1651
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Serre D, Lee BH, Ting AH. MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome. Nucleic Acids Res 2009; 38:391-9. [PMID: 19906696 PMCID: PMC2811030 DOI: 10.1093/nar/gkp992] [Citation(s) in RCA: 286] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
DNA methylation is an epigenetic modification involved in both normal developmental processes and disease states through the modulation of gene expression and the maintenance of genomic organization. Conventional methods of DNA methylation analysis, such as bisulfite sequencing, methylation sensitive restriction enzyme digestion and array-based detection techniques, have major limitations that impede high-throughput genome-wide analysis. We describe a novel technique, MBD-isolated Genome Sequencing (MiGS), which combines precipitation of methylated DNA by recombinant methyl-CpG binding domain of MBD2 protein and sequencing of the isolated DNA by a massively parallel sequencer. We utilized MiGS to study three isogenic cancer cell lines with varying degrees of DNA methylation. We successfully detected previously known methylated regions in these cells and identified hundreds of novel methylated regions. This technique is highly specific and sensitive and can be applied to any biological settings to identify differentially methylated regions at the genomic scale.
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Affiliation(s)
- David Serre
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Ave, mail code NE50, Cleveland, OH 44195, USA.
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1652
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Vitzthum VJ. The ecology and evolutionary endocrinology of reproduction in the human female. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2009; 140 Suppl 49:95-136. [DOI: 10.1002/ajpa.21195] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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1653
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Latzel V, Hájek T, Klimešová J, Gómez S. Nutrients and disturbance history in twoPlantagospecies: maternal effects as a clue for observed dichotomy between resprouting and seeding strategies. OIKOS 2009. [DOI: 10.1111/j.1600-0706.2009.17767.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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1654
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Epigenetic side-effects of common pharmaceuticals: A potential new field in medicine and pharmacology. Med Hypotheses 2009; 73:770-80. [DOI: 10.1016/j.mehy.2008.10.039] [Citation(s) in RCA: 158] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Revised: 09/29/2008] [Accepted: 10/01/2008] [Indexed: 11/22/2022]
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1655
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Ding Y, Lapko H, Ndamukong I, Xia Y, Al-Abdallat A, Lalithambika S, Sadder M, Saleh A, Fromm M, Riethoven JJ, Lu G, Avramova Z. The Arabidopsis chromatin modifier ATX1, the myotubularin-like AtMTM and the response to drought. PLANT SIGNALING & BEHAVIOR 2009; 4:1049-58. [PMID: 19901554 PMCID: PMC2819512 DOI: 10.4161/psb.4.11.10103] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Accepted: 09/15/2009] [Indexed: 05/19/2023]
Abstract
Plants respond to environmental stresses by altering transcription of genes involved in the response. The chromatin modifier ATX1 regulates expression of a large number of genes; consequently, factors that affect ATX1 activity would also influence expression from ATX1-regulated genes. Here, we demonstrate that dehydration is such a factor implicating ATX1 in the plant's response to drought. In addition, we report that a hitherto unknown Arabidopsis gene, At3g10550, encodes a phosphoinositide 3'-phosphatase related to the animal myotubularins (AtMTM1). Myotubularin activities in plants have not been described and herein, we identify an overlapping set of genes co-regulated by ATX1 and AtMTM under drought conditions. We propose that these shared genes represent the ultimate targets of partially overlapping branches of the pathways of the nuclear ATX1 and the cytoplasmic AtMTM1. Our analyses offer first genome-wide insights into the relationship of an epigenetic factor and a lipid phosphatase from the other end of a shared drought responding pathway in Arabidopsis.
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Affiliation(s)
- Yong Ding
- UNL Center for Biotechnology and Plant Science Initiative; UNL; Lincoln, NE USA
| | - Hanna Lapko
- School of Biological Sciences; UNL; Lincoln, NE USA
| | | | - Yuannan Xia
- Genomics Core Research Facility; Center for Biotechnology UNL; Lincoln, NE USA
| | - Ayed Al-Abdallat
- UNL Center for Biotechnology and Plant Science Initiative; UNL; Lincoln, NE USA
- Faculty of Agriculture; University of Jordan; Amman, Jordan
| | | | - Monther Sadder
- School of Biological Sciences; UNL; Lincoln, NE USA
- Faculty of Agriculture; University of Jordan; Amman, Jordan
| | | | - Michael Fromm
- UNL Center for Biotechnology and Plant Science Initiative; UNL; Lincoln, NE USA
| | - Jean-Jack Riethoven
- Bioinformatics Core Research Facility; Center for Biotechnology UNL; Lincoln, NE USA
| | - Guoqing Lu
- Department of Biology; University of Nebraska at Omaha; Omaha, NE USA
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1656
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Abstract
The contribution of horizontal gene transfer to evolution has been controversial since it was suggested to be a force driving evolution in the microbial world. In this paper, I review the current standpoint on horizontal gene transfer in evolutionary thinking and discuss how important horizontal gene transfer is in evolution in the broad sense, and particularly in prokaryotic evolution. I review recent literature, asking, first, which processes are involved in the evolutionary success of transferred genes and, secondly, about the extent of horizontal gene transfer towards different evolutionary times. Moreover, I discuss the feasibility of reconstructing ancient phylogenetic relationships in the face of horizontal gene transfer. Finally, I discuss how horizontal gene transfer fits in the current neo-Darwinian evolutionary paradigm and conclude there is a need for a new evolutionary paradigm that includes horizontal gene transfer as well as other mechanisms in the explanation of evolution.
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Affiliation(s)
- Luis Boto
- Departamento Biodiversidad y Biología Evolutiva, Museo Nacional Ciencias Naturales, CSIC, C/José Gutierrez Abascal 2, 28006 Madrid, Spain.
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1657
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Kim MS, Kondo T, Takada I, Youn MY, Yamamoto Y, Takahashi S, Matsumoto T, Fujiyama S, Shirode Y, Yamaoka I, Kitagawa H, Takeyama KI, Shibuya H, Ohtake F, Kato S. DNA demethylation in hormone-induced transcriptional derepression. Nature 2009; 461:1007-12. [PMID: 19829383 DOI: 10.1038/nature08456] [Citation(s) in RCA: 199] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2008] [Accepted: 08/24/2009] [Indexed: 12/23/2022]
Abstract
Epigenetic modifications at the histone level affect gene regulation in response to extracellular signals. However, regulated epigenetic modifications at the DNA level, especially active DNA demethylation, in gene activation are not well understood. Here we report that DNA methylation/demethylation is hormonally switched to control transcription of the cytochrome p450 27B1 (CYP27B1) gene. Reflecting vitamin-D-mediated transrepression of the CYP27B1 gene by the negative vitamin D response element (nVDRE), methylation of CpG sites ((5m)CpG) is induced by vitamin D in this gene promoter. Conversely, treatment with parathyroid hormone, a hormone known to activate the CYP27B1 gene, induces active demethylation of the (5m)CpG sites in this promoter. Biochemical purification of a complex associated with the nVDRE-binding protein (VDIR, also known as TCF3) identified two DNA methyltransferases, DNMT1 and DNMT3B, for methylation of CpG sites, as well as a DNA glycosylase, MBD4 (ref. 10). Protein-kinase-C-phosphorylated MBD4 by parathyroid hormone stimulation promotes incision of methylated DNA through glycosylase activity, and a base-excision repair process seems to complete DNA demethylation in the MBD4-bound promoter. Such parathyroid-hormone-induced DNA demethylation and subsequent transcriptional derepression are impaired in Mbd4(-/-) mice. Thus, the present findings suggest that methylation switching at the DNA level contributes to the hormonal control of transcription.
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Affiliation(s)
- Mi-Sun Kim
- ERATO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchisi, Saitama 332-0012, Japan
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1658
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Saffery R, Ellis J, Morley R. A convergent model for placental dysfunction encompassing combined sub-optimal one-carbon donor and vitamin D bioavailability. Med Hypotheses 2009; 73:1023-8. [PMID: 19819084 DOI: 10.1016/j.mehy.2009.03.057] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Revised: 03/18/2009] [Accepted: 03/22/2009] [Indexed: 01/08/2023]
Abstract
We hypothesise that the risk of placental dysfunction/insufficiency rises cumulatively in response to several interdependent risk factors that convergently regulate 1,25-dihydroxyvitamin D (the biologically active form of vitamin D, [1,25-(OH)(2)D]) levels at the feto-maternal interface. These factors include; (i) disturbances in genetic or epigenetic regulation of one-carbon metabolism and/or vitamin D metabolism and (ii) insufficiency in maternal vitamin D or in dietary intake of micronutrients that are involved in one-carbon donation. We predict that the sub-optimal functioning of folate and vitamin D metabolic pathways, in concert, represents a potential novel risk pathway for adverse pregnancy outcomes. We base this prediction on five observations: In order to test this model, future epidemiological studies aimed at identifying risk factors for disorders linked to sub-optimal placental development and functioning, should: (a) measure circulating precursor molecules (including folate, vitamin B12, homocysteine, and vitamin D) in maternal and cord blood; (b) collect samples for examination of genotypic variation in both one-carbon and vitamin D regulatory genes and, (c) collect samples for examination of epigenetic status of genes regulating vitamin D homeostasis and action in the placenta.
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Affiliation(s)
- Richard Saffery
- Department of Paediatrics, Developmental Epigenetics, Murdoch Childrens Research Institute, University of Melbourne, Parkville, Victoria 3052, Australia.
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1659
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Abstract
Epigenetics is focused on understanding the control of gene expression beyond what is encoded in the sequence of DNA. Central to growing interest in the field is the hope that more can be learned about the epigenetic regulatory mechanisms underlying processes of human development and disease. Researchers have begun to examine epigenetic alterations - such as changes in promoter DNA methylation, genomic imprinting, and expression of miRNA - to learn more about epigenetic regulation in the placenta, an organ whose proper development and function are crucial to the health, growth, and survival of the developing fetus. A number of studies are now making important links between alterations to appropriate epigenetic regulation in the placenta and diseases of gestation and early life. In addition, these studies are adding important insight into our understanding of trophoblast biology and differentiation as well as placental immunology. Examining epigenetic alterations in the placenta will prove especially important in the search for biomarkers of exposure, pathology, and disease risk and can provide critical insights into the biology of development and pathogenesis of disease. Thus, epigenetic alterations may aid in disease diagnosis and prognosis as well as in targeting new treatment and prevention strategies.
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Affiliation(s)
- Matthew A Maccani
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02912, USA
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1660
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Chordate roots of the vertebrate nervous system: expanding the molecular toolkit. Nat Rev Neurosci 2009; 10:736-46. [PMID: 19738625 DOI: 10.1038/nrn2703] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The vertebrate brain is highly complex with millions to billions of neurons. During development, the neural plate border region gives rise to the neural crest, cranial placodes and, in anamniotes, to Rohon-Beard sensory neurons, whereas the boundary region of the midbrain and hindbrain develops organizer properties. Comparisons of developmental gene expression and neuroanatomy between vertebrates and the basal chordate amphioxus, which has only thousands of neurons and lacks a neural crest, most placodes and a midbrain-hindbrain organizer, indicate that these vertebrate features were built on a foundation already present in the ancestral chordate. Recent advances in genomics have provided insights into the elaboration of the molecular toolkit at the invertebrate-vertebrate transition that may have facilitated the evolution of these vertebrate characteristics.
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1661
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Abstract
The term health is commonplace in both everyday parlance and professional discourse. Unfortunately, the term has little objective specification, especially in physiologic terms. When critically examined, even time-honored terms such as homeostasis lack specific measurable referents. The last three decades, however, have witnessed an explosion of information from diverse fields regarding the dynamical basis of biology. This brief review explores a few main ideas, which appear to be coming together to provide biosignatures of health.
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Affiliation(s)
- Joseph P Zbilut
- Adult Health Nursing, College of Nursing, and Molecular Biophysics and Physiology, Rush Medical College, Chicago, Illinois, USA
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1662
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Singh RP, Shiue K, Schomberg D, Zhou FC. Cellular epigenetic modifications of neural stem cell differentiation. Cell Transplant 2009; 18:1197-211. [PMID: 19660178 DOI: 10.3727/096368909x12483162197204] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Emerging information indicates that epigenetic modification (i.e., histone code and DNA methylation) may be integral to the maintenance and differentiation of neural stem cells (NSCs), but their actual involvement has not yet been illustrated. In this study, we demonstrated the dynamic nature of epigenetic marks during the differentiation of quiescent adult rat NSCs in neurospheres. A subpopulation of OCT4(+) NSCs in the neurosphere contained histone marks, trimethylated histone 3 on lysine 27 (3me-H3K27), 2me-H3K4, and acetylated H4 (Ac-H4). A major decrease of these marks was found prior to or during differentiation, and was further diminished or reprogrammed in diverse subpopulations of migrated NSCs expressing nestin or beta-III-tubulin. The DNA methylation mark 5-methyl-cytosine (5-MeC), and DNA methyltransferase (DNMT) 1 and 3a expression also correlated to the state of differentiation; they were highly present in undifferentiated NSCs but downregulated in migrated populations. In contrast, DNA methyl-CpG-binding protein (MBD1) was low in undifferentiated NSCs in neurospheres, but highly appeared in differentiating NSCs. Furthermore, we found an outward translocation of DNA methylation marker 5-MeC, DNMT1, DNMT3a, and MBD1 in NSCs as differentiation began and proceeded; 5-MeC from homogeneous nucleus to peripheral nucleus, and DMNT1a and 3a from nuclear to cytoplasm, indicating chromatin remodeling. Treatment with DNA methylation inhibitor, 5-aza-cytidine, altered DNA methylation and disrupted migration as indicated by a reduction of migrated neurons and differentiation. These results indicate that chromatin is dynamically remodeled when NSCs transform from the quiescent state to active growth, and that DNA methylation modification is essential for neural stem cell differentiation.
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Affiliation(s)
- Rabindra P Singh
- Departments of Anatomy & Cell Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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1663
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Lobo FP, Mota BEF, Pena SDJ, Azevedo V, Macedo AM, Tauch A, Machado CR, Franco GR. Virus-host coevolution: common patterns of nucleotide motif usage in Flaviviridae and their hosts. PLoS One 2009; 4:e6282. [PMID: 19617912 PMCID: PMC2707012 DOI: 10.1371/journal.pone.0006282] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Accepted: 06/17/2009] [Indexed: 12/18/2022] Open
Abstract
Virus-host biological interaction is a continuous coevolutionary process involving both host immune system and viral escape mechanisms. Flaviviridae family is composed of fast evolving RNA viruses that infects vertebrate (mammals and birds) and/or invertebrate (ticks and mosquitoes) organisms. These host groups are very distinct life forms separated by a long evolutionary time, so lineage-specific anti-viral mechanisms are likely to have evolved. Flaviviridae viruses which infect a single host lineage would be subjected to specific host-induced pressures and, therefore, selected by them. In this work we compare the genomic evolutionary patterns of Flaviviridae viruses and their hosts in an attempt to uncover coevolutionary processes inducing common features in such disparate groups. Especially, we have analyzed dinucleotide and codon usage patterns in the coding regions of vertebrate and invertebrate organisms as well as in Flaviviridae viruses which specifically infect one or both host types. The two host groups posses very distinctive dinucleotide and codon usage patterns. A pronounced CpG under-representation was found in the vertebrate group, possibly induced by the methylation-deamination process, as well as a prominent TpA decrease. The invertebrate group displayed only a TpA frequency reduction bias. Flaviviridae viruses mimicked host nucleotide motif usage in a host-specific manner. Vertebrate-infecting viruses possessed under-representation of CpG and TpA, and insect-only viruses displayed only a TpA under-representation bias. Single-host Flaviviridae members which persistently infect mammals or insect hosts (Hepacivirus and insect-only Flavivirus, respectively) were found to posses a codon usage profile more similar to that of their hosts than to related Flaviviridae. We demonstrated that vertebrates and mosquitoes genomes are under very distinct lineage-specific constraints, and Flaviviridae viruses which specifically infect these lineages appear to be subject to the same evolutionary pressures that shaped their host coding regions, evidencing the lineage-specific coevolutionary processes between the viral and host groups.
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Affiliation(s)
- Francisco P Lobo
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
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1664
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Hitchler MJ, Domann FE. Metabolic defects provide a spark for the epigenetic switch in cancer. Free Radic Biol Med 2009; 47:115-27. [PMID: 19362589 PMCID: PMC2728018 DOI: 10.1016/j.freeradbiomed.2009.04.010] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Revised: 04/07/2009] [Accepted: 04/08/2009] [Indexed: 12/18/2022]
Abstract
Cancer is a pathology that is associated with aberrant gene expression and an altered metabolism. Whereas changes in gene expression have historically been attributed to mutations, it has become apparent that epigenetic processes also play a critical role in controlling gene expression during carcinogenesis. Global changes in epigenetic processes, including DNA methylation and histone modifications, have been observed in cancer. These epigenetic alterations can aberrantly silence or activate gene expression during the formation of cancer; however, the process leading to this epigenetic switch in cancer remains unknown. Carcinogenesis is also associated with metabolic defects that increase mitochondrially derived reactive oxygen species, create an atypical redox state, and change the fundamental means by which cells produce energy. Here, we summarize the influence of these metabolic defects on epigenetic processes. Metabolic defects affect epigenetic enzymes by limiting the availability of cofactors like S-adenosylmethionine. Increased production of reactive oxygen species alters DNA methylation and histone modifications in tumor cells by oxidizing DNMTs and HMTs or through direct oxidation of nucleotide bases. Last, the Warburg effect and increased glutamine consumption in cancer influence histone acetylation and methylation by affecting the activity of sirtuins and histone demethylases.
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Affiliation(s)
- Michael J Hitchler
- Department of Radiation Oncology, Free Radical and Radiation Biology Program, University of Iowa, Iowa City, IA 52242, USA
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1665
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Histone acetyl transferases as emerging drug targets. Drug Discov Today 2009; 14:942-8. [PMID: 19577000 DOI: 10.1016/j.drudis.2009.06.008] [Citation(s) in RCA: 230] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 06/24/2009] [Accepted: 06/24/2009] [Indexed: 02/07/2023]
Abstract
Post-translational modifications, such as acetylation or phosphorylation, play a crucial role in the regulation of gene transcription in eukaryotes. Different subtypes of histone acetyl transferases (HATs) catalyze the acetylation of histones on specific lysine residues. A potential role of HATs in the pathology of cancer, asthma, COPD and viral infection has been described. This indicates that specific HAT inhibitors are potential tools for pharmacological research and might find therapeutic applications. This review focuses on the role of the HATs p300, CBP, PCAF and GCN5 in different diseases and the development of small-molecule inhibitors of these enzymes as potential drugs.
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1666
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Bhatti I, Lee A, Lund J, Larvin M. Small RNA: a large contributor to carcinogenesis? J Gastrointest Surg 2009; 13:1379-88. [PMID: 19373515 DOI: 10.1007/s11605-009-0887-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2008] [Accepted: 03/24/2009] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Homeostasis in normal tissue includes balancing cell proliferation and apoptosis (programmed cell death). Mutations in proto-oncogenes or tumor suppressor genes may lead to disruption of normal cellular function, uncontrolled cell proliferation, and subsequent carcinogenesis. DISCUSSION Micro-RNAs (miRNAs) are short (19-24 nucleotide) noncoding RNA sequences that inhibit protein translation and can cause the degradation of subsequent messenger RNA, thus playing an important role in the regulation of gene expression. Aberrant expression of miRNAs has been shown to inhibit tumor suppressor genes or inappropriately activate oncogenes initiating the cancer process. Unique miRNA expression profiles have been found in different cancer types at different stages, suggesting a possible diagnostic application. This review summarizes the current evidence supporting a link between aberrant miRNA expression and carcinogenesis and its possible role in improving diagnosis and treatment of cancers, particularly of gastrointestinal origin.
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Affiliation(s)
- Imran Bhatti
- Division of Surgery, School of Graduate Entry Medicine and Health, University of Nottingham Medical School at Derby, Derby City General Hospital, Uttoxeter Road, Derby, DE22 3DT, UK.
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1667
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Abstract
The stunning possibility of "reprogramming" differentiated somatic cells to express a pluripotent stem cell phenotype (iPS, induced pluripotent stem cell) and the "ground state" character of pluripotency reveal fundamental features of cell fate regulation that lie beyond existing paradigms. The rarity of reprogramming events appears to contradict the robustness with which the unfathomably complex phenotype of stem cells can reliably be generated. This apparent paradox, however, is naturally explained by the rugged "epigenetic landscape" with valleys representing "preprogrammed" attractor states that emerge from the dynamical constraints of the gene regulatory network. This article provides a pedagogical primer to the fundamental principles of gene regulatory networks as integrated dynamic systems and reviews recent insights in gene expression noise and fate determination, thereby offering a formal framework that may help us to understand why cell fate reprogramming events are inherently rare and yet so robust.
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Affiliation(s)
- Sui Huang
- Institute for Biocomplexity and Informatics, University of Calgary, Calgary, AB, Canada.
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1668
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Corballis MC. The evolution and genetics of cerebral asymmetry. Philos Trans R Soc Lond B Biol Sci 2009; 364:867-79. [PMID: 19064358 DOI: 10.1098/rstb.2008.0232] [Citation(s) in RCA: 176] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Handedness and cerebral asymmetry are commonly assumed to be uniquely human, and even defining characteristics of our species. This is increasingly refuted by the evidence of behavioural asymmetries in non-human species. Although complex manual skill and language are indeed unique to our species and are represented asymmetrically in the brain, some non-human asymmetries appear to be precursors, and others are shared between humans and non-humans. In all behavioural and cerebral asymmetries so far investigated, a minority of individuals reverse or negate the dominant asymmetry, suggesting that such asymmetries are best understood in the context of the overriding bilateral symmetry of the brain and body, and a trade-off between the relative advantages and disadvantages of symmetry and asymmetry. Genetic models of handedness, for example, typically postulate a gene with two alleles, one disposing towards right-handedness and the other imposing no directional influence. There is as yet no convincing evidence as to the location of this putative gene, suggesting that several genes may be involved, or that the gene may be monomorphic with variations due to environmental or epigenetic influences. Nevertheless, it is suggested that, in behavioural, neurological and evolutionary terms, it may be more profitable to examine the degree rather than the direction of asymmetry.
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Affiliation(s)
- Michael C Corballis
- Department of Psychology, University of Auckland, Auckland 1142, New Zealand.
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1669
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Rust W, Balakrishnan T, Zweigerdt R. Cardiomyocyte enrichment from human embryonic stem cell cultures by selection of ALCAM surface expression. Regen Med 2009; 4:225-37. [PMID: 19317642 DOI: 10.2217/17460751.4.2.225] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
AIMS The production of a homogenous population of human cardiomyocytes that can be expanded in vitro may facilitate development of replacement tissue lost as a result of cardiac disease and injury. MATERIALS AND METHODS We evaluated the utility of activated leukocyte cell-adhesion molecule, CD166 (ALCAM) expression as a marker for isolating cardiomyocytes from differentiating cultures of human embryonic stem cells (hESCs). Using RT-qPCR, immunohistochemistry and DNA methylation studies, we evaluated the developmental age of hESC-derived cardiomyocytes. RESULTS AND CONCLUSIONS We demonstrate that cardiomyocytes derived from hESC cultures express ALCAM and that this surface antigen can be used to select a population of differentiated cells that are enriched for cardiomyocytes. Expression of contractile proteins and ion channels, and DNA methylation patterns, suggest that ALCAM-enriched cardiomyocytes have an embryonic phenotype. Selected cardiomyocyte populations survive sorting, adhere to collagen-coated tissue culture plastic and proliferate in short-term culture. Long-term in vitro survival of cardiomyocytes was achieved by culturing cells in 3D aggregates.
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Affiliation(s)
- William Rust
- Lonza Walkersville, Inc., 8830 Biggs Ford Road, Walkersville, MD 21793, USA.
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1670
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Abstract
Epigenetic phenomena, and in particular heritable epigenetic changes, or transgenerational effects, are the subject of much discussion in the current literature. This article presents a model of transgenerational epigenetic inheritance and explores the effect of epigenetic inheritance on the risk and recurrence risk of a complex disease. The model assumes that epigenetic modifications of the genome are gained and lost at specified rates and that each modification contributes multiplicatively to disease risk. The potentially high rate of loss of epigenetic modifications causes the probability of identity in state in close relatives to be smaller than is implied by their relatedness. As a consequence, the recurrence risk to close relatives is reduced. Although epigenetic modifications may contribute substantially to average risk, they will not contribute much to recurrence risk and heritability unless they persist on average for many generations. If they do persist for long times, they are equivalent to mutations and hence are likely to be in linkage disequilibrium with SNPs surveyed in genomewide association studies. Thus epigenetic modifications are a potential solution to the problem of missing causality of complex diseases but not to the problem of missing heritability. The model highlights the need for empirical estimates of the persistence times of heritable epialleles.
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1671
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Deciphering morphology in Triatominae: the evolutionary signals. Acta Trop 2009; 110:101-11. [PMID: 19026978 DOI: 10.1016/j.actatropica.2008.09.026] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2008] [Revised: 09/30/2008] [Accepted: 09/30/2008] [Indexed: 11/20/2022]
Abstract
Many species of Triatominae show evidence for morphological plasticity. Frequent taxonomic questions arose from this variability leading to disputes about describing new subspecies, species or even genera. We suggest this phenotypic flexibility is primarily an intraspecific feature, but with potential for evolutionary changes. We present arguments for a selection regime leading to the separation of species having low developmental canalization into morphologically distinct ecotypes. We suggest that these ecotypes, or morphs, or forms, may have evolutionary importance even if gene flow still exists between them. Thus, although we consider the morphological plasticity of Triatominae as an intraspecific trait, we defend the idea that it might represent a common evolutionary route to new species. Speciation processes in Triatominae could result from disruptive selection regimes combined with weak developmental canalization. Added to this basic pattern, accidental events could hasten evolutionary change. We suggest the heterosis as one of them.
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1672
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1673
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Abstract
In mammals, imprinted genes are clustered and at least one gene in each imprinted cluster is a long i.e., macro non-coding (nc) RNA. Most genes in a cluster show concordant parental-specific expression but the ncRNA is the odd one out, and is expressed from the opposite parental chromosome. While reciprocal expression between imprinted macro non-coding RNAs and flanking mRNA genes is indicative of a functional role, only two of three tested macro ncRNAs have been shown to induce imprinted gene expression. The two known functional imprinted macro non-coding RNAs are both RNAPII transcripts with unusual transcriptional properties that may be functionally relevant and their analysis may shed light on the function of non-coding RNAs that have been shown to comprise the majority of the mammalian transcriptome.
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Affiliation(s)
- Paulina A Latos
- CeMM-Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
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1674
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Abstract
Epigenetic mechanisms participate in the regulation of gene transcription in eukaryotes. Two studies in yeast have revealed an additional mechanism for controlling global gene transcription that is based on an inherited self-perpetuating change in the conformation of two different components of key transcriptional regulatory complexes.
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1675
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Wills PR. Informed Generation: Physical origin and biological evolution of genetic codescript interpreters. J Theor Biol 2009; 257:345-58. [DOI: 10.1016/j.jtbi.2008.12.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2008] [Revised: 11/18/2008] [Accepted: 12/17/2008] [Indexed: 11/26/2022]
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1676
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Probst AV, Dunleavy E, Almouzni G. Epigenetic inheritance during the cell cycle. Nat Rev Mol Cell Biol 2009; 10:192-206. [PMID: 19234478 DOI: 10.1038/nrm2640] [Citation(s) in RCA: 564] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Studies that concern the mechanism of DNA replication have provided a major framework for understanding genetic transmission through multiple cell cycles. Recent work has begun to gain insight into possible means to ensure the stable transmission of information beyond just DNA, and has led to the concept of epigenetic inheritance. Considering chromatin-based information, key candidates have arisen as epigenetic marks, including DNA and histone modifications, histone variants, non-histone chromatin proteins, nuclear RNA as well as higher-order chromatin organization. Understanding the dynamics and stability of these marks through the cell cycle is crucial in maintaining a given chromatin state.
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Affiliation(s)
- Aline V Probst
- Laboratory of Nuclear Dynamics and Genome Plasticity, UMR218 Centre National de la Recherche Scientifique/Institut Curie, 26, rue d'Ulm, 75231 Paris Cedex 05, France
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1677
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Abstract
Common DNA sequence variants inadequately explain variability in fat mass among individuals. Abnormal body weights are characteristic of specific imprinted-gene disorders. However, the relevance of imprinted genes to our understanding of obesity among the general population is uncertain. Hitherto unidentified imprinted genes and epigenetic mosaicism are two of the challenges for this emerging field of epigenetics. Subtle epigenetic differences in imprinted genes and gene networks are likely to be present among cells, tissues and individuals. In order to advance obesity research it will be necessary to use genome-wide, next-generation sequencing approaches that allow the detection of such epigenetic differences.
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Affiliation(s)
- Reinhard Stöger
- Department of Biology, University of Washington, 156 Kincaid Hall, Box 351800, Seattle, WA, 98195-1800, USA.
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1678
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Moser A, Guza R, Tretyakova N, York DM. Density Functional Study of the Influence of C5 Cytosine Substitution in Base Pairs with Guanine. Theor Chem Acc 2009; 122:179-188. [PMID: 19890472 PMCID: PMC2771868 DOI: 10.1007/s00214-008-0497-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The present study employs density-functional electronic structure methods to investigate the effect of chemical modification at the C5 position of cytosine. A series of experimentally motivated chemical modifications are considered, including alkyl, halogen, aromatic, fused ring, and strong σ and π withdrawing functional groups. The effect of these modifications on cytosine geometry, electronic structure, proton affinities, gas phase basicities, cytosine-guanine base-pair hydrogen bond network and corresponding nucleophilicity at guanine are examined. Ultimately, these results play a part in dissecting the effect of endogenous cytosine methylation on the reactivity of neighboring guanine toward carcinogens and DNA alkylating agents.
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Affiliation(s)
- Adam Moser
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455–0431, USA
| | - Rebecca Guza
- Department of Medicinal Chemistry and the Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Natalia Tretyakova
- Department of Medicinal Chemistry and the Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Darrin M. York
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455–0431, USA. E-mail:
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1679
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Genetics and epigenetics: stability and plasticity during cellular differentiation. Trends Genet 2009; 25:129-36. [PMID: 19185382 DOI: 10.1016/j.tig.2008.12.005] [Citation(s) in RCA: 188] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Revised: 12/22/2008] [Accepted: 12/23/2008] [Indexed: 11/21/2022]
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1680
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Does promoter methylation of the SLC30A5 (ZnT5) zinc transporter gene contribute to the ageing-related decline in zinc status? Proc Nutr Soc 2009; 68:142-7. [PMID: 19245740 DOI: 10.1017/s0029665109001104] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A decline in Zn status with ageing may contribute to the development of frailty, including impaired immune function, and increased incidence of age-related degenerative diseases. This decline may be a result of reduced dietary Zn intake and/or impaired Zn absorption in the gut. The Zn transporter ZnT5 may play a key role in the absorption of dietary Zn. The corresponding gene (SLC30A5) has a CpG island in its promoter region, so could be regulated by epigenetic mechanisms. It is hypothesised that methylation of the SLC30A5 promoter region is increased with age and that a resulting reduction in ZnT5 expression contributes to the decline in Zn status observed with ageing. This hypothesis has been addressed through (1) studies of effects of SLC30A5 promoter methylation on gene expression in vitro and (2) in vivo measurements of the DNA methylation status of this gene domain. It has been established in vitro that methylation of the human SLC30A5 promoter region results in reduced expression of an associated reporter gene. Second, this gene region shows variable levels of methylation in vivo. Correlation between the level of methylation at this locus and age would support the hypothesis that age-related hypermethylation of this region has the potential to modulate dietary Zn absorption. This premise is being investigated by analysis of additional samples from a human adult cohort to test the hypothesis that methylation of the SLC30A5 promoter region contributes to the age-related decline in Zn status.
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1681
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Balleza E, López-Bojorquez LN, Martínez-Antonio A, Resendis-Antonio O, Lozada-Chávez I, Balderas-Martínez YI, Encarnación S, Collado-Vides J. Regulation by transcription factors in bacteria: beyond description. FEMS Microbiol Rev 2009; 33:133-51. [PMID: 19076632 PMCID: PMC2704942 DOI: 10.1111/j.1574-6976.2008.00145.x] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Transcription is an essential step in gene expression and its understanding has been one of the major interests in molecular and cellular biology. By precisely tuning gene expression, transcriptional regulation determines the molecular machinery for developmental plasticity, homeostasis and adaptation. In this review, we transmit the main ideas or concepts behind regulation by transcription factors and give just enough examples to sustain these main ideas, thus avoiding a classical ennumeration of facts. We review recent concepts and developments: cis elements and trans regulatory factors, chromosome organization and structure, transcriptional regulatory networks (TRNs) and transcriptomics. We also summarize new important discoveries that will probably affect the direction of research in gene regulation: epigenetics and stochasticity in transcriptional regulation, synthetic circuits and plasticity and evolution of TRNs. Many of the new discoveries in gene regulation are not extensively tested with wetlab approaches. Consequently, we review this broad area in Inference of TRNs and Dynamical Models of TRNs. Finally, we have stepped backwards to trace the origins of these modern concepts, synthesizing their history in a timeline schema.
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Affiliation(s)
- Enrique Balleza
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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1682
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Foley DL, Craig JM, Morley R, Olsson CA, Dwyer T, Smith K, Saffery R. Prospects for epigenetic epidemiology. Am J Epidemiol 2009; 169:389-400. [PMID: 19139055 DOI: 10.1093/aje/kwn380] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Epigenetic modification can mediate environmental influences on gene expression and can modulate the disease risk associated with genetic variation. Epigenetic analysis therefore holds substantial promise for identifying mechanisms through which genetic and environmental factors jointly contribute to disease risk. The spatial and temporal variance in epigenetic profile is of particular relevance for developmental epidemiology and the study of aging, including the variable age at onset for many common diseases. This review serves as a general introduction to the topic by describing epigenetic mechanisms, with a focus on DNA methylation; genetic and environmental factors that influence DNA methylation; epigenetic influences on development, aging, and disease; and current methodology for measuring epigenetic profile. Methodological considerations for epidemiologic studies that seek to include epigenetic analysis are also discussed.
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Affiliation(s)
- Debra L Foley
- Orygen Youth Health Research Centre & Department of Psychiatry, University of Melbourne, Australia
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1683
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Dahl JA, Reiner AH, Collas P. Fast genomic muChIP-chip from 1,000 cells. Genome Biol 2009; 10:R13. [PMID: 19208222 PMCID: PMC2688267 DOI: 10.1186/gb-2009-10-2-r13] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2008] [Revised: 01/16/2009] [Accepted: 02/10/2009] [Indexed: 01/17/2023] Open
Abstract
A new method for rapid genome-wide μChIP-chip from as few as 1,000 cells. Genome-wide location analysis of histone modifications and transcription factor binding relies on chromatin immunoprecipitation (ChIP) assays. These assays are, however, time-consuming and require large numbers of cells, hindering their application to the analysis of many interesting cell types. We report here a fast microChIP (μChIP) assay for 1,000 cells in combination with microarrays to produce genome-scale surveys of histone modifications. μChIP-chip reliably reproduces data obtained by large-scale assays: H3K9ac and H3K9m3 enrichment profiles are conserved and nucleosome-free regions are revealed.
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Affiliation(s)
- John Arne Dahl
- Institute of Basic Medical Sciences, Department of Biochemistry, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway
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1684
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Abstract
Although early replication has long been associated with accessible chromatin, replication timing is not included in most discussions of epigenetic marks. This is partly due to a lack of understanding of the mechanisms behind this association but the issue has also been confounded by studies concluding that there are very few changes in replication timing during development. Recently, the first genome-wide study of replication timing during the course of differentiation revealed extensive changes that were strongly associated with changes in transcriptional activity and subnuclear organization. Domains of temporally coordinate replication delineate discrete units of chromosome structure and function that are characteristic of particular differentiation states. Hence, although we are still a long way from understanding the functional significance of replication timing, it is clear that replication timing is a distinct epigenetic signature of cell differentiation state.
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Affiliation(s)
- Ichiro Hiratani
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
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1685
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Brickner JH. Transcriptional memory at the nuclear periphery. Curr Opin Cell Biol 2009; 21:127-33. [PMID: 19181512 DOI: 10.1016/j.ceb.2009.01.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Revised: 12/15/2008] [Accepted: 01/08/2009] [Indexed: 10/21/2022]
Abstract
A number of inducible yeast genes are targeted to the nuclear periphery upon transcriptional activation. However, when repressed again, the INO1 and GAL1 genes remain at the nuclear periphery for multiple generations. Retention at the nuclear periphery represents a novel type of transcriptional memory; the peripherally localized, recently repressed state of GAL1 is activated more rapidly than the nucleoplasmically localized long-term repressed state of GAL1. This rapid reactivation involves localization at the nuclear periphery, the SWI/SNF chromatin remodeling complex, the histone variant H2A.Z and the Gal1 protein itself. Here, I review what we have learned about this type of transcriptional memory in yeast, what remains to be resolved and the challenges associated with understanding such epigenetic phenomena.
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Affiliation(s)
- Jason H Brickner
- Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, IL, USA.
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1686
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Abstract
Gene-environment interaction (G x E) has been treated as both a statistical phenomenon and a biological reality. It is argued that, although there are important statistical issues that need to be considered, the focus has to be on the biological implications of G x E. Four reports of G x E deriving from the Dunedin longitudinal study are used as exemplars of the biological considerations that should lead to an hypothesis-driven choice of the specific genetic polymorphisms and the specific environmental influence to be investigated. The same four studies are used to discuss how the assessment of internal and external validity can be undertaken and how experimental approaches in humans and with animal models may be informative in the elucidation of the relevant operative biological mechanisms.
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1687
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Histone modification patterns and epigenetic codes. Biochim Biophys Acta Gen Subj 2009; 1790:863-8. [PMID: 19168116 DOI: 10.1016/j.bbagen.2008.12.006] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2008] [Revised: 12/22/2008] [Accepted: 12/29/2008] [Indexed: 01/19/2023]
Abstract
The eukaryotic DNA is wrapped around histone octamers, which consist of four different histones, H2A, H2B, H3 and H4. The N-terminal tail of each histone is post-transcriptionally modified. The modification patterns constitute codes that regulate chromatin organisation and DNA utilization processes, including transcription. Recent progress in technology development has made it possible to perform systematic genome-wide studies of histone modifications. This helps immensely in deciphering the histone codes and their biological influence. In this review, we discuss the histone modification patterns found in genome-wide studies in different biological models and how they influence cell differentiation and carcinogenesis.
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1688
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Abstract
Breast cancer is a complex disease caused by the progressive accumulation of multiple gene mutations combined with epigenetic dysregulation of critical genes and protein pathways. There is substantial interindividual variability in both the age at diagnosis and phenotypic expression of the disease. With an estimated 1,152,161 new breast cancer cases diagnosed worldwide per year, cancer control efforts in the postgenome era should be focused at both population and individual levels to develop novel risk assessment and treatment strategies that will further reduce the morbidity and mortality associated with the disease. The discovery that mutations in the BRCA1 and BRCA2 genes increase the risk of breast and ovarian cancers has radically transformed our understanding of the genetic basis of breast cancer, leading to improved management of high-risk women. A better understanding of tumor host biology has led to improvements in the multidisciplinary management of breast cancer, and traditional pathologic evaluation is being complemented by more sophisticated genomic approaches. A number of genomic biomarkers have been developed for clinical use, and increasingly, pharmacogenetic end points are being incorporated into clinical trial design. For women diagnosed with breast cancer, prognostic or predictive information is most useful when coupled with targeted therapeutic approaches, very few of which exist for women with triple-negative breast cancer or those with tumors resistant to chemotherapy. The immediate challenge is to learn how to use the molecular characteristics of an individual and their tumor to improve detection and treatment, and ultimately to prevent the development of breast cancer. The five articles in this edition of CCR Focus highlight recent advances and future directions on the pathway to individualized approaches for the early detection, treatment, and prevention of breast cancer.
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Affiliation(s)
- Olufunmilayo I Olopade
- Department of Medicine, Section of Hematology/Oncology, Center for Clinical Cancer Genetics, University of Chicago, Chicago, Illinois 60637, USA.
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1689
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Pei Y, Zhang T, Renault V, Zhang X. An overview of hepatocellular carcinoma study by omics-based methods. Acta Biochim Biophys Sin (Shanghai) 2009; 41:1-15. [PMID: 19129945 DOI: 10.1093/abbs/gmn001] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most deadly malignancies worldwide. Scientists have been studying the molecular mechanism of HCC for years, but the understanding of it remains incomplete and scattered across the literature at different molecular levels. Chromosomal aberrations, epigenetic abnormality and changes of gene expression have been reported in HCC. High-throughput omics technologies have been widely applied, aiming at the discovery of candidate biomarkers for cancer staging, prediction of recurrence and prognosis, and treatment selection. Large amounts of data on genetic and epigenetic abnormalities, gene expression profiles, microRNA expression profiles and proteomics have been accumulating, and bioinformatics is playing a more and more important role. In this paper, we review the current omics-based studies on HCC at the levels of genomics, transcriptomics and proteomics. Integrating observations from multiple aspects is an essential step toward the systematic understanding of the disease.
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Affiliation(s)
- Yunfei Pei
- TNLIST/Department of Automation, Bioinformatics and Bioinformatics Division, MOE Key Laboratory, Tsinghua University, Beijing, China
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1690
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Zhu J, Yao X. Use of DNA methylation for cancer detection: Promises and challenges. Int J Biochem Cell Biol 2009; 41:147-54. [DOI: 10.1016/j.biocel.2008.09.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 09/08/2008] [Accepted: 09/10/2008] [Indexed: 01/12/2023]
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1691
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Abstract
The Physiome Project, exemplified by the Cardiac Physiome, is now 10 years old. In this article, we review past progress and future challenges in developing a quantitative framework for understanding human physiology that incorporates both genetic inheritance and environmental influence. Despite the enormity of the challenge, which is certainly greater than that facing the pioneers of the human genome project 20 years ago, there is reason for optimism that real and accelerating progress is being made.
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1692
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Brick K, Watanabe J, Pizzi E. Core promoters are predicted by their distinct physicochemical properties in the genome of Plasmodium falciparum. Genome Biol 2008; 9:R178. [PMID: 19094208 PMCID: PMC2646282 DOI: 10.1186/gb-2008-9-12-r178] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Revised: 11/03/2008] [Accepted: 12/18/2008] [Indexed: 11/23/2022] Open
Abstract
A method is presented to computationally identify core promoters in the Plasmodium falciparum genome using only DNA physicochemical properties. Little is known about the structure and distinguishing features of core promoters in Plasmodium falciparum. In this work, we describe the first method to computationally identify core promoters in this AT-rich genome. This prediction algorithm uses solely DNA physicochemical properties as descriptors. Our results add to a growing body of evidence that a physicochemical code for eukaryotic genomes plays a crucial role in core promoter recognition.
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Affiliation(s)
- Kevin Brick
- Dipartimento di Malattie Infettive, Parassitarie ed Immunomediate - Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161 Rome, Italy.
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1693
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Lee JH, Bugarija B, Millan EJ, Walton NM, Gaetz J, Fernandes CJ, Yu WH, Mekel-Bobrov N, Vallender TW, Snyder GE, Xiang AP, Lahn BT. Systematic identification of cis-silenced genes by trans complementation. Hum Mol Genet 2008; 18:835-46. [PMID: 19050040 PMCID: PMC2640206 DOI: 10.1093/hmg/ddn409] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
A gene's transcriptional output is the combined product of two inputs: diffusible factors in the cellular milieu acting in trans, and chromatin state acting in cis. Here, we describe a strategy for dissecting the relative contribution of cis versus trans mechanisms to gene regulation. Referred to as trans complementation, it entails fusing two disparate cell types and searching for genes differentially expressed between the two genomes of fused cells. Any differential expression can be causally attributed to cis mechanisms because the two genomes of fused cells share a single homogenized milieu in trans. This assay uncovered a state of transcriptional competency that we termed 'occluded' whereby affected genes are silenced by cis-acting mechanisms in a manner that blocks them from responding to the trans-acting milieu of the cell. Importantly, occluded genes in a given cell type tend to include master triggers of alternative cell fates. Furthermore, the occluded state is maintained during cell division and is extraordinarily stable under a wide range of physiological conditions. These results support the model that the occlusion of lineage-inappropriate genes is a key mechanism of cell fate restriction. The identification of occluded genes by our assay provides a hitherto unavailable functional readout of chromatin state that is distinct from and complementary to gene expression status.
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Affiliation(s)
- Jae Hyun Lee
- Department of Human Genetics, Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, USA
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1694
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Morphometrics applied to medical entomology. INFECTION GENETICS AND EVOLUTION 2008; 8:875-90. [DOI: 10.1016/j.meegid.2008.07.011] [Citation(s) in RCA: 147] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2008] [Revised: 07/28/2008] [Accepted: 07/30/2008] [Indexed: 11/18/2022]
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1695
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Delistraty D. Radioprotection of nonhuman biota. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2008; 99:1863-1869. [PMID: 18952327 DOI: 10.1016/j.jenvrad.2008.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2008] [Accepted: 09/08/2008] [Indexed: 05/27/2023]
Abstract
Radioprotection has historically focused on humans with the assumption that human protection confers protection of nonhuman biota. However, there is a need to scientifically and independently demonstrate protection of nonhuman biota. Approaches to address impacts of radiation on nonhuman biota include applying an ecological risk assessment paradigm, setting dose limits, defining reference organisms, and assessing a geographic region. Recommendations include harmonization of a radioprotection framework for both humans and nonhuman biota, a consistent methodology to evaluate radionuclide and nonradionuclide contaminants, a graded assessment approach, development of dosimetric models for reference organisms, compilation of a radiological effects database, and periodic expert review of methodology.
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1696
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Nestler EJ. Review. Transcriptional mechanisms of addiction: role of DeltaFosB. Philos Trans R Soc Lond B Biol Sci 2008; 363:3245-55. [PMID: 18640924 DOI: 10.1098/rstb.2008.0067] [Citation(s) in RCA: 275] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Regulation of gene expression is considered a plausible mechanism of drug addiction, given the stability of behavioural abnormalities that define an addicted state. Among many transcription factors known to influence the addiction process, one of the best characterized is DeltaFosB, which is induced in the brain's reward regions by chronic exposure to virtually all drugs of abuse and mediates sensitized responses to drug exposure. Since DeltaFosB is a highly stable protein, it represents a mechanism by which drugs produce lasting changes in gene expression long after the cessation of drug use. Studies are underway to explore the detailed molecular mechanisms by which DeltaFosB regulates target genes and produces its behavioural effects. We are approaching this question using DNA expression arrays coupled with the analysis of chromatin remodelling--changes in the posttranslational modifications of histones at drug-regulated gene promoters--to identify genes that are regulated by drugs of abuse via the induction of DeltaFosB and to gain insight into the detailed molecular mechanisms involved. Our findings establish chromatin remodelling as an important regulatory mechanism underlying drug-induced behavioural plasticity, and promise to reveal fundamentally new insight into how DeltaFosB contributes to addiction by regulating the expression of specific target genes in brain reward pathways.
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Affiliation(s)
- Eric J Nestler
- Department of Neuroscience, Mount Sinai School of Medicine, New York, NY 10029, USA.
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1697
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Laland KN, Odling-Smee J, Gilbert SF. EvoDevo and niche construction: building bridges. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2008; 310:549-66. [DOI: 10.1002/jez.b.21232] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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1698
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Turner JD, Pelascini LPL, Macedo JA, Muller CP. Highly individual methylation patterns of alternative glucocorticoid receptor promoters suggest individualized epigenetic regulatory mechanisms. Nucleic Acids Res 2008; 36:7207-18. [PMID: 19004867 PMCID: PMC2602793 DOI: 10.1093/nar/gkn897] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The transcription start sites (TSS) and promoters of many genes are located in upstream CpG islands. Methylation within such islands is known for both imprinted and oncogenes, although poorly studied for other genes, especially those with complex CpG islands containing multiple first exons and promoters. The glucocorticoid receptor (GR) CpG island contains seven alternative first exons and their promoters. Here we show for the five GR promoters activated in PBMCs that methylation patterns are highly variable between individuals. The majority of positions were methylated at levels >25% in at least one donor affecting each promoter and TSS. We also examined the evolutionarily conserved transcription factor binding sites (TFBS) using an improved in silico phylogenetic footprinting technique. The majority of these contain methylatable CpG sites, suggesting that methylation may orchestrates alternative first exon usage, silencing and controlling tissue-specific expression. The heterogeneity observed may reflect epigenetic mechanisms of GR fine tuning, programmed by early life environment and events. With 78% of evolutionarily conserved alternative first exons falling into such complex CpG islands, their internal structure and epigenetic modifications are bound to be biologically important, and may be a common transcriptional control mechanism used throughout many phyla.
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Affiliation(s)
- Jonathan D Turner
- Institute of Immunology, Laboratoire National de Santé, Luxembourg, Germany
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1699
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1700
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Feil R. Epigenetics, an emerging discipline with broad implications. C R Biol 2008; 331:837-43. [DOI: 10.1016/j.crvi.2008.07.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2008] [Accepted: 07/28/2008] [Indexed: 12/19/2022]
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