNA-binding factor actions on chromatin. In the present review, the current knowledge of the mechanisms regulating nuclear receptor occupancy at cis-regulatory elements is discussed, with particular emphasis on the glucocorticoid, oestrogen and androgen receptors. Epigenetic regulation of genomic elements direct cell-specific regulatory factor binding and contribute to human variation in factor occupancy. Through regulating nuclear receptor activity, the epigenome is a critical checkpoint in nuclear receptor induced gene expression in health and disease.
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Affiliation(s)
- S C Biddie
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, Faculty of Medicine and Dentistry, University of Bristol, Bristol, UK.
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1552
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Sartorelli V, Juan AH. Sculpting chromatin beyond the double helix: epigenetic control of skeletal myogenesis. Curr Top Dev Biol 2011; 96:57-83. [PMID: 21621067 DOI: 10.1016/b978-0-12-385940-2.00003-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Satellite cells (SCs) are the main source of adult skeletal muscle stem cells responsible for muscle growth and regeneration. By interpreting extracellular cues, developmental regulators control quiescence, proliferation, and differentiation of SCs by influencing coordinate gene expression. The scope of this review is limited to the description and discussion of protein complexes that introduce and decode heritable histone and chromatin modifications and how these modifications are relevant for SC biology.
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Affiliation(s)
- Vittorio Sartorelli
- Laboratory of Muscle Stem Cell and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
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1553
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Yakovlev IA, Asante DKA, Fossdal CG, Junttila O, Johnsen Ø. Differential gene expression related to an epigenetic memory affecting climatic adaptation in Norway spruce. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2011; 180:132-9. [PMID: 21421355 DOI: 10.1016/j.plantsci.2010.07.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Revised: 06/24/2010] [Accepted: 07/06/2010] [Indexed: 05/04/2023]
Abstract
In Norway spruce, the temperature during zygotic embryogenesis appears to adjust an adaptive epigenetic memory in the progeny that may regulate bud phenology and cold acclimation. Conditions colder than normal advance the timing whilst temperatures above normal delay the onset of these processes and altered performance is long lasting in progeny with identical genetic background. As a step toward unraveling the molecular mechanism behind an epigenetic memory, transcriptional analysis was performed on seedlings from seeds of six full-sib families produced at different embryogenesis temperature-cold (CE) vs warm (WE) under long and short day conditions. We prepared two suppressive subtracted cDNA libraries, forward and reverse, representing genes predominantly expressed in plants from seeds obtained after CE and WE embryogenesis following short day treatment (inducing bud set). Sequencing and annotation revealed considerable differences in the transcriptome of WE versus CE originated plants. By using qRT-PCR we studied the expression patterns of 32 selected candidate genes chosen from subtractive cDNA libraries analysis and nine siRNA pathways genes by a direct candidate approach. Eight genes, two transposons related genes, three with no match to Databases sequences and three genes from siRNA pathways (PaDCL1 and 2, PaSGS3) showed differential expression in progeny from CE and WE correlated with the family phenotypic differences. These findings may contribute to our understanding of the epigenetic mechanisms underlying adaptive changes acquired during embryogenesis.
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Affiliation(s)
- Igor A Yakovlev
- Norwegian Forest and Landscape Institute, Hogskoleveien 8, P.O. Box 115, N-1431 Ås, Norway.
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1554
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Robins JC, Marsit CJ, Padbury JF, Sharma SS. Endocrine disruptors, environmental oxygen, epigenetics and pregnancy. Front Biosci (Elite Ed) 2011; 3:690-700. [PMID: 21196344 DOI: 10.2741/e279] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The placenta and its myriad functions are central to successful reproductive outcomes. These functions can be influenced by the environment encountered throughout pregnancy, thereby altering the appropriate genetic programming needed to allow for sustained pregnancy and appropriate fetal development. This altered programming may result from epigenetic alterations related to environmental exposures. Epigenetic alterations are now being linked to several important reproductive outcomes, including early pregnancy loss, intrauterine growth restriction, congenital syndromes, preterm birth, and preeclampsia. The diversity of environmental exposures linked to adverse reproductive effects continues to grow. Much attention has focused on the role of endocrine disruptors in infertility, but recent work suggests that these chemicals may also have adverse effects in pregnancy and development. Environmental oxygen is also critical in pregnancy success. There are clear links between altered oxygen levels and placentation amongst other effects. As research continues to enhance our understanding of the molecular processes including epigenetic regulation that influence pregnancy, it will be critical to specifically examine how the environment, broadly defined, may play a role in altering these critical functions.
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Affiliation(s)
- Jared C Robins
- Division of Reproductive Endocrinology and Infertility, Women and Infants Hospital of Rhode Island, Providence, RI, USA
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1555
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Larsen PF, Schulte PM, Nielsen EE. Gene expression analysis for the identification of selection and local adaptation in fishes. JOURNAL OF FISH BIOLOGY 2011; 78:1-22. [PMID: 21235543 DOI: 10.1111/j.1095-8649.2010.02834.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In recent years, variation in gene expression has been recognized as an important component of environmental adaptation in multiple model species, including a few fish species. There is, however, still little known about the genetic basis of adaptation in gene expression resulting from variation in the aquatic environment (e.g. temperature, salinity and oxygen) and the physiological effect and costs of such differences in gene expression. This review presents and discusses progress and pitfalls of applying gene expression analyses to fishes and suggests simple frameworks to get started with gene expression analysis. It is emphasized that well-planned gene expression studies can serve as an important tool for the identification of selection in local populations of fishes, even for non-traditional model species where limited genomic information is available. Recent studies focusing on gene expression variation among natural fish populations are reviewed, highlighting the latest applications that combine genetic evidence from neutral markers and gene expression data.
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Affiliation(s)
- P F Larsen
- Department of Biological Sciences, Aarhus Universit, Ny Munkegade, DK-8000 Aarhus C, Denmark.
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1556
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Abstract
Breast carcinogenesis is a multistep process involving both genetic and epigenetic changes. Epigenetics is defined as reversible changes in gene expression, not accompanied by alteration in gene sequence. DNA methylation, histone modification, and nucleosome remodeling are the major epigenetic changes that are dysregulated in breast cancer. Several genes involved in proliferation, anti-apoptosis, invasion, and metastasis have been shown to undergo epigenetic changes in breast cancer. Because epigenetic changes are potentially reversible processes, much effort has been directed toward understanding this mechanism with the goal of finding effective therapies that target these changes. Both demethylating agents and the histone deacetylase inhibitors (HDACi) are under investigation as single agents or in combination with other systemic therapies in the treatment of breast cancer. In this review, we discuss the role of epigenetic regulation in breast cancer, in particular focusing on the clinical trials using therapies that modulate epigenetic mechanisms.
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Affiliation(s)
- Maryam B Lustberg
- Division of Hematology and Oncology, Comprehensive Cancer Center, The Ohio State University Medical Center, Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA
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1557
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Abstract
Obesity is a complex disease with multiple well-defined risk factors. Nevertheless, susceptibility to obesity and its sequelae within obesogenic environments varies greatly from one person to the next, suggesting a role for gene × environment interactions in the etiology of the disorder. Epigenetic regulation of the human genome provides a putative mechanism by which specific environmental exposures convey risk for obesity and other human diseases and is one possible mechanism that underlies the gene × environment/treatment interactions observed in epidemiological studies and clinical trials. A study published in BMC Medicine this month by Wang et al. reports on an examination of DNA methylation in peripheral blood leukocytes of lean and obese adolescents, comparing methylation patterns between the two groups. The authors identified two genes that were differentially methylated, both of which have roles in immune function. Here we overview the findings from this study in the context of those emerging from other recent genetic and epigenetic studies, discuss the strengths and weaknesses of the study and speculate on the future of epigenetics in chronic disease research.
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Affiliation(s)
- Paul W Franks
- Department of Clinical Sciences, Skåne University Hospital, Lund University, Malmö, Sweden.
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1558
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Abstract
Body fat distribution plays an important role in determining metabolic health. Whereas central obesity is closely associated with the development of CVD and type 2 diabetes, lower body fat appears to be protective and is paradoxically associated with improved metabolic and cardiovascular profiles. Physiological studies have demonstrated that fatty acid handling differs between white adipose tissue depots, with lower body white adipose tissue acting as a more efficient site for long-term lipid storage. The regulatory mechanisms governing these regional differences in function remain to be elucidated. Although the local microenvironment is likely to be a contributing factor, recent findings point towards the tissues being intrinsically distinct at the level of the adipocyte precursor cells (pre-adipocytes). The multi-potent pre-adipocytes are capable of generating cells of the mesenchymal lineage, including adipocytes. Regional differences in the adipogenic and replicative potential of these cells, as well as metabolic and biochemical activity, have been reported. Intriguingly, the genetic and metabolic characteristics of these cells can be retained through multiple generations when the cells are cultured in vitro. The rapidly emerging field of epigenetics may hold the key for explaining regional differences in white adipose tissue gene expression and function. Epigenetics describes the regulation of gene expression that occurs independently of changes in DNA sequence, for instance, DNA methylation or histone protein modification. In this review, we will discuss the contribution of DNA methylation to the determination of cells of adipogenic fate as well as the role DNA methylation may play during adipocyte terminal differentiation.
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1559
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Abstract
Parental effects are a major source of phenotypic plasticity and may influence offspring phenotype in concert with environmental demands. Studies of "environmental epigenetics" suggest that (1) DNA methylation states are variable and that both demethylation and remethylation occur in post-mitotic cells, and (2) that remodeling of DNA methylation can occur in response to environmentally driven intracellular signaling pathways. Studies of mother-offspring interactions in rodents suggest that parental signals influence the DNA methylation, leading to stable changes in gene expression. If parental effects do indeed enhance the "match" between prevailing environmental demands and offspring phenotype, then the potential for variation in environmental conditions over time would suggest a mechanism that requires active maintenance across generations through parental signaling. We suggest that parental regulation of DNA methylation states is thus an ideal candidate mechanism for parental effects on phenotypic variation.
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Affiliation(s)
- Laurent Kappeler
- Sackler Program for Epigenetics and Psychobiology, Douglas Mental Health University Institute, McGill University, Montréal, Québec, Canada
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1560
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Targeting Epigenetic Modifications for the Treatment and Prevention of Breast Cancer. CURRENT BREAST CANCER REPORTS 2010. [DOI: 10.1007/s12609-010-0027-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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1561
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Latzel V, Klimešová J. Year-to-year changes in expression of maternal effects in perennial plants. Basic Appl Ecol 2010. [DOI: 10.1016/j.baae.2010.09.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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1562
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Abstract
Epigenetic modifications are widely accepted as playing a critical role in the regulation of gene expression and thereby contributing to the determination of the phenotype of multicellular organisms. In general, these marks are cleared and re-established each generation, but there have been reports in a number of model organisms that at some loci in the genome this clearing is incomplete. This phenomenon is referred to as transgenerational epigenetic inheritance. Moreover, recent evidence shows that the environment can stably influence the establishment of the epigenome. Together, these findings suggest that an environmental event in one generation could affect the phenotype in subsequent generations, and these somewhat Lamarckian ideas are stimulating interest from a broad spectrum of biologists, from ecologists to health workers.
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Affiliation(s)
- Lucia Daxinger
- Epigenetics Laboratory, Queensland Institute of Medical Research, Herston, Brisbane, Queensland 4006, Australia
| | - Emma Whitelaw
- Epigenetics Laboratory, Queensland Institute of Medical Research, Herston, Brisbane, Queensland 4006, Australia
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1563
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Abstract
Obesity is a result of excess body fat accumulation. This excess is associated with adverse health effects such as CVD, type 2 diabetes, and cancer. The development of obesity has an evident environmental contribution, but as shown by heritability estimates of 40% to 70%, a genetic susceptibility component is also needed. Progress in understanding the etiology has been slow, with findings largely restricted to monogenic, severe forms of obesity. However, technological and analytical advances have enabled detection of more than 20 obesity susceptibility loci. These contain genes suggested to be involved in the regulation of food intake through action in the central nervous system as well as in adipocyte function. These results provide plausible biological pathways that may, in the future, be targeted as part of treatment or prevention strategies. Although the proportion of heritability explained by these genes is small, their detection heralds a new phase in understanding the etiology of common obesity.
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Affiliation(s)
- Blanca M. Herrera
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN UK
| | - Cecilia M. Lindgren
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN UK
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1564
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Turner JD, Alt SR, Cao L, Vernocchi S, Trifonova S, Battello N, Muller CP. Transcriptional control of the glucocorticoid receptor: CpG islands, epigenetics and more. Biochem Pharmacol 2010; 80:1860-8. [DOI: 10.1016/j.bcp.2010.06.037] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Revised: 06/18/2010] [Accepted: 06/21/2010] [Indexed: 12/16/2022]
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1565
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Russo P, Lauria F, Siani A. Heritability of body weight: moving beyond genetics. Nutr Metab Cardiovasc Dis 2010; 20:691-697. [PMID: 21094029 DOI: 10.1016/j.numecd.2010.09.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Revised: 09/07/2010] [Accepted: 09/16/2010] [Indexed: 11/23/2022]
Abstract
Obesity is a complex disease, arising from the interaction between several genetic and environmental factors. Until recently, the genetic basis of complex diseases in general, and of obesity in particular, were poorly characterized. While the relatively rare monogenic and syndromic forms of obesity clearly recognize a genetic origin, the actual worldwide epidemics of obesity represent a challenge for the identification of the genetic factors involved, being likely the effect of several loci each having a subtle influence on the phenotypic expression. Progress in DNA analysis techniques and in computational tools, and the increasing level of characterization of the variability of the human genome has recently allowed to study comprehensively the association between genetic variants and obesity. To date, well-conducted and powered genome-wide association studies allowed to consistently identify genomic regions - lying on different chromosomes and affecting different metabolic pathways - influencing the predisposition to the accumulation of body fat, ultimately leading to overweight and obesity. However, the population attributable risk for obesity linked to the most statistically significant loci, like FTO and MC4R, remains discouragingly low, explaining only small fractions of the overall variance of body weight. In the last few years, the role of the complex interaction between genetic determinants and environmental factors in the rapid global increase of obesity has been further challenged by the entry of new players, that is the transcriptional and post-transcriptional regulation, summarized under the emerging discipline of epigenetics. The key challenge now is to move from the identification of causal genes and variants to the integration of different "omics" disciplines, finally allowing the molecular understanding of obesity and related conditions.
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Affiliation(s)
- P Russo
- Unit of Epidemiology and Population Genetics, Institute of Food Sciences, CNR, Avellino, Italy
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1566
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Abstract
Epigenetics is a steadily growing research area. In many human diseases, especially in cancers, but also in autoimmune diseases, epigenetic aberrations have been found. Rheumatoid arthritis is an autoimmune disease characterized by chronic inflammation and destruction of synovial joints. Even though the etiology is not yet fully understood, rheumatoid arthritis is generally considered to be caused by a combination of genetic predisposition, deregulated immunomodulation, and environmental influences. To gain a better understanding of this disease, researchers have become interested in studying epigenetic changes in rheumatoid arthritis. Here, we want to review the current knowledge on epigenetics in rheumatoid arthritis.
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Affiliation(s)
- Michelle Trenkmann
- Center of Experimental Rheumatology and Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Zurich, Switzerland
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1567
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Epigenetic regulation of the neural transcriptome: the meaning of the marks. Nat Neurosci 2010; 13:1313-8. [PMID: 20975754 DOI: 10.1038/nn1110-1313] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The field of epigenetics provides neurobiologists with candidate mechanisms for experience-dependent changes in gene transcription. The ability to realize the potential of epigenetics in defining the causal pathways lying between environmental signals, transcriptional regulation and neural function will depend on moving beyond correlational studies focusing on individual epigenetic marks. Here we attempt to provide a conceptual framework for integrative research on nucleotide sequence, chromatin modifications, RNA signaling and their interactions in understanding experience-dependent phenotypic plasticity. Studies in genomic imprinting may serve as an existing model for such approaches.
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1568
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Abstract
Memory formation and storage require long-lasting changes in memory-related neuronal circuits. Recent evidence indicates that DNA methylation may serve as a contributing mechanism in memory formation and storage. These emerging findings suggest a role for an epigenetic mechanism in learning and long-term memory maintenance and raise apparent conundrums and questions. For example, it is unclear how DNA methylation might be reversed during the formation of a memory, how changes in DNA methylation alter neuronal function to promote memory formation, and how DNA methylation patterns differ between neuronal structures to enable both consolidation and storage of memories. Here we evaluate the existing evidence supporting a role for DNA methylation in memory, discuss how DNA methylation may affect genetic and neuronal function to contribute to behavior, propose several future directions for the emerging subfield of neuroepigenetics, and begin to address some of the broader implications of this work.
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Affiliation(s)
- Jeremy J Day
- Department of Neurobiology and Evelyn F. McKnight Brain Institute, University of Alabama at Birmingham, Birmingham, Alabama, USA
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1569
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Murr R. Interplay between different epigenetic modifications and mechanisms. ADVANCES IN GENETICS 2010; 70:101-41. [PMID: 20920747 DOI: 10.1016/b978-0-12-380866-0.60005-8] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Cellular functions including transcription regulation, DNA repair, and DNA replication need to be tightly regulated. DNA sequence can contribute to the regulation of these mechanisms. This is exemplified by the consensus sequences that allow the binding of specific transcription factors, thus regulating transcription rates. Another layer of regulation resides in modifications that do not affect the DNA sequence itself but still results in the modification of chromatin structure and properties, thus affecting the readout of the underlying DNA sequence. These modifications are dubbed as "epigenetic modifications" and include, among others, histone modifications, DNA methylation, and small RNAs. While these events can independently regulate cellular mechanisms, recent studies indicate that joint activities of different epigenetic modifications could result in a common outcome. In this chapter, I will attempt to recapitulate the best known examples of collaborative activities between epigenetic modifications. I will emphasize mostly on the effect of crosstalks between epigenetic modifications on transcription regulation, simply because it is the most exposed and studied aspect of epigenetic interactions. I will also summarize the effect of epigenetic interactions on DNA damage response and DNA repair. The involvement of epigenetic crosstalks in cancer formation, progression, and treatment will be emphasized throughout the manuscript. Due to space restrictions, additional aspects involving histone replacements [Park, Y. J., and Luger, K. (2008). Histone chaperones in nucleosome eviction and histone exchange. Curr. Opin. Struct. Biol.18, 282-289.], histone variants [Boulard, M., Bouvet, P., Kundu, T. K., and Dimitrov, S. (2007). Histone variant nucleosomes: Structure, function and implication in disease. Subcell. Biochem. 41, 71-89; Talbert, P. B., and Henikoff, S. (2010). Histone variants-Ancient wrap artists of the epigenome. Nat. Rev. Mol. Cell Biol.11, 264-275.], and histone modification readers [de la Cruz, X., Lois, S., Sanchez-Molina, S., and Martinez-Balbas, M. A. (2005). Do protein motifs read the histone code? Bioessays27, 164-175; Grewal, S. I., and Jia, S. (2007). Heterochromatin revisited. Nat. Rev. Genet.8, 35-46.] will not be addressed in depth in this chapter, and the reader is referred to the reviews cited here.
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Affiliation(s)
- Rabih Murr
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66,4058 Basel, Switzerland
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1570
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1571
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Du Z, Song J, Wang Y, Zhao Y, Guda K, Yang S, Kao HY, Xu Y, Willis J, Markowitz SD, Sedwick D, Ewing RM, Wang Z. DNMT1 stability is regulated by proteins coordinating deubiquitination and acetylation-driven ubiquitination. Sci Signal 2010; 3:ra80. [PMID: 21045206 DOI: 10.1126/scisignal.2001462] [Citation(s) in RCA: 253] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
DNA methyltransferase 1 (DNMT1) is the primary enzyme that maintains DNA methylation. We describe a previously unknown mode of regulation of DNMT1 protein stability through the coordinated action of an array of DNMT1-associated proteins. DNMT1 was destabilized by acetylation by the acetyltransferase Tip60, which triggered ubiquitination by the E3 ligase UHRF1, thereby targeting DNMT1 for proteasomal degradation. In contrast, DNMT1 was stabilized by histone deacetylase 1 (HDAC1) and the deubiquitinase HAUSP (herpes virus-associated ubiquitin-specific protease). Analysis of the abundance of DNMT1 and Tip60, as well as the association between HAUSP and DNMT1, suggested that during the cell cycle the initiation of DNMT1 degradation was coordinated with the end of DNA replication and the need for DNMT activity. In human colon cancers, the abundance of DNMT1 correlated with that of HAUSP. HAUSP knockdown rendered colon cancer cells more sensitive to killing by HDAC inhibitors both in tissue culture and in tumor xenograft models. Thus, these studies provide a mechanism-based rationale for the development of HDAC and HAUSP inhibitors for combined use in cancer therapy.
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Affiliation(s)
- Zhanwen Du
- Department of Genetics, Case Western Reserve University, Cleveland, OH 44106, USA
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1572
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The possible role of epigenetics in gestational diabetes: cause, consequence, or both. Obstet Gynecol Int 2010; 2010:605163. [PMID: 21052542 PMCID: PMC2968420 DOI: 10.1155/2010/605163] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Accepted: 08/22/2010] [Indexed: 12/20/2022] Open
Abstract
Gestational diabetes mellitus (GDM) is defined as the glucose intolerance that is not present or recognized prior to pregnancy. Several risk factors of GDM depend on environmental factors that are thought to regulate the genome through epigenetic mechanisms. Thus, epigenetic regulation could be involved in the development of GDM. In addition, the adverse intrauterine environment in patients with GDM could also have a negative impact on the establishment of the epigenomes of the offspring.
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1573
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Abstract
Epigenetic signals are responsible for the establishment, maintenance, and reversal of metastable transcriptional states that are fundamental for the cell's ability to "remember" past events, such as changes in the external environment or developmental cues. Complex epigenetic states are orchestrated by several converging and reinforcing signals, including transcription factors, noncoding RNAs, DNA methylation, and histone modifications. Although all of these pathways modulate transcription from chromatin in vivo, the mechanisms by which epigenetic information is transmitted through cell division remain unclear. Because epigenetic states are metastable and change in response to the appropriate signals, a deeper understanding of their molecular framework will allow us to tackle the dysregulation of epigenetics in disease.
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Affiliation(s)
- Roberto Bonasio
- Howard Hughes Medical Institute and Department of Biochemistry, School of Medicine, New York University, New York, NY 10016, USA
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1574
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Abstract
Epigenetic research is at the forefront of plant biology and molecular genetics. Studies on higher plants underscore the significant role played by epigenetics in both plant development and stress response. Relatively recent advances in analytical methodology have allowed for a significant expansion of what is known about genome-wide mapping of DNA methylation and histone modifications. In this review, we explore the different modification patterns in plant epigenetics, and the key factors involved in the epigenetic process, in order to illustrate various putative mechanisms. Experimental technology to exploit these modifications, and proposed focus areas for future plant epigenetic research, are also presented.
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Affiliation(s)
- Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China.
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1575
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Abstract
As part of the PLoS Epigenetics Collection, Caroline Relton and George Davey Smith discuss the potential of epigenetics for the treatment and prevention of common complex diseases, including cancer.
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Affiliation(s)
- Caroline L Relton
- Human Nutrition Research Centre, Institute of Human Genetics, Newcastle University, Newcastle upon Tyne, United Kingdom.
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1576
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Fischer A, Sananbenesi F, Mungenast A, Tsai LH. Targeting the correct HDAC(s) to treat cognitive disorders. Trends Pharmacol Sci 2010; 31:605-17. [PMID: 20980063 DOI: 10.1016/j.tips.2010.09.003] [Citation(s) in RCA: 285] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Revised: 09/15/2010] [Accepted: 09/16/2010] [Indexed: 01/18/2023]
Abstract
Changes in gene expression in the brain may underlie cognitive deficits inherent to normal aging and neurodegenerative disease. However, the mechanisms underlying pathological alterations in the brain transcriptome are incompletely understood. Epigenetic mechanisms such as DNA methylation and histone acetylation have been shown to be important for memory processes in the adult brain. There is accumulating evidence that altered chromatin plasticity and histone acetylation are also involved in cognitive aging, neurodegeneration, and neuropsychiatric diseases. Inhibitors of histone deacetylase (HDAC) exhibit neuroprotective and neuroregenerative properties in animal models of various brain diseases. As such, targeting of HDACs seems to be a promising therapeutic strategy. In this review, we discuss the specific roles of each HDAC protein and the possible function of distinct histone modifications. We hope that this knowledge will aid in the development of diagnostic tools and in designing more potent and specific treatment for neurological disorders targeting selective HDAC proteins.
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Affiliation(s)
- André Fischer
- Laboratory for Aging and Cognitive Diseases, European Neuroscience Institute, Grisebach Str. 5, D-37077 Goettingen, Germany.
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1577
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Nelissen ECM, van Montfoort APA, Dumoulin JCM, Evers JLH. Epigenetics and the placenta. Hum Reprod Update 2010; 17:397-417. [PMID: 20959349 DOI: 10.1093/humupd/dmq052] [Citation(s) in RCA: 259] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The placenta is of utmost importance for intrauterine fetal development and growth. Deregulation of placentation can lead to adverse outcomes for both mother and fetus, e.g. gestational trophoblastic disease (GTD), pre-eclampsia and fetal growth retardation. A significant factor in placental development and function is epigenetic regulation. METHODS This review summarizes the current knowledge in the field of epigenetics in relation to placental development and function. Relevant studies were identified by searching PubMed, Medline and reference sections of all relevant studies and reviews. RESULTS Epigenetic regulation of the placenta evolves during preimplantation development and further gestation. Epigenetic marks, like DNA methylation, histone modifications and non-coding RNAs, affect gene expression patterns. These expression patterns, including the important parent-of-origin-dependent gene expression resulting from genomic imprinting, play a pivotal role in proper fetal and placental development. Disturbed placental epigenetics has been demonstrated in cases of intrauterine growth retardation and small for gestational age, and also appears to be involved in the pathogenesis of pre-eclampsia and GTD. Several environmental effects have been investigated so far, e.g. ethanol, oxygen tension as well as the effect of several aspects of assisted reproduction technologies on placental epigenetics. CONCLUSIONS Studies in both animals and humans have made it increasingly clear that proper epigenetic regulation of both imprinted and non-imprinted genes is important in placental development. Its disturbance, which can be caused by various environmental factors, can lead to abnormal placental development and function with possible consequences for maternal morbidity, fetal development and disease susceptibility in later life.
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Affiliation(s)
- Ewka C M Nelissen
- Department of Obstetrics and Gynaecology, Research Institute Growth & Development (GROW), Center for Reproductive Medicine, Maastricht University Medical Centre, MUMC+, PO Box 5800, 6202 AZ Maastricht, The Netherlands.
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1578
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Gräff J, Franklin TB, Mansuy IM. [Epigenetics and memory]. Biol Aujourdhui 2010; 204:131-7. [PMID: 20950557 DOI: 10.1051/jbio/2010007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2010] [Indexed: 11/15/2022]
Abstract
The epigenetic marking of chromatin in the brain has recently been recognized as an essential mechanism for brain functions such as learning and memory formation. It allows nerve cells not only to respond to environmental stimuli and modulate their profile of gene expression, but also to establish and maintain their own identity. The epigenetic code is conferred by a set of covalent modifications on the basic elements of chromatin, DNA and histone proteins. These changes are catalyzed by specific enzymes and mechanisms, which include DNA methylation, and post-translational modifications of histone proteins such as acetylation, phosphorylation, methylation and ubiquitination. They are both stable and highly dynamic, and are triggered during stimulation of neuronal circuits but can also persist thereafter. Their study in animal models has demonstrated their importance, and revealed some of their modes of function.
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Affiliation(s)
- Johannes Gräff
- Brain Research Institute, University of Zurich, Zurich, Switzerland
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1579
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Selvi BR, Cassel JC, Kundu TK, Boutillier AL. Tuning acetylation levels with HAT activators: Therapeutic strategy in neurodegenerative diseases. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2010; 1799:840-53. [DOI: 10.1016/j.bbagrm.2010.08.012] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Revised: 08/24/2010] [Accepted: 08/27/2010] [Indexed: 10/19/2022]
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1580
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Environmental epigenetics of asthma: an update. J Allergy Clin Immunol 2010; 126:453-65. [PMID: 20816181 DOI: 10.1016/j.jaci.2010.07.030] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Revised: 07/27/2010] [Accepted: 07/29/2010] [Indexed: 12/29/2022]
Abstract
Asthma, a chronic inflammatory disorder of the airway, is influenced by interplay between genetic and environmental factors now known to be mediated by epigenetics. Aberrant DNA methylation, altered histone modifications, specific microRNA expression, and other chromatin alterations orchestrate a complex early-life reprogramming of immune T-cell response, dendritic cell function, macrophage activation, and a breach of airway epithelial barrier that dictates asthma risk and severity in later life. Adult-onset asthma is under analogous regulation. The sharp increase in asthma prevalence over the past 2 or 3 decades and the large variations among populations of similar racial/ethnic background but different environmental exposures favors a strong contribution of environmental factors. This review addresses the fundamental question of whether environmental influences on asthma risk, severity, and steroid resistance are partly due to differential epigenetic modulations. Current knowledge on the epigenetic effects of tobacco smoke, microbial allergens, oxidants, airborne particulate matter, diesel exhaust particles, polycyclic aromatic hydrocarbons, dietary methyl donors and other nutritional factors, and dust mites is discussed. Exciting findings have been generated by rapid technological advances and well-designed experimental and population studies. The discovery and validation of epigenetic biomarkers linked to exposure, asthma, or both might lead to better epigenotyping of risk, prognosis, treatment prediction, and development of novel therapies.
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1581
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Meeran SM, Ahmed A, Tollefsbol TO. Epigenetic targets of bioactive dietary components for cancer prevention and therapy. Clin Epigenetics 2010; 1:101-116. [PMID: 21258631 PMCID: PMC3024548 DOI: 10.1007/s13148-010-0011-5] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The emergent interest in cancer epigenetics stems from the fact that epigenetic modifications are implicated in virtually every step of tumorigenesis. More interestingly, epigenetic changes are reversible heritable changes that are not due to the alteration in DNA sequence but have potential to alter gene expression. Dietary agents consist of many bioactive ingredients which actively regulate various molecular targets involved in tumorigenesis. We present evidence that numerous bioactive dietary components can interfere with various epigenetic targets in cancer prevention and therapy. These agents include curcumin (turmeric), genistein (soybean), tea polyphenols (green tea), resveratrol (grapes), and sulforaphane (cruciferous vegetables). These bioactive components alter the DNA methylation and histone modifications required for gene activation or silencing in cancer prevention and therapy. Bioactive components mediate epigenetic modifications associated with the induction of tumor suppressor genes such as p21WAF1/CIP1 and inhibition of tumor promoting genes such as the human telomerase reverse transcriptase during tumorigenesis processes. Here, we present considerable evidence that bioactive components and their epigenetic targets are associated with cancer prevention and therapy which should facilitate novel drug discovery and development. In addition, remarkable advances in our understanding of basic epigenetic mechanisms as well as the rapid progress that is being made in developing powerful new technologies, such as those for sensitive and quantitative detection of epigenetic and epigenomic changes in cancer biology, hold great promise for novel epigenetic approaches to cancer prevention and therapy.
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Affiliation(s)
- Syed M. Meeran
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Campbell Hall 175, Birmingham, AL 35294-1170 USA
| | - Amiya Ahmed
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Campbell Hall 175, Birmingham, AL 35294-1170 USA
| | - Trygve O. Tollefsbol
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Campbell Hall 175, Birmingham, AL 35294-1170 USA
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL USA
- Center for Aging, University of Alabama at Birmingham, Birmingham, AL USA
- Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL USA
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1582
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Helmreich EJ. Ways and means of coping with uncertainties of the relationship of the genetic blue print to protein structure and function in the cell. Cell Commun Signal 2010; 8:26. [PMID: 20849616 PMCID: PMC2954850 DOI: 10.1186/1478-811x-8-26] [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] [Received: 07/19/2010] [Accepted: 09/17/2010] [Indexed: 11/24/2022] Open
Abstract
As one of the disciplines of systems biology, proteomics is central to enabling the elucidation of protein function within the cell; furthermore, the question of how to deduce protein structure and function from the genetic readout has gained new significance. This problem is of particular relevance for proteins engaged in cell signalling. In dealing with this question, I shall critically comment on the reliability and predictability of transmission and translation of the genetic blue print into the phenotype, the protein. Based on this information, I will then evaluate the intentions and goals of today's proteomics and gene-networking and appraise their chances of success. Some of the themes commented on in this publication are explored in greater detail with particular emphasis on the historical roots of concepts and techniques in my forthcoming book, published in German: Von Molekülen zu Zellen. 100 Jahre experimentelle Biologie. Betrachtungen eines Biochemikers.
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1583
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Fernandez AZ, Siebel AL, El-Osta A. Atherogenic factors and their epigenetic relationships. Int J Vasc Med 2010; 2010:437809. [PMID: 21152193 PMCID: PMC2989709 DOI: 10.1155/2010/437809] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Accepted: 08/25/2010] [Indexed: 02/08/2023] Open
Abstract
Hypercholesterolemia, homocysteine, oxidative stress, and hyperglycemia have been recognized as the major risk factors for atherogenesis. Their impact on the physiology and biochemistry of vascular cells has been widely demonstrated for the last century. However, the recent discovery of the role of epigenetics in human disease has opened up a new field in the study of atherogenic factors. Thus, epigenetic tags in endothelial, smooth muscle, and immune cells seem to be differentially affected by similar atherogenic stimuli. This paper summarizes some recent works on expression of histone-modifying enzymes and DNA methylation directly linked to the presence of risk factors that could lead to the development or prevention of the atherosclerotic process.
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Affiliation(s)
- Ana Z. Fernandez
- Hemostasia and Vascular Genetics Laboratory, Biophysics and Biochemistry Center, Venezuelan Institute for Scientific Research IVIC, Carretera Panamericana km11, P.O. 26973, Caracas 1020, Venezuela
- Epigenetics in Human Health and Disease Laboratory, Baker IDI Heart and Diabetes Institute, Melbourne, VIC 3004, Australia
| | - Andrew L. Siebel
- Epigenetics in Human Health and Disease Laboratory, Baker IDI Heart and Diabetes Institute, Melbourne, VIC 3004, Australia
| | - Assam El-Osta
- Epigenetics in Human Health and Disease Laboratory, Baker IDI Heart and Diabetes Institute, Melbourne, VIC 3004, Australia
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1584
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Cancer: evolutionary, genetic and epigenetic aspects. Clin Epigenetics 2010; 1:85-100. [PMID: 22704202 PMCID: PMC3365664 DOI: 10.1007/s13148-010-0010-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Accepted: 08/31/2010] [Indexed: 12/22/2022] Open
Abstract
There exist two paradigms about the nature of cancer. According to the generally accepted one, cancer is a by-product of design limitations of a multi-cellular organism (Greaves, Nat Rev Cancer 7:213–221, 2007). The essence of the second resides in the question “Does cancer kill the individual and save the species?” (Sommer, Hum Mutat 3:166–169, 1994). Recent data on genetic and epigenetic mechanisms of cell transformation summarized in this review support the latter point of view, namely that carcinogenesis is an evolutionary conserved phenomenon—a programmed death of an organism. It is assumed that cancer possesses an important function of altruistic nature: as a mediator of negative selection, it serves to preserve integrity of species gene pool and to mediate its evolutionary adjustment. Cancer fulfills its task due apparently to specific killer function, understanding mechanism of which may suggest new therapeutic strategy.
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1585
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1586
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Plazas-Mayorca MD, Vrana KE. Proteomic investigation of epigenetics in neuropsychiatric disorders: a missing link between genetics and behavior? J Proteome Res 2010; 10:58-65. [PMID: 20735116 DOI: 10.1021/pr100463y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Neuropsychiatric disorders affect a large segment of the human population and result in large costs to society. The majority of such disorders have unknown underlying causes. Recent evidence suggests an important role for epigenetic regulation in the emergence of neuropsychiatric disease. Epigenetics may provide a link between genetic and environmental factors and behavior. Epigenetic signaling involves changes on the structure of chromatin; such changes are often triggered and maintained by the post-translational modification of chromatin proteins and/or DNA. Recent proteomic technologies have enabled the study of epigenetic mechanisms in a high-throughput manner. This review will provide an overview of the major epigenetic pathways and modern techniques for their study, before focusing on experimental evidence supporting a strong role for epigenetics in selected psychiatric disorders such as depression, schizophrenia, and drug addiction. These results highlight a great need for the inclusion of the proteomic characterization of epigenetic mechanisms in the study of gene/disease associations in psychiatric disorders.
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Affiliation(s)
- Mariana D Plazas-Mayorca
- Department of Pharmacology, Penn State University College of Medicine, Hershey, Pennsylvania, USA
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1587
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Diguet A, Mani NK, Geoffroy M, Sollogoub M, Baigl D. Photosensitive Surfactants with Various Hydrophobic Tail Lengths for the Photocontrol of Genomic DNA Conformation with Improved Efficiency. Chemistry 2010; 16:11890-6. [DOI: 10.1002/chem.201001579] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Antoine Diguet
- Department of Chemistry, Ecole Normale Superieure, 24 rue Lhomond, 75005 Paris (France), Fax: (+33) 1‐4432‐2402
| | - Naresh Kumar Mani
- Department of Chemistry, Ecole Normale Superieure, 24 rue Lhomond, 75005 Paris (France), Fax: (+33) 1‐4432‐2402
| | - Marie Geoffroy
- Department of Chemistry, Ecole Normale Superieure, 24 rue Lhomond, 75005 Paris (France), Fax: (+33) 1‐4432‐2402
| | - Matthieu Sollogoub
- UPMC Univ Paris 06, Institut Parisien de Chimie Moléculaire (UMR CNRS 7201), FR 2769, C. 181, 4 Place Jussieu, 75005 Paris (France)
| | - Damien Baigl
- Department of Chemistry, Ecole Normale Superieure, 24 rue Lhomond, 75005 Paris (France), Fax: (+33) 1‐4432‐2402
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1588
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Münzel M, Lercher L, Müller M, Carell T. Chemical discrimination between dC and 5MedC via their hydroxylamine adducts. Nucleic Acids Res 2010; 38:e192. [PMID: 20813757 PMCID: PMC2995083 DOI: 10.1093/nar/gkq724] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The presence of the methylated nucleobase 5MedC in CpG islands is a key factor that determines gene silencing. False methylation patterns are responsible for deteriorated cellular development and are a hallmark of many cancers. Today genes can be sequenced for the content of 5MedC only with the help of the bisulfite reagent, which is based exclusively on chemical reactivity differences established by the additional methyl group. Despite intensive optimization of the bisulfite protocol, the method still has specificity problems. Most importantly ∼95% of the DNA analyte is degraded during the analysis procedure. We discovered that the reagent O-allylhydroxylamine is able to discriminate between dC and 5MedC. The reagent, in contrast to bisulfite, does not exploit reactivity differences but gives directly different reaction products. The reagent forms a stable mutagenic adduct with dC, which can exist in two states (E versus Z). In case of dC the allylhydroxylamine adduct switches into the E-isomeric form, which generates dC to dT transition mutations that can easily be detected by established methods. Significantly, the 5MedC-adduct adopts exclusively the Z-isomeric form, which causes the polymerase to stop. O-allylhydroxylamine does allow differentiation between dC and 5MedC with high accuracy, leading towards a novel and mild chemistry for methylation analysis.
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Affiliation(s)
- Martin Münzel
- Department of Chemistry, Center for Integrated Protein Science Munich, Ludwig-Maximilians University, Butenandtstr. 5-13, 81377 Munich, Germany
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1589
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Natoli G. Maintaining cell identity through global control of genomic organization. Immunity 2010; 33:12-24. [PMID: 20643336 DOI: 10.1016/j.immuni.2010.07.006] [Citation(s) in RCA: 149] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2010] [Indexed: 02/06/2023]
Abstract
Cell differentiation entails early lineage choices leading to the activation, and the subsequent maintenance, of the gene expression program characteristic of each cell type. Alternative lineage choices involve the activation of different regulatory and coding regions of the genome, a process instructed by lineage-determining transcription factors, and at least in part mediated by the deposition of chromatin marks that modify functionality and accessibility of the underlying genome. According to classic epigenetics, subsequent maintenance of chromatin marks across mitoses and in spite of environmental perturbations occurs largely through autonomous and unsupervised mechanisms. However, paradigmatic genetic and biochemical studies in immune system and hematopoietic cells strongly point to the concept that both induction and maintenance of the differentiated state require constant supervision by lineage-determining transcription factors, which may act to globally organize the genome in both the one- and the three-dimensional space.
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Affiliation(s)
- Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy
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1590
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Bale TL, Baram TZ, Brown AS, Goldstein JM, Insel TR, McCarthy MM, Nemeroff CB, Reyes TM, Simerly RB, Susser ES, Nestler EJ. Early life programming and neurodevelopmental disorders. Biol Psychiatry 2010; 68:314-9. [PMID: 20674602 PMCID: PMC3168778 DOI: 10.1016/j.biopsych.2010.05.028] [Citation(s) in RCA: 643] [Impact Index Per Article: 45.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Revised: 05/17/2010] [Accepted: 05/20/2010] [Indexed: 02/06/2023]
Abstract
For more than a century, clinical investigators have focused on early life as a source of adult psychopathology. Early theories about psychic conflict and toxic parenting have been replaced by more recent formulations of complex interactions of genes and environment. Although the hypothesized mechanisms have evolved, a central notion remains: early life is a period of unique sensitivity during which experience confers enduring effects. The mechanisms for these effects remain almost as much a mystery today as they were a century ago. Recent studies suggest that maternal diet can program offspring growth and metabolic pathways, altering lifelong susceptibility to diabetes and obesity. If maternal psychosocial experience has similar programming effects on the developing offspring, one might expect a comparable contribution to neurodevelopmental disorders, including affective disorders, schizophrenia, autism, and eating disorders. Due to their early onset, prevalence, and chronicity, some of these disorders, such as depression and schizophrenia, are among the highest causes of disability worldwide according to the World Health Organization 2002 report. Consideration of the early life programming and transcriptional regulation in adult exposures supports a critical need to understand epigenetic mechanisms as a critical determinant in disease predisposition. Incorporating the latest insight gained from clinical and epidemiological studies with potential epigenetic mechanisms from basic research, the following review summarizes findings from a workshop on Early Life Programming and Neurodevelopmental Disorders held at the University of Pennsylvania in 2009.
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1591
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Abstract
Variations in phenotype reflect the influence of environmental conditions during development on cellular functions, including that of the genome. The recent integration of epigenetics into developmental psychobiology illustrates the processes by which environmental conditions in early life structurally alter DNA, providing a physical basis for the influence of the perinatal environmental signals on phenotype over the life of the individual. This review focuses on the enduring effects of naturally occurring variations in maternal care on gene expression and phenotype to provide an example of environmentally driven plasticity at the level of the DNA, revealing the interdependence of gene and environmental in the regulation of phenotype.
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1592
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Grafodatskaya D, Chung B, Szatmari P, Weksberg R. Autism spectrum disorders and epigenetics. J Am Acad Child Adolesc Psychiatry 2010; 49:794-809. [PMID: 20643313 DOI: 10.1016/j.jaac.2010.05.005] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Revised: 05/05/2010] [Accepted: 05/10/2010] [Indexed: 10/18/2022]
Abstract
OBJECTIVE Current research suggests that the causes of autism spectrum disorders (ASD) are multifactorial and include both genetic and environmental factors. Several lines of evidence suggest that epigenetics also plays an important role in ASD etiology and that it might, in fact, integrate genetic and environmental influences to dysregulate neurodevelopmental processes. The objective of this review is to illustrate how epigenetic modifications that are known to alter gene expression without changing primary DNA sequence may play a role in the etiology of ASD. METHOD In this review, we summarize current knowledge about epigenetic modifications to genes and genomic regions possibly involved in the etiology of ASD. RESULTS Several genetic syndromes comorbid with ASD, which include Rett, Fragile X, Prader-Willi, Angelman, and CHARGE (Coloboma of the eye, Heart defects, Atresia of the nasal choanae, Retardation of growth and/or development, Genital and/or urinary abnormalities, and Ear abnormalities and deafness), all demonstrate dysregulation of epigenetic marks or epigenetic mechanisms. We report also on genes or genomic regions exhibiting abnormal epigenetic regulation in association with either syndromic (15q11-13 maternal duplication) or nonsyndromic forms of ASD. Finally, we discuss the state of current knowledge regarding the etiologic role of environmental factors linked to both the development of ASD and epigenetic dysregulation. CONCLUSION Data reviewed in this article highlight a variety of situations in which epigenetic dysregulation is associated with the development of ASD, thereby supporting a role for epigenetics in the multifactorial etiologies of ASD.
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1593
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Abstract
Adult muscle is extremely plastic. However, the muscle precursor cells associated with those fibres show stable and heritable differences in gene expression indicative of epigenetic imprinting. Epigenetic processes in the development of skeletal muscle have been appreciated for over a decade; however, there are a paucity of studies looking at whether epigenetics determines the phenotype of adult and/or ageing skeletal muscle. This review presents the evidence that epigenetics plays a role in determining adult muscle function and a series of unanswered questions that would greatly increase our understanding of how epigenetics works in adult muscle. With the increased interest in epigenetics, over the next few years this field will begin to unfold in unimaginable directions.
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Affiliation(s)
- K Baar
- Department of Neurobiology, Physiology, and Behavior, University of California, Davis, CA 95616, USA.
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1594
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Bagot RC, Meaney MJ. Epigenetics and the biological basis of gene x environment interactions. J Am Acad Child Adolesc Psychiatry 2010; 49:752-71. [PMID: 20643310 DOI: 10.1016/j.jaac.2010.06.001] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Revised: 05/31/2010] [Accepted: 06/07/2010] [Indexed: 10/18/2022]
Abstract
OBJECTIVE Child and adolescent psychiatry is rife with examples of the sustained effects of early experience on brain function. The study of behavioral genetics provides evidence for a relation between genomic variation and personality and with the risk for psychopathology. A pressing challenge is that of conceptually integrating findings from genetics into the study of personality without regressing to arguments concerning the relative importance of genomic variation versus nongenomic or environmental influences. METHOD Epigenetics refers to functionally relevant modifications to the genome that do not involve a change in nucleotide sequence. This review examines epigenetics as a candidate biological mechanism for gene x environment interactions, with a focus on environmental influences that occur during early life and that yield sustained effects on neural development and function. RESULTS The studies reviewed suggest that epigenetic remodeling occurs in response to the environmental activation of cellular signalling pathways associated with synaptic plasticity, epigenetic marks are actively remodeled during early development in response to environmental events that regulate neural development and function, and epigenetic marks are subject to remodeling by environmental influences even at later stages in development. CONCLUSION Epigenetic remodeling might serve as an ideal mechanism for phenotypic plasticity--the process whereby the environment interacts with the genome to produce individual differences in the expression of specific traits.
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Affiliation(s)
- Rosemary C Bagot
- Sackler Program for Epigenetics and Psychobiology, McGill University and Douglas Mental Health University Institute, Montreal, Canada
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1595
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Baye TM, Martin LJ, Khurana Hershey GK. Application of genetic/genomic approaches to allergic disorders. J Allergy Clin Immunol 2010; 126:425-36; quiz 437-8. [PMID: 20638111 DOI: 10.1016/j.jaci.2010.05.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Revised: 04/28/2010] [Accepted: 05/07/2010] [Indexed: 11/16/2022]
Abstract
Completion of the human genome project and rapid progress in genetics and bioinformatics have enabled the development of large public databases, which include genetic and genomic data linked to clinical health data. With the massive amount of information available, clinicians and researchers have the unique opportunity to complement and integrate their daily practice with the existing resources to clarify the underlying cause of complex phenotypes, such as allergic diseases. The genome itself is now often used as a starting point for many studies, and multiple innovative approaches have emerged applying genetic/genomic strategies to key questions in the field of allergy and immunology. There have been several successes that have uncovered new insights into the biologic underpinnings of allergic disorders. Herein we will provide an in-depth review of genomic approaches to identifying genes and biologic networks involved in allergic diseases. We will discuss genetic and phenotypic variation, statistical approaches for gene discovery, public databases, functional genomics, clinical implications, and the challenges that remain.
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Affiliation(s)
- Tesfaye M Baye
- Division of Asthma Research, University of Cincinnati, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
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1596
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Bredy TW, Sun YE, Kobor MS. How the epigenome contributes to the development of psychiatric disorders. Dev Psychobiol 2010; 52:331-42. [PMID: 20127889 DOI: 10.1002/dev.20424] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Epigenetics commonly refers to the developmental process by which cellular traits are established and inherited without a change in DNA sequence. These mechanisms of cellular memory also orchestrate gene expression in the adult brain and recent evidence suggests that the "epigenome" represents a critical interface between environmental signals, activation, repression and maintenance of genomic responses, and persistent behavior. We here review the current state of knowledge regarding the contribution of the epigenome toward the development of psychiatric disorders.
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Affiliation(s)
- Timothy W Bredy
- Queensland Brain Institute, University of Queensland, Brisbane, QC 4072, Australia.
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1597
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Yu XY, Geng YJ, Liang JL, Lin QX, Lin SG, Zhang S, Li Y. High levels of glucose induce apoptosis in cardiomyocyte via epigenetic regulation of the insulin-like growth factor receptor. Exp Cell Res 2010; 316:2903-9. [PMID: 20633551 DOI: 10.1016/j.yexcr.2010.07.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Revised: 07/02/2010] [Accepted: 07/06/2010] [Indexed: 12/28/2022]
Abstract
Diabetic hyperglycemia result in cardiovascular complications, but the mechanisms by which high levels of glucose (HG) cause diabetic cardiomyopathy are not known. We investigate whether HG-induced repression of insulin-like growth factor 1 receptor (IGF-1R) mediated by epigenetic modifications is one potential mechanism. We found that HG resulted in decreased IGF-1 receptor (IGF-1R) mRNA levels, and IGF-1R protein when compared with H9C2 rat cardiomyocyte cells incubated in normal glucose. HG also induced apoptosis of H9C2 cells. The effects of HG on reduced expression of IGF-1R and increased apoptosis were blocked by silencing p53 with small interference RNA but not by non-targeting scrambled siRNA. Moreover, HG negatively regulated IGF-1R promoter activity as determined by ChIP analysis, which was dependent on p53 since siRNA-p53 attenuated the effects of HG on IGF-1R promoter activity. HG also increased the association of p53 with histone deacetylase 1 (HDAC1), and decreased the association of acetylated histone-4 with the IGF-1R promoter. Furthermore, HDAC inhibitor relieved the repression of IGF-1R following HG state. These results suggest that HG-induced repression of IGF-1R is mediated by the association of p53 with the IGF-1R promoter, and by the subsequent enhanced recruitment of chromatin-modifying proteins, such as HDAC1, to the IGF-1R promoter-p53 complex. In conclusion, our data demonstrate that HG decreases expression of IGF-1R and decreases the association of acetylated histone-4 with the IGF-1R promoter. These studies may help delineate the complex pathways regulating diabetic cardiomyopathy, and have implications for the development of novel therapeutic strategies to prevent diabetic cardiomyopathy by epigenetic regulation of IGF-1R.
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Affiliation(s)
- Xi-Yong Yu
- Medical Research Center, Guangdong General Hospital, Guangdong Provincial Cardiovascular Institute, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, P.R. China.
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1598
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Iborra M, Bernuzzi F, Invernizzi P, Danese S. MicroRNAs in autoimmunity and inflammatory bowel disease: crucial regulators in immune response. Autoimmun Rev 2010; 11:305-14. [PMID: 20627134 DOI: 10.1016/j.autrev.2010.07.002] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Accepted: 07/08/2010] [Indexed: 02/07/2023]
Abstract
MicroRNAs (miRNAs) have recently emerged as a new class of modulators of gene expression at the post-transcriptional level. The function of miRNA is the control of protein production by targeting mRNAs for translational repression or degradation. MiRNAs play a critical role in many biological processes such as cellular proliferation and maturation, apoptosis, regulation of chronic inflammation and development of cancer. It has recently been discovered that miRNAs are differentially expressed in autoimmune diseases (AID) and miRNA regulation may impact in the development or prevention of AID. In this paper we review the importance of miRNAs in AID in particular in inflammatory bowel disease (IBD). IBD is an AID whose pathophysiology remains uncertain. It is generally hypothesized that IBD is caused by the enteric microflora in genetically predisposed patients with an immune dysregulation in the gastrointestinal tract. Knowing the typical miRNA pattern of IBD will improve our knowledge of the pathogenesis of this disease and will lead to future well-focused projects to study the regulatory function of such miRNAs. Furthermore, it is possible that some miRNAs are specific to IBD and could serve as biomarkers with clinical applications for the diagnosis or assessment of disease activity.
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Affiliation(s)
- Marisa Iborra
- Fundacion Hospital Universitari La Fe, Department of Gastroenterology, Hospital Universitari La Fe, Valencia, Spain
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Blanchet S, Clobert J, Danchin E. The role of public information in ecology and conservation: an emphasis on inadvertent social information. Ann N Y Acad Sci 2010; 1195:149-68. [PMID: 20536822 DOI: 10.1111/j.1749-6632.2010.05477.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Public information is an emerging major topic in ecology and evolution. We review the literature about the role of public information in ecology and conservation while mainly focusing on inadvertent social information (ISI), which constitutes a major form of public information. We first define the terms of biological information that we use. We then review the accruing evidence for ISI use in many fitness-affecting decisions in plants and animals. We generalize concepts of information to encompass interspecific interactions. We then develop how intra- and interspecific information flows actually shape ecological and evolutionary dynamics. We then discuss some of the application of adopting an information-driven approach to ecology and evolution in conservation biology. Our hope is to favor the transfer of knowledge from ecology and evolution to conservation biology. We claim that this is the only way to design efficient conservation actions and illustrate how ignoring concepts of information may lead us to design conservation actions that drive endangered populations toward rather than away from extinction.
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Affiliation(s)
- Simon Blanchet
- CNRS, EDB (Laboratoire Evolution et Diversité Biologique), Toulouse, France
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