dna methylation

Summary

Summary: Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.

Top Publications

  1. pmc Human DNA methylomes at base resolution show widespread epigenomic differences
    Ryan Lister
    Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
    Nature 462:315-22. 2009
  2. ncbi DNA methylation patterns and epigenetic memory
    Adrian Bird
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK
    Genes Dev 16:6-21. 2002
  3. pmc Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1
    Mamta Tahiliani
    Department of Pathology, Harvard Medical School and Immune Disease Institute, 200 Longwood Avenue, Boston, MA 02115, USA
    Science 324:930-5. 2009
  4. pmc The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores
    Rafael A Irizarry
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
    Nat Genet 41:178-86. 2009
  5. doi Epigenetics in cancer
    Manel Esteller
    Cancer Epigenetics Laboratory, Spanish National Cancer Research Center, Madrid, Spain
    N Engl J Med 358:1148-59. 2008
  6. ncbi MGMT gene silencing and benefit from temozolomide in glioblastoma
    Monika E Hegi
    Laboratory of Tumor Biology and Genetics, Department of Neurosurgery, University Hospital Lausanne, Lausanne, Switzerland
    N Engl J Med 352:997-1003. 2005
  7. pmc Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs
    John L Rinn
    Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Cell 129:1311-23. 2007
  8. pmc Increased methylation variation in epigenetic domains across cancer types
    Kasper Daniel Hansen
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
    Nat Genet 43:768-75. 2011
  9. pmc Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA
    Yu Fei He
    Group of DNA Metabolism, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
    Science 333:1303-7. 2011
  10. pmc Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma
    Houtan Noushmehr
    USC Epigenome Center, University of Southern California, Los Angeles, CA 90033, USA
    Cancer Cell 17:510-22. 2010

Detail Information

Publications278 found, 100 shown here

  1. pmc Human DNA methylomes at base resolution show widespread epigenomic differences
    Ryan Lister
    Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
    Nature 462:315-22. 2009
    ..These reference epigenomes provide a foundation for future studies exploring this key epigenetic modification in human disease and development...
  2. ncbi DNA methylation patterns and epigenetic memory
    Adrian Bird
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK
    Genes Dev 16:6-21. 2002
  3. pmc Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1
    Mamta Tahiliani
    Department of Pathology, Harvard Medical School and Immune Disease Institute, 200 Longwood Avenue, Boston, MA 02115, USA
    Science 324:930-5. 2009
    ..hmC is present in the genome of mouse embryonic stem cells, and hmC levels decrease upon RNA interference-mediated depletion of TET1. Thus, TET proteins have potential roles in epigenetic regulation through modification of 5mC to hmC...
  4. pmc The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores
    Rafael A Irizarry
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
    Nat Genet 41:178-86. 2009
    For the past 25 years, it has been known that alterations in DNA methylation (DNAm) occur in cancer, including hypomethylation of oncogenes and hypermethylation of tumor suppressor genes...
  5. doi Epigenetics in cancer
    Manel Esteller
    Cancer Epigenetics Laboratory, Spanish National Cancer Research Center, Madrid, Spain
    N Engl J Med 358:1148-59. 2008
  6. ncbi MGMT gene silencing and benefit from temozolomide in glioblastoma
    Monika E Hegi
    Laboratory of Tumor Biology and Genetics, Department of Neurosurgery, University Hospital Lausanne, Lausanne, Switzerland
    N Engl J Med 352:997-1003. 2005
    ....
  7. pmc Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs
    John L Rinn
    Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Cell 129:1311-23. 2007
    ..Thus, transcription of ncRNA may demarcate chromosomal domains of gene silencing at a distance; these results have broad implications for gene regulation in development and disease states...
  8. pmc Increased methylation variation in epigenetic domains across cancer types
    Kasper Daniel Hansen
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
    Nat Genet 43:768-75. 2011
    ..We suggest a model for cancer involving loss of epigenetic stability of well-defined genomic domains that underlies increased methylation variability in cancer that may contribute to tumor heterogeneity...
  9. pmc Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA
    Yu Fei He
    Group of DNA Metabolism, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
    Science 333:1303-7. 2011
    ..These data suggest that oxidation of 5mC by Tet proteins followed by TDG-mediated base excision of 5caC constitutes a pathway for active DNA demethylation...
  10. pmc Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma
    Houtan Noushmehr
    USC Epigenome Center, University of Southern California, Los Angeles, CA 90033, USA
    Cancer Cell 17:510-22. 2010
    We have profiled promoter DNA methylation alterations in 272 glioblastoma tumors in the context of The Cancer Genome Atlas (TCGA)...
  11. pmc CpG islands and the regulation of transcription
    Aimée M Deaton
    The Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
    Genes Dev 25:1010-22. 2011
    ..CGIs are therefore generically equipped to influence local chromatin structure and simplify regulation of gene activity...
  12. pmc Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells
    Ryan Lister
    Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
    Nature 471:68-73. 2011
    ..However, it remains unknown how complete the reestablishment of ES-cell-like DNA methylation patterns is throughout the genome...
  13. ncbi Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome
    Michael Weber
    Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH 4058 Basel, Switzerland
    Nat Genet 39:457-66. 2007
    To gain insight into the function of DNA methylation at cis-regulatory regions and its impact on gene expression, we measured methylation, RNA polymerase occupancy and histone modifications at 16,000 promoters in primary human somatic ..
  14. ncbi Generation of germline-competent induced pluripotent stem cells
    Keisuke Okita
    Department of Stem Cell Biology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606 8507, Japan
    Nature 448:313-7. 2007
    ..proliferation and teratoma formation; however, they are different with regards to gene expression and DNA methylation patterns, and fail to produce adult chimaeras...
  15. pmc Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine
    Shinsuke Ito
    Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 7295, USA
    Science 333:1300-3. 2011
    ..Thus, we identify two previously unknown cytosine derivatives in genomic DNA as the products of Tet proteins. Our study raises the possibility that DNA demethylation may occur through Tet-catalyzed oxidation followed by decarboxylation...
  16. doi Functions of DNA methylation: islands, start sites, gene bodies and beyond
    Peter A Jones
    USC Norris Comprehensive Cancer Center, Keck School of Medicine of University of Southern California, Los Angeles, California 90089 99176, USA
    Nat Rev Genet 13:484-92. 2012
    b>DNA methylation is frequently described as a 'silencing' epigenetic mark, and indeed this function of 5-methylcytosine was originally proposed in the 1970s...
  17. doi Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation
    Gabriella Ficz
    Laboratory of Developmental Genetics and Imprinting, The Babraham Institute, Cambridge CB22 3AT, UK
    Nature 473:398-402. 2011
    ..We propose that the balance between hydroxymethylation and methylation in the genome is inextricably linked with the balance between pluripotency and lineage commitment...
  18. doi DNA methylation landscapes: provocative insights from epigenomics
    Miho M Suzuki
    The Wellcome Trust Centre for Cell Biology, The University of Edinburgh, Michael Swann Building, The King s Buildings, Edinburgh EH9 3JR, UK
    Nat Rev Genet 9:465-76. 2008
    ..New techniques are making it easier to map DNA methylation patterns on a large scale and the results have already provided surprises...
  19. ncbi Reprogramming of human somatic cells to pluripotency with defined factors
    In Hyun Park
    Division of Pediatric Hematology Oncology, Children s Hospital Boston and Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
    Nature 451:141-6. 2008
    ..These data demonstrate that defined factors can reprogramme human cells to pluripotency, and establish a method whereby patient-specific cells might be established in culture...
  20. ncbi DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development
    M Okano
    Cardiovascular Research Center, Massachusetts General Hospital, Department of Medicine, Harvard Medical School, Charlestown 02129, USA
    Cell 99:247-57. 1999
    The establishment of DNA methylation patterns requires de novo methylation that occurs predominantly during early development and gametogenesis in mice...
  21. pmc DNA demethylation dynamics
    Nidhi Bhutani
    Baxter Laboratory for Stem Cell Biology, Institute for Stem Cell Biology and Regenerative Medicine, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305 5175, USA
    Cell 146:866-72. 2011
    ..These reports highlight that in certain contexts, DNA methylation is not fixed but dynamic, requiring continuous regulation.
  22. pmc Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts
    Akiko Doi
    Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
    Nat Genet 41:1350-3. 2009
    Induced pluripotent stem (iPS) cells are derived by epigenetic reprogramming, but their DNA methylation patterns have not yet been analyzed on a genome-wide scale...
  23. pmc Conserved role of intragenic DNA methylation in regulating alternative promoters
    Alika K Maunakea
    Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA
    Nature 466:253-7. 2010
    Although it is known that the methylation of DNA in 5' promoters suppresses gene expression, the role of DNA methylation in gene bodies is unclear...
  24. pmc Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation
    Maria E Figueroa
    Weill Cornell Medical College, New York, NY 10065, USA
    Cancer Cell 18:553-67. 2010
    ..Finally, either expression of mutant IDH1/2 or Tet2 depletion impaired hematopoietic differentiation and increased stem/progenitor cell marker expression, suggesting a shared proleukemogenic effect...
  25. pmc Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain
    Junjie U Guo
    Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Cell 145:423-34. 2011
    ..Our study suggests a TET1-induced oxidation-deamination mechanism for active DNA demethylation in mammals...
  26. doi Principles and challenges of genomewide DNA methylation analysis
    Peter W Laird
    USC Epigenome Center, University of Southern California, Keck School of Medicine, Los Angeles, 90089 9601, USA
    Nat Rev Genet 11:191-203. 2010
    ..Therefore, profiling DNA methylation across the genome is vital to understanding the influence of epigenetics...
  27. pmc Genome-scale DNA methylation maps of pluripotent and differentiated cells
    Alexander Meissner
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 454:766-70. 2008
    b>DNA methylation is essential for normal development and has been implicated in many pathologies including cancer...
  28. pmc TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity
    Kristine Williams
    Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
    Nature 473:343-8. 2011
    ..We propose that TET1 fine-tunes transcription, opposes aberrant DNA methylation at CpG-rich sequences and thereby contributes to the regulation of DNA methylation fidelity.
  29. doi Cancer epigenetics reaches mainstream oncology
    Manuel Rodríguez-Paredes
    Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L Hospitalet, and Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Spain
    Nat Med 17:330-9. 2011
    ..The field has moved from just one recognized marker, DNA methylation, to a variety of others, including a wide spectrum of histone modifications...
  30. pmc DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines
    Jordana T Bell
    Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
    Genome Biol 12:R10. 2011
    b>DNA methylation is an essential epigenetic mechanism involved in gene regulation and disease, but little is known about the mechanisms underlying inter-individual variation in methylation profiles...
  31. pmc Epigenome-wide association studies for common human diseases
    Vardhman K Rakyan
    Blizard Institute of Cell and Molecular Science, Barts and the London School of Medicine and Dentistry, Queen Mary, University of London, London, UK
    Nat Rev Genet 12:529-41. 2011
    ..to initiate large-scale studies of human disease-associated epigenetic variation, specifically variation in DNA methylation. Such epigenome-wide association studies (EWASs) present novel opportunities but also create new challenges ..
  32. ncbi Epigenetic reprogramming in mammalian development
    W Reik
    Laboratory of Developmental Genetics and Imprinting, The Babraham Institute, Cambridge CB2 4AT, UK
    Science 293:1089-93. 2001
    b>DNA methylation is a major epigenetic modification of the genome that regulates crucial aspects of its function. Genomic methylation patterns in somatic differentiated cells are generally stable and heritable...
  33. ncbi Genome-wide evolutionary analysis of eukaryotic DNA methylation
    Assaf Zemach
    Department of Plant and Microbial Biology, 211 Koshland Hall, University of California, Berkeley, CA 94720, USA
    Science 328:916-9. 2010
    ..We quantified DNA methylation in 17 eukaryotic genomes and found that gene body methylation is conserved between plants and animals, ..
  34. doi Linking DNA methylation and histone modification: patterns and paradigms
    Howard Cedar
    Department of Developmental Biology and Cancer Research, Hebrew University Medical School, Ein Kerem, Jerusalem 91120, Israel
    Nat Rev Genet 10:295-304. 2009
    Both DNA methylation and histone modification are involved in establishing patterns of gene repression during development...
  35. pmc Establishing, maintaining and modifying DNA methylation patterns in plants and animals
    Julie A Law
    Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, 90095 1606, USA
    Nat Rev Genet 11:204-20. 2010
    Cytosine DNA methylation is a stable epigenetic mark that is crucial for diverse biological processes, including gene and transposon silencing, imprinting and X chromosome inactivation...
  36. pmc Thymine DNA glycosylase is essential for active DNA demethylation by linked deamination-base excision repair
    Salvatore Cortellino
    Cancer Biology Program and Epigenetics and Progenitor Cells Keystone Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
    Cell 146:67-79. 2011
    b>DNA methylation is a major epigenetic mechanism for gene silencing...
  37. ncbi MethPrimer: designing primers for methylation PCRs
    Long Cheng Li
    Department of Urology, Veterans Affairs Medical Center, and University of California San Francisco, San Francisco, CA 94121, USA
    Bioinformatics 18:1427-31. 2002
    b>DNA methylation is an epigenetic mechanism of gene regulation...
  38. pmc Persistent epigenetic differences associated with prenatal exposure to famine in humans
    Bastiaan T Heijmans
    Departments of Molecular Epidemiology, Medical Statistics, and Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
    Proc Natl Acad Sci U S A 105:17046-9. 2008
    ..who were prenatally exposed to famine during the Dutch Hunger Winter in 1944-45 had, 6 decades later, less DNA methylation of the imprinted IGF2 gene compared with their unexposed, same-sex siblings...
  39. doi CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing
    Sanjeev Shukla
    Center for Cancer Research, Mouse Cancer Genetics Program, National Cancer Institute at Frederick, Frederick, Maryland 21702, USA
    Nature 479:74-9. 2011
    ..reports have identified distinct histone methylation patterns, elevated nucleosome occupancy and enriched DNA methylation at exons relative to introns...
  40. doi DNA-binding factors shape the mouse methylome at distal regulatory regions
    Michael B Stadler
    Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
    Nature 480:490-5. 2011
    ..This study provides methylome references for the mouse and shows that DNA-binding factors locally influence DNA methylation, enabling the identification of active regulatory regions.
  41. doi Mechanisms of polycomb gene silencing: knowns and unknowns
    Jeffrey A Simon
    Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis 55455, USA
    Nat Rev Mol Cell Biol 10:697-708. 2009
    ..These findings have an impact on the epigenetic programming of gene expression in many biological systems...
  42. ncbi Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals
    Rudolf Jaenisch
    Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
    Nat Genet 33:245-54. 2003
    ..Research over the past few years has focused on two molecular mechanisms that mediate epigenetic phenomena: DNA methylation and histone modifications...
  43. pmc Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency
    Christian Popp
    Laboratory of Developmental Genetics and Imprinting, The Babraham Institute, Cambridge, UK
    Nature 463:1101-5. 2010
    ..Here we profiled DNA methylation throughout the genome by unbiased bisulphite next generation sequencing in wild-type and AID-deficient mouse ..
  44. ncbi Epigenetic programming by maternal behavior
    Ian C G Weaver
    Douglas Hospital Research Center, 6875 LaSalle Blvd, Montreal, Quebec H4H 1R3, Canada
    Nat Neurosci 7:847-54. 2004
    ..Offspring of mothers that showed high levels of LG and ABN were found to have differences in DNA methylation, as compared to offspring of 'low-LG-ABN' mothers...
  45. pmc A unique regulatory phase of DNA methylation in the early mammalian embryo
    Zachary D Smith
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Nature 484:339-44. 2012
    b>DNA methylation is highly dynamic during mammalian embryogenesis...
  46. ncbi Environmental epigenomics and disease susceptibility
    Randy L Jirtle
    Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina 27710, USA
    Nat Rev Genet 8:253-62. 2007
    ..Methods are now becoming available to investigate the relevance of these phenomena to human disease...
  47. pmc Epigenetic differences arise during the lifetime of monozygotic twins
    Mario F Fraga
    Epigenetics Laboratory, Spanish National Cancer Centre CNIO, Melchor Fernandez Almagro 3, 28029 Madrid, Spain
    Proc Natl Acad Sci U S A 102:10604-9. 2005
    ..To address this issue, we examined the global and locus-specific differences in DNA methylation and histone acetylation of a large cohort of monozygotic twins...
  48. ncbi Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome
    Juan Sandoval
    Cancer Epigenetics and Biology Program PEBC, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute IDIBELL, Spain
    Epigenetics 6:692-702. 2011
    b>DNA methylation is the most studied epigenetic mark and CpG methylation is central to many biological processes and human diseases...
  49. doi Evaluation of the Infinium Methylation 450K technology
    Sarah Dedeurwaerder
    Laboratory of Cancer Epigenetics, Universite Libre de Bruxelles, Faculty of Medicine, Brussels, Belgium
    Epigenomics 3:771-84. 2011
    ..In particular, we compare the methylation values of the Infinium I and Infinium II assays...
  50. doi Epigenetic modifications and human disease
    Anna Portela
    Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, Barcelona, Catalonia, Spain
    Nat Biotechnol 28:1057-68. 2010
    ..These allow the mapping of epigenetic marks, such as DNA methylation, histone modifications and nucleosome positioning, which are critical for regulating gene and noncoding RNA ..
  51. pmc Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications
    Felix Krueger
    Bioinformatics Group, The Babraham Institute, CB22 3AT, Cambridge, UK
    Bioinformatics 27:1571-2. 2011
    ..Its output discriminates between cytosines in CpG, CHG and CHH context and enables bench scientists to visualize and interpret their methylation data soon after the sequencing run is completed...
  52. pmc A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters
    Serge Saxonov
    Biomedical Informatics Program, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 103:1412-7. 2006
    ....
  53. pmc Epigenetic regulation of the glucocorticoid receptor in human brain associates with childhood abuse
    Patrick O McGowan
    Douglas Mental Health University Institute, 6875 LaSalle Boulevard, Montreal, Quebec, H4H 1R3, Canada
    Nat Neurosci 12:342-8. 2009
    ..These findings translate previous results from rat to humans and suggest a common effect of parental care on the epigenetic regulation of hippocampal glucocorticoid receptor expression...
  54. pmc Dynamic changes in the human methylome during differentiation
    Louise Laurent
    UCSD Medical Center, Department of Reproductive Medicine, San Diego, California 92103, USA
    Genome Res 20:320-31. 2010
    b>DNA methylation is a critical epigenetic regulator in mammalian development...
  55. pmc Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain
    J Raphael Gibbs
    Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS Genet 6:e1000952. 2010
    ..We present a set of integrated experiments that investigate the effects of common genetic variability on DNA methylation and mRNA expression in four human brain regions each from 150 individuals (600 samples total)...
  56. pmc DNA methylation profiling of human chromosomes 6, 20 and 22
    Florian Eckhardt
    Epigenomics AG, Kleine Präsidentstrasse 1, 10178 Berlin, Germany
    Nat Genet 38:1378-85. 2006
    b>DNA methylation is the most stable type of epigenetic modification modulating the transcriptional plasticity of mammalian genomes...
  57. pmc Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning
    Shawn J Cokus
    Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California 90095, USA
    Nature 452:215-9. 2008
    Cytosine DNA methylation is important in regulating gene expression and in silencing transposons and other repetitive sequences...
  58. pmc Epigenetic reprogramming in plant and animal development
    Suhua Feng
    Howard Hughes Medical Institute and Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
    Science 330:622-7. 2010
    ..The mechanisms of genome-wide erasure of DNA methylation, which involve modifications to 5-methylcytosine and DNA repair, are being unraveled...
  59. pmc Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells
    William A Pastor
    Harvard Medical School, Immune Disease Institute and Program in Cellular and Molecular Medicine, Children s Hospital Boston, Boston, Massachusetts 02115, USA
    Nature 473:394-7. 2011
    ..Our results indicate that 5hmC has a probable role in transcriptional regulation, and suggest a model in which 5hmC contributes to the 'poised' chromatin signature found at developmentally-regulated genes in ES cells...
  60. pmc Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis
    Pan Du
    Northwestern University Biomedical Informatics Center NUBIC, NUCATS, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
    BMC Bioinformatics 11:587. 2010
    High-throughput profiling of DNA methylation status of CpG islands is crucial to understand the epigenetic regulation of genes...
  61. ncbi The mammalian epigenome
    Bradley E Bernstein
    Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA
    Cell 128:669-81. 2007
    ..Here we review current research efforts, with an emphasis on large-scale studies, emerging technologies, and challenges ahead...
  62. doi The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes
    Tian Peng Gu
    Group of DNA Metabolism, The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
    Nature 477:606-10. 2011
    ..Therefore, Tet3-mediated DNA hydroxylation is involved in epigenetic reprogramming of the zygotic paternal DNA following natural fertilization and may also contribute to somatic cell nuclear reprogramming during animal cloning...
  63. ncbi DNA methylation and human disease
    Keith D Robertson
    Department of Biochemistry and Molecular Biology, Shands Cancer Center, University of Florida, Gainesville, Florida 32610, USA
    Nat Rev Genet 6:597-610. 2005
    b>DNA methylation is a crucial epigenetic modification of the genome that is involved in regulating many cellular processes...
  64. pmc Distinct epigenomic landscapes of pluripotent and lineage-committed human cells
    R David Hawkins
    Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
    Cell Stem Cell 6:479-91. 2010
    ..of potential regulatory sequences also exhibit a high degree of dynamics in chromatin modifications and DNA methylation. Additionally, we observe novel, context-dependent relationships between DNA methylation and chromatin ..
  65. pmc Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines
    Christoph Bock
    Broad Institute, Cambridge, MA 02142, USA
    Cell 144:439-52. 2011
    ..Toward this goal we have established genome-wide reference maps of DNA methylation and gene expression for 20 previously derived human ES lines and 12 human iPS cell lines, and we have ..
  66. doi Directly reprogrammed fibroblasts show global epigenetic remodeling and widespread tissue contribution
    Nimet Maherali
    Massachusetts General Hospital Cancer Center and Center for Regenerative Medicine, Harvard Stem Cell Institute, 185 Cambridge Street, Boston, MA 02114, USA
    Cell Stem Cell 1:55-70. 2007
    ....
  67. pmc A microRNA DNA methylation signature for human cancer metastasis
    Amaia Lujambio
    Cancer Epigenetics Laboratory, Spanish National Cancer Research Center, Melchor Fernandez Almagro 3, 28029 Madrid, Spain
    Proc Natl Acad Sci U S A 105:13556-61. 2008
    ..Our findings indicate that DNA methylation-associated silencing of tumor suppressor miRNAs contributes to the development of human cancer metastasis.
  68. pmc MicroRNA-29 family reverts aberrant methylation in lung cancer by targeting DNA methyltransferases 3A and 3B
    Muller Fabbri
    Department of Molecular Virology, Immunology, and Medical Genetics, Comprehensive Cancer Center, and College of Pharmacy, Ohio State University, Columbus, OH 43210, USA
    Proc Natl Acad Sci U S A 104:15805-10. 2007
    ..3'-UTRs of DNA methyltransferase (DNMT)3A and -3B (de novo methyltransferases), two key enzymes involved in DNA methylation, that are frequently up-regulated in lung cancer and associated with poor prognosis...
  69. ncbi Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution
    Michael J Booth
    Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
    Science 336:934-7. 2012
    ..Our results open new questions on 5hmC dynamics and sequence-specific targeting by TETs...
  70. pmc Dissecting direct reprogramming through integrative genomic analysis
    Tarjei S Mikkelsen
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 454:49-55. 2008
    ..We demonstrate that RNA inhibition of transcription factors can facilitate reprogramming, and that treatment with DNA methyltransferase inhibitors can improve the overall efficiency of the reprogramming process...
  71. pmc Intra-individual change over time in DNA methylation with familial clustering
    Hans T Bjornsson
    Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
    JAMA 299:2877-83. 2008
    Changes over time in epigenetic marks, which are modifications of DNA such as by DNA methylation, may help explain the late onset of common human diseases...
  72. ncbi The fundamental role of epigenetic events in cancer
    Peter A Jones
    USC Norris Comprehensive Cancer Center, Department of Urology, Keck School of Medicine, University of Southern California, 1441 Eastlake Avenue, MS 8302L, Los Angeles, California 90089 9181, USA
    Nat Rev Genet 3:415-28. 2002
    Patterns of DNA methylation and chromatin structure are profoundly altered in neoplasia and include genome-wide losses of, and regional gains in, DNA methylation...
  73. pmc Conservation and divergence of methylation patterning in plants and animals
    Suhua Feng
    Howard Hughes Medical Institute, Department of Molecular, Cell and Developmental Biology, and Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 107:8689-94. 2010
    Cytosine DNA methylation is a heritable epigenetic mark present in many eukaryotic organisms...
  74. doi CpG islands--'a rough guide'
    Robert S Illingworth
    Wellcome Trust Centre for Cell Biology, Michael Swann Building, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JR, United Kingdom
    FEBS Lett 583:1713-20. 2009
    ..CGIs generally lack DNA methylation and associate with the majority of annotated gene promoters...
  75. ncbi Epigenetics in human disease and prospects for epigenetic therapy
    Gerda Egger
    Department of Biochemistry and Molecular Biology, USC Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, 1441 Eastlake Avenue, Room 8302L, Los Angeles, California 90089 9181, USA
    Nature 429:457-63. 2004
    ....
  76. ncbi Specific activation of microRNA-127 with downregulation of the proto-oncogene BCL6 by chromatin-modifying drugs in human cancer cells
    Yoshimasa Saito
    Department of Urology, Biochemistry, and Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90089, USA
    Cancer Cell 9:435-43. 2006
    ..These results suggest that DNA demethylation and histone deacetylase inhibition can activate expression of miRNAs that may act as tumor suppressors...
  77. doi Targets and dynamics of promoter DNA methylation during early mouse development
    Julie Borgel
    Institute of Molecular Genetics, Centre National de la Recherche Scientifique CNRS UMR 5535, Universite Montpellier 2, Universite Montpellier 1, Montpellier, France
    Nat Genet 42:1093-100. 2010
    b>DNA methylation is extensively reprogrammed during the early phases of mammalian development, yet genomic targets of this process are largely unknown...
  78. pmc The relationship of DNA methylation with age, gender and genotype in twins and healthy controls
    Marco P Boks
    Rudolf Magnus Institute of Neuroscience, Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands
    PLoS ONE 4:e6767. 2009
    ..In addition to influences of age and gender, genetic control of DNA methylation levels has recently been described...
  79. pmc Quantitative comparison of genome-wide DNA methylation mapping technologies
    Christoph Bock
    Broad Institute, Cambridge, Massachusetts, USA
    Nat Biotechnol 28:1106-14. 2010
    b>DNA methylation plays a key role in regulating eukaryotic gene expression...
  80. ncbi Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex
    X Nan
    Institute of Cell and Molecular Biology, University of Edinburgh, UK
    Nature 393:386-9. 1998
    ..The data suggest that two global mechanisms of gene regulation, DNA methylation and histone deacetylation, can be linked by MeCP2.
  81. pmc DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA
    Steen K T Ooi
    Department of Genetics and Development, College of Physicians and Surgeons of Columbia University, New York, New York 10032, USA
    Nature 448:714-7. 2007
    Mammals use DNA methylation for the heritable silencing of retrotransposons and imprinted genes and for the inactivation of the X chromosome in females...
  82. pmc Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells
    Madeleine P Ball
    Department of Genetics, Harvard Medical School, Cambridge, MA, USA
    Nat Biotechnol 27:361-8. 2009
    ..Our observations highlight the usefulness of techniques that are not inherently or intentionally biased towards particular subsets like CpG islands or promoter regions...
  83. pmc Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains
    Vardhman K Rakyan
    Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
    Genome Res 20:434-9. 2010
    ....
  84. pmc Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
    R Alan Harris
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
    Nat Biotechnol 28:1097-105. 2010
    Analysis of DNA methylation patterns relies increasingly on sequencing-based profiling methods...
  85. pmc Comprehensive methylome map of lineage commitment from haematopoietic progenitors
    Hong Ji
    Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, 570 Rangos, 725 N Wolfe St, Baltimore, Maryland 21205, USA
    Nature 467:338-42. 2010
    ..Although DNA methylation is critical for myeloid versus lymphoid differentiation, as demonstrated by the myeloerythroid bias in Dnmt1 ..
  86. pmc L1 retrotransposition in neurons is modulated by MeCP2
    Alysson R Muotri
    University of California San Diego, School of Medicine, Department of Pediatrics Rady Children s Hospital San Diego, La Jolla, California 92093 0695, USA
    Nature 468:443-6. 2010
    ..in rodents are increased in the absence of methyl-CpG-binding protein 2 (MeCP2), a protein involved in global DNA methylation and human neurodevelopmental diseases...
  87. pmc A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice
    Alexei A Aravin
    Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Mol Cell 31:785-99. 2008
    ..The Piwi pathway lies upstream of known mediators of DNA methylation, since piRNAs are still produced in dnmt3L mutants, which fail to methylate transposons...
  88. pmc Rethinking how DNA methylation patterns are maintained
    Peter A Jones
    Peter A Jones and Gangning Liang are at the Department of Urology, Biochemistry and Molecular Biology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089 9181, USA
    Nat Rev Genet 10:805-11. 2009
    b>DNA methylation patterns are set up early in mammalian development and are then copied during the division of somatic cells...
  89. doi DNA methylation profiles in monozygotic and dizygotic twins
    Zachary A Kaminsky
    Centre for Addiction and Mental Health, Toronto, Ontario M5T 1R8, Canada
    Nat Genet 41:240-5. 2009
    ..As epigenetic factors can contribute to phenotypic outcomes, we conducted a DNA methylation analysis in white blood cells (WBC), buccal epithelial cells and gut biopsies of 114 monozygotic (MZ) twins ..
  90. ncbi Dietary protein restriction of pregnant rats induces and folic acid supplementation prevents epigenetic modification of hepatic gene expression in the offspring
    Karen A Lillycrop
    Development and Cell Biology, University of Southampton, UK
    J Nutr 135:1382-6. 2005
    ..This suggests persistent alteration of gene transcription. DNA methylation, which is largely established in utero, provides a causal mechanism by which unbalanced prenatal nutrition ..
  91. pmc CpG islands influence chromatin structure via the CpG-binding protein Cfp1
    John P Thomson
    Wellcome Trust Centre for Cell Biology, Michael Swann Building, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JR, UK
    Nature 464:1082-6. 2010
    ..Most human gene promoters are embedded within CGIs that lack DNA methylation and coincide with sites of histone H3 lysine 4 trimethylation (H3K4me3), irrespective of transcriptional ..
  92. doi Cyclical DNA methylation of a transcriptionally active promoter
    Raphaël Métivier
    Universite de Rennes I, CNRS, UMR 6026 Equipe SPARTE, IFR 140 GFAS, Campus de Beaulieu, 35042 Rennes Cedex, France
    Nature 452:45-50. 2008
    ..b>DNA methylation on CpGs constitutes an epigenetic mark generally correlated with transcriptionally silent condensed chromatin...
  93. ncbi In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state
    Marius Wernig
    Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
    Nature 448:318-24. 2007
    ..Here we show that DNA methylation, gene expression and chromatin state of such induced reprogrammed stem cells are similar to those of ES cells...
  94. ncbi Molecular pathogenesis of human hepatocellular carcinoma
    Snorri S Thorgeirsson
    Laboratory of Experimental Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Nat Genet 31:339-46. 2002
    ..New strategies should enable these variants to be characterized...
  95. doi Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation
    Kristi Kerkel
    Institute for Cancer Genetics, Columbia University Medical Center, New York, New York 10032, USA
    Nat Genet 40:904-8. 2008
    Allele-specific DNA methylation (ASM) is a hallmark of imprinted genes, but ASM in the larger nonimprinted fraction of the genome is less well characterized...
  96. pmc The Dnmt3a PWWP domain reads histone 3 lysine 36 trimethylation and guides DNA methylation
    Arunkumar Dhayalan
    Biochemistry Laboratory, School of Engineering and Science, Jacobs University Bremen, Bremen, Germany
    J Biol Chem 285:26114-20. 2010
    ..H3K36me3 is known to be a repressive modification correlated with DNA methylation in mammals and heterochromatin in Schizosaccharomyces pombe...
  97. pmc Chromatin methylation activity of Dnmt3a and Dnmt3a/3L is guided by interaction of the ADD domain with the histone H3 tail
    Yingying Zhang
    Biochemistry Laboratory, School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
    Nucleic Acids Res 38:4246-53. 2010
    ..To establish a functional role of the ADD domain binding to unmodified H3 tails, we analyzed the DNA methylation of in vitro reconstituted chromatin with Dnmt3a2, the Dnmt3a2/Dnmt3L complex, and the catalytic domain of ..
  98. pmc Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming
    Jie Deng
    Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
    Nat Biotechnol 27:353-60. 2009
    Current DNA methylation assays are limited in the flexibility and efficiency of characterizing a large number of genomic targets...
  99. pmc Reprogramming towards pluripotency requires AID-dependent DNA demethylation
    Nidhi Bhutani
    Baxter Laboratory for Stem Cell Biology, Institute for Stem Cell Biology and Regenerative Medicine, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305 5175, USA
    Nature 463:1042-7. 2010
    ..These data provide new evidence that mammalian AID is required for active DNA demethylation and initiation of nuclear reprogramming towards pluripotency in human somatic cells...
  100. pmc Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer
    Andrew E Teschendorff
    University College London, London WC1E 6BT, UK
    Genome Res 20:440-6. 2010
    ..These findings shed substantial novel insights into the epigenetic effects of aging and support the view that age may predispose to malignant transformation by irreversibly stabilizing stem cell features...

Research Grants97

  1. DNA methylation in aging, race and prostate cancer
    Rajvir Dahiya; Fiscal Year: 2006
    ..Specific hypotheses: 1) The DNA methylation status of most frequently deleted genes [ERs, E-cadherin, CD44 and GSTPI (glutathione S-transferase pi)] will ..
  2. Dietary Methyl Score, Genomic DNA Methylation and Colorectal Cancer
    Eunyoung Cho; Fiscal Year: 2009
    ..cancer risk in large prospective studies and expect that individuals with reduced levels of genomic DNA methylation are at increased risk of colorectal cancer...
  3. Variation in M. tuberculosis in response to host selection
    Sarah Fortune; Fiscal Year: 2009
    ..In these studies, we expect to provide fundamental insights into the mechanisms and targets of diversifying immune selection in M. tuberculosis. ..
  4. DNA methylation in aging, race and prostate cancer
    Rajvir Dahiya; Fiscal Year: 2004
    ..Specific hypotheses: 1) The DNA methylation status of most frequently deleted genes [ERs, E-cadherin, CD44 and GSTPI (glutathione S-transferase pi)] will ..
  5. DNA methylation in aging, race and prostate cancer
    Rajvir Dahiya; Fiscal Year: 2005
    ..Specific hypotheses: 1) The DNA methylation status of most frequently deleted genes [ERs, E-cadherin, CD44 and GSTPI (glutathione S-transferase pi)] will ..
  6. DNA methylation in aging, race and prostate cancer
    Rajvir Dahiya; Fiscal Year: 2003
    ..Specific hypotheses: 1) The DNA methylation status of most frequently deleted genes [ERs, E-cadherin, CD44 and GSTPI (glutathione S-transferase pi)] will ..
  7. DNA methylation in aging, race and prostate cancer
    Rajvir Dahiya; Fiscal Year: 2002
    ..Specific hypotheses: 1) The DNA methylation status of most frequently deleted genes [ERs, E-cadherin, CD44 and GSTPI (glutathione S-transferase pi)] will ..
  8. Targeting aberrant epigenetics by nanomedicine
    Shujun Liu; Fiscal Year: 2010
    ..Inhibition of aberrant DNA methylation by decitabine or 5-azacitidine restores normal patterns of cell proliferation, differentiation and apoptosis, ..
  9. Dietary Methyl Score, Genomic DNA Methylation and Colorectal Cancer
    Eunyoung Cho; Fiscal Year: 2010
    ..cancer risk in large prospective studies and expect that individuals with reduced levels of genomic DNA methylation are at increased risk of colorectal cancer...
  10. DNA methylation alterations in response to pesticides exposure
    Lifang Hou; Fiscal Year: 2010
    ..Altered DNA methylation, an emerging hallmark of cancer, is not considered in the EPA testing system...
  11. DNA methylation alterations in response to pesticides exposure
    Lifang Hou; Fiscal Year: 2009
    ..Altered DNA methylation, an emerging hallmark of cancer, is not considered in the EPA testing system...
  12. Regulated Accessibility of a cytokine gene locus.
    Anjana Rao; Fiscal Year: 2011
    ..in activated as well as silenced cytokine genes, as judged by changes in DNase I hypersensitive (DH) sites, DNA methylation and histone modification;explored the transcriptional and chromatin-based programs underlying CD8 T cell ..
  13. Regulated Accessibility of a cytokine gene locus.
    Anjana Rao; Fiscal Year: 2010
    ..in activated as well as silenced cytokine genes, as judged by changes in DNase I hypersensitive (DH) sites, DNA methylation and histone modification;explored the transcriptional and chromatin-based programs underlying CD8 T cell ..
  14. Chemical modulators of Tet-family proteins
    Anjana Rao; Fiscal Year: 2010
    ..In mammalian cells, DNA methylation occurs almost exclusively as symmetrical methylation of cytosine in the context of the dinucleotide CpG...
  15. Chemical modulators of Tet-family proteins
    Anjana Rao; Fiscal Year: 2009
    ..In mammalian cells, DNA methylation occurs almost exclusively as symmetrical methylation of cytosine in the context of the dinucleotide CpG...
  16. Antenatal Dietary Supplementation is a Risk Factor for Infant Atopy Through Epige
    DAVID ALBERT SCHWARTZ; Fiscal Year: 2010
    ..disease during a vulnerable period of fetal development through epigenetic regulation in the form of enhanced DNA methylation. Remarkably, the increase in atopic diseases appears to correlate with the institution of widespread ..
  17. Antenatal Dietary Supplementation is a Risk Factor for Infant Atopy Through Epige
    Erwin Gelfand; Fiscal Year: 2009
    ..disease during a vulnerable period of fetal development through epigenetic regulation in the form of enhanced DNA methylation. Remarkably, the increase in atopic diseases appears to correlate with the institution of widespread ..
  18. DNA Methylation Control Hematopoietic Stem Cell Lineage Differentiation
    GRANT ANTHONY CHALLEN; Fiscal Year: 2010
    ..Research: From my post-doctoral work, I have identified a project concerning the role of DNA methylation in hematopoietic stem cell (HSC) lineage fate specification...
  19. Exploring persistent epigenetic changes after prenatal famine exposure in humans
    L Lumey; Fiscal Year: 2009
    ..b>DNA methylation, one type of epigenetic change, may play an important role in disease causation by altering the proteins that ..
  20. Regulation of Airway Mucin Gene Expression by Epigenetic Mechanism
    Reen Wu; Fiscal Year: 2010
    ..Based on these results, we hypothesize that epigenetic changes, especially changes in DNA methylation status, is one of the major mechanisms involved in the persistence of mucin gene expression, especially ..
  21. Exploring persistent epigenetic changes after prenatal famine exposure in humans
    L H Lumey; Fiscal Year: 2010
    ..b>DNA methylation, one type of epigenetic change, may play an important role in disease causation by altering the proteins that ..
  22. Impact of PAH carcinogen-DNA adducts on DNA methylation
    Nicholas Geacintov; Fiscal Year: 2002
    ..of cytosine (displacement of bases, bending, and destabilisation of the double helix) should facilitate DNA methylation. The purpose of this project is to reveal the relationship between DNA methylation and carcinogenic DNA ..
  23. Impact of PAH carcinogen-DNA adducts on DNA methylation
    Nicholas Geacintov; Fiscal Year: 2001
    ..of cytosine (displacement of bases, bending, and destabilisation of the double helix) should facilitate DNA methylation. The purpose of this project is to reveal the relationship between DNA methylation and carcinogenic DNA ..
  24. Impact of PAH carcinogen-DNA adducts on DNA methylation
    Nicholas Geacintov; Fiscal Year: 2003
    ..of cytosine (displacement of bases, bending, and destabilisation of the double helix) should facilitate DNA methylation. The purpose of this project is to reveal the relationship between DNA methylation and carcinogenic DNA ..
  25. Exploring the Role of the Brain Epigenome: Cognitive Decline and Life Experiences
    David Bennett; Fiscal Year: 2009
    ..Building on our prior work, we propose to conduct epigenome-wide DNA methylation scans on brain tissue from participants in an Exploratory Cohort consisting of the Rush Memory and Aging ..
  26. Carcinogenesis of Nickel and Epigenetic Control
    Max Costa; Fiscal Year: 2009
    ..region of genes is one of the most important chromatin marks and is commonly associated with nucleosomal DNA methylation and gene silencing...
  27. Carcinogenesis of Nickel and Epigenetic Control
    Max Costa; Fiscal Year: 2007
    ..region of genes is one of the most important chromatin marks and is commonly associated with nucleosomal DNA methylation and gene silencing...
  28. Genome-scale anaylsis of DNA methylation in CpG Islands with bisulfite sequencing
    Kun Zhang; Fiscal Year: 2009
    ..b>DNA methylation is the most stable form of epigenetic modification that leads to transcriptional silencing, X chromosome ..
  29. Genome-scale anaylsis of DNA methylation in CpG Islands with bisulfite sequencing
    KUN contact ZHANG; Fiscal Year: 2010
    ..b>DNA methylation is the most stable form of epigenetic modification that leads to transcriptional silencing, X chromosome ..
  30. Genome-scale anaylsis of DNA methylation in CpG Islands with bisulfite sequencing
    Kun Zhang; Fiscal Year: 2009
    ..b>DNA methylation is the most stable form of epigenetic modification that leads to transcriptional silencing, X chromosome ..
  31. Epigenetic predicators of asthma in neonates
    Donata Vercelli; Fiscal Year: 2009
    ..To test this hypothesis, we propose to assess genome-wide patterns of DNA methylation, a robust and quantifiable epigenetic mark...
  32. DNA methylation markers for cervical intraepithelial neoplasia III
    Qinghua Feng; Fiscal Year: 2009
    DESCRIPTION (provided by applicant): The overall objective of this grant is to identify novel DNA methylation markers for detection of cervical intraepithelial neoplasia 3 (CIN-3) and carcinoma in situ (CIS), to access their clinical ..
  33. The New England Family Study: Fifty Year Post-Perinatal Follow-Up for Life Course
    ERIC contact LOUCKS; Fiscal Year: 2010
    ..cortisol levels, maternal smoking and socioeconomic adversity) with epigenetic processes (often measured as DNA methylation) that could alter gene expression and disease outcomes...
  34. The New England Family Study: Fifty Year Post-Perinatal Follow-Up for Life Course
    ERIC LOUCKS; Fiscal Year: 2009
    ..cortisol levels, maternal smoking and socioeconomic adversity) with epigenetic processes (often measured as DNA methylation) that could alter gene expression and disease outcomes...
  35. Alcohol and Iron Derived Oxidant Stress Impact Epigenetic Regulation
    JOHN contact WILKINSON IV; Fiscal Year: 2010
    ..the methyl donor pool in cells has the potential to affect epigenetic regulation, specifically by attenuating DNA methylation. Epigenetic changes that result in altered expression of critical genes involved in control of proliferation, ..
  36. DNA Methyltransferase Inhibition by Intercalating Agents
    KEITH ROBERTSON; Fiscal Year: 2009
    ..Epigenetic genome modifications, in particular DNA methylation, have now been recognized as major regulators of gene activity and genomic stability...
  37. DNA Methyltransferase Inhibition by Intercalating Agents
    KEITH ROBERTSON; Fiscal Year: 2006
    ..Epigenetic genome modifications, in particular DNA methylation, have now been recognized as major regulators of gene activity and genomic stability...
  38. DNA Methyltransferase Inhibition by Intercalating Agents
    KEITH ROBERTSON; Fiscal Year: 2007
    ..Epigenetic genome modifications, in particular DNA methylation, have now been recognized as major regulators of gene activity and genomic stability...
  39. DNA METHYLATION AND PILI GENE REGULATION
    David Low; Fiscal Year: 2006
    ..This work will serve as a paradigm to understand how DNA methylation patterns control heritable gene expression states...
  40. Epigenetic Effects of Particles and Metals on Cardiac Health of an Aging Cohort
    Joel Schwartz; Fiscal Year: 2006
    ..and humans have shown that air particles and metals, which are constituents of particulate pollution, alter DNA methylation status...
  41. DNA METHYLATION AND PILI GENE REGULATION
    David Low; Fiscal Year: 2003
    ..This work will serve as a paradigm to understand how DNA methylation patterns control heritable gene expression states...
  42. Epigenetic Effects of Particles and Metals on Cardiac Health of an Aging Cohort
    Joel Schwartz; Fiscal Year: 2009
    ..and humans have shown that air particles and metals, which are constituents of particulate pollution, alter DNA methylation status...
  43. Epigenetic Effects of Particles and Metals on Cardiac Health of an Aging Cohort
    Joel Schwartz; Fiscal Year: 2007
    ..and humans have shown that air particles and metals, which are constituents of particulate pollution, alter DNA methylation status...
  44. DNA Methylation Control Hematopoietic Stem Cell Lineage Differentiation
    GRANT ANTHONY CHALLEN; Fiscal Year: 2012
    ..Research: From my post-doctoral work, I have identified a project concerning the role of DNA methylation in hematopoietic stem cell (HSC) lineage fate specification...
  45. EPIGENETIC TRANSGENERATIONAL ENDOCRINE DISRUPTOR ACTIONS
    Michael Skinner; Fiscal Year: 2009
    ..e. DNA methylation) of the male germ line that then, through alterations in critical epigenetic regulatory mechanism(s), ..
  46. Epigenetic regulation of programmed genome instability in O. trifallax
    JOHN RUSSELL BRACHT; Fiscal Year: 2012
    ..Genome stability is compromised when DNA methylation patterns are disrupted in cancer or in developmental disease...
  47. Genetics of DNA methylation patterning of arabidopsis.
    Steven Jacobsen; Fiscal Year: 2009
    Project Summary/Abstract Cytosine DNA methylation is an epigenetic mark for gene silencing that is important in many gene regulatory systems including mammalian imprinting, X-chromosome inactivation, and the silencing of transposons and ..
  48. Genetics of DNA methylation patterning of arabidopsis.
    Steven E Jacobsen; Fiscal Year: 2010
    Project Summary/Abstract Cytosine DNA methylation is an epigenetic mark for gene silencing that is important in many gene regulatory systems including mammalian imprinting, X-chromosome inactivation, and the silencing of transposons and ..
  49. Molecular Mechanisms of GSTP1 Reactivation by Green Tea Polyphenols
    Sanjay Gupta; Fiscal Year: 2007
    Aberrant DNA methylation and chromatin remodeling are common epigenetic changes that play critical role in gene silencing; implicated in the development and progression of prostate cancer...
  50. Molecular Mechanisms of GSTP1 Reactivation by Green Tea Polyphenols
    Sanjay Gupta; Fiscal Year: 2009
    DESCRIPTION (provided by applicant): Aberrant DNA methylation and chromatin remodeling are common epigenetic changes that play critical role in gene silencing;implicated in the development and progression of prostate cancer...
  51. Reactivation of Tumor Suppressor Genes in Breast Cancer by Dietary Supplements as
    Zhongfa Liu; Fiscal Year: 2009
    ..In contrast to genetic mutation, DNA methylation is susceptible to change and reversible;therefore, it represents an excellent target to develop DNA ..
  52. Reactivation of Tumor Suppressor Genes in Breast Cancer by Dietary Supplements as
    Zhongfa Liu; Fiscal Year: 2010
    ..In contrast to genetic mutation, DNA methylation is susceptible to change and reversible;therefore, it represents an excellent target to develop DNA ..
  53. CPG METHYLATION AND MUTATION
    Gerd P Pfeifer; Fiscal Year: 2010
    ..This application will focus on mechanistic studies that will investigate the molecular pathways leading to DNA methylation changes in tumors with emphasis on DNA hypermethylation...
  54. CPG METHYLATION AND MUTATION
    GERD PFEIFER; Fiscal Year: 2009
    ..This application will focus on mechanistic studies that will investigate the molecular pathways leading to DNA methylation changes in tumors with emphasis on DNA hypermethylation...
  55. DNA Methyltransferase Inhibition by Intercalating Agents
    Keith D Robertson; Fiscal Year: 2010
    ..Epigenetic genome modifications, in particular DNA methylation, have now been recognized as major regulators of gene activity and genomic stability...
  56. Roles for Global Chromatin Structure in C. elegans Longevity
    SIU LEE; Fiscal Year: 2009
    ..Epigenetic changes, such as altered levels or patterns of DNA methylation and post-translational histone modifications, have been observed in a variety of aging mammalian tissues and ..
  57. Epigenetic Alterations in IPF Fibroblastic Foci
    James Hagood; Fiscal Year: 2009
    ..Recent data indicate re-expression of developmental gene signatures in IPF. Epigenetic regulation, including DNA methylation and histone modification, which often occurs during development and in response to aging and environmental ..
  58. Genome Wide Analysis of DNA Methylation
    Joseph Ecker; Fiscal Year: 2005
    This proposal aims to identify functional, non-coding elements in eukaryotic genomes by surveying genome-wide DNA methylation. Cytosine DNA methylation controls developmental gene expression in mammals during genomic imprinting and X-..
  59. Regulation of Genomic and Epigenomic Stability at CpG Sites
    Alfonso Bellacosa; Fiscal Year: 2010
    ..b>DNA methylation is an important epigenetic modification of the mammalian genome consisting in the formation of 5-..
  60. Genome Wide Analysis of DNA Methylation
    Joseph Ecker; Fiscal Year: 2006
    ..This proposal aims to identify functional, non-coding elements in eukaryotic genomes by surveying genome-wide DNA methylation. Cytosine DNA methylation controls developmental gene expression in mammals during genomic imprinting and X-..
  61. Genome Wide Analysis of DNA Methylation
    Joseph Ecker; Fiscal Year: 2004
    This proposal aims to identify functional, non-coding elements in eukaryotic genomes by surveying genome-wide DNA methylation. Cytosine DNA methylation controls developmental gene expression in mammals during genomic imprinting and X-..
  62. Epigenetic regulation of HIV latency
    ERIC M VERDIN; Fiscal Year: 2012
    ..We have recently reported that DNA methylation of the HIV promoter plays an important role in the establishment and maintenance of HIV latency...
  63. DNA Methylation Profiles in a Polygenic Mouse Model of Diet-Induced Obesity
    Jan Bressler; Fiscal Year: 2007
    ..It is the long-term goal of this proposal to evaluate whether modifications in DNA methylation patterns that may result in either activation or silencing of genes can be detected when comparing obese and ..
  64. Epigenetic regulation of HIV latency
    ERIC M VERDIN; Fiscal Year: 2010
    ..We have recently reported that DNA methylation of the HIV promoter plays an important role in the establishment and maintenance of HIV latency...
  65. Genome-wide DNA Methylation Profiles Associated with Abnormal Intrauterine Growth
    Francine Einstein; Fiscal Year: 2009
    ..We offer a novel hypothesis that conditions during fetal development alter epigenetic patterns of DNA methylation in non-embryonic stem cells, which may be a marker for, or contribute to, susceptibility to T2DM and other ..
  66. Genome-wide DNA Methylation Profiles Associated with Abnormal Intrauterine Growth
    Cristina Montagna; Fiscal Year: 2010
    ..We offer a novel hypothesis that conditions during fetal development alter epigenetic patterns of DNA methylation in non-embryonic stem cells, which may be a marker for, or contribute to, susceptibility to T2DM and other ..
  67. GENETIC ASPECTS OF DNA METHYLATION
    ERIC SELKER; Fiscal Year: 1992
    ..a link has been demonstrated between methylation and inactivity of DNA, the function and mechanism of DNA methylation remains unclear...
  68. GENETIC ASPECTS OF DNA METHYLATION
    ERIC SELKER; Fiscal Year: 1993
    ..a link has been demonstrated between methylation and inactivity of DNA, the function and mechanism of DNA methylation remains unclear...
  69. GENETIC ASPECTS OF DNA METHYLATION
    ERIC SELKER; Fiscal Year: 1991
    ..a link has been demonstrated between methylation and inactivity of DNA, the function and mechanism of DNA methylation remains unclear...
  70. The Role of DNMT3B in the DNA Methylation of Cancer Cells
    LUCY ANN GODLEY; Fiscal Year: 2010
    Epigenetic changes, such as DNA methylation and histone modifications, alter chromatin structure and regulate gene transcription...
  71. Epigenetic Regulation of MMP-13
    MARY GOLDRING; Fiscal Year: 2007
    ..is not only controlled by transcriptional activators and repressors, but also depends on the epigenetic DNA methylation of the promoter, which is the mechanism whereby genes that are never expressed by a somatic cell are ..
  72. GENETIC ASPECTS OF DNA METHYLATION
    ERIC SELKER; Fiscal Year: 2007
    b>DNA methylation is required for normal development of higher eukaryotes. Methylation is required for X-inactivation and genomic imprinting in mammals, and abnormal methylation is associated with cancer...
  73. GENETIC ASPECTS OF DNA METHYLATION
    ERIC SELKER; Fiscal Year: 2003
    b>DNA methylation is required for normal development of higher eukaryotes. Methylation is required for X-inactivation and genomic imprinting in mammals, and abnormal methylation is associated with cancer...
  74. GENETIC ASPECTS OF DNA METHYLATION
    ERIC SELKER; Fiscal Year: 2006
    b>DNA methylation is required for normal development of higher eukaryotes. Methylation is required for X-inactivation and genomic imprinting in mammals, and abnormal methylation is associated with cancer...
  75. METHYLATION-ASSOCIATED SILENCING OF MOUSE HSP70 GENES
    Benette Phillips; Fiscal Year: 1999
    DESCRIPTION: The significance of DNA methylation has been an open issue for some time. Many people believe that methylated genes are incapable or less capable of being transcribed than their unmethylated or hypomethylated counterparts...
  76. Role of T-cells in the induction of lupus
    Bruce Richardson; Fiscal Year: 2009
    ..from the Richardson lab indicates that environmental agents may contribute to human lupus through effects on DNA methylation, an epigenetic mechanism determining chromatin structure...
  77. Epigenetic Mechanisms of Memory Storage
    EDWIN TED G ABEL; Fiscal Year: 2010
    DESCRIPTION (provided by applicant): Epigenetic modifications such as histone acetylation and DNA methylation are critical for the long-lasting regulation of gene expression during development and may be a major mechanism of information ..
  78. DNA METHYLOME ANALYSIS IN BIPOLAR DISORDER
    ART PETRONIS; Fiscal Year: 2009
    ..In our recent study, we used 12,192- feature containing CpG-island microarrays to identify DNA methylation changes in the prefrontal cortex of individuals affected with BPD and schizophrenia...
  79. MECHANISMS OF DE NOVO METHYLATION IN CANCER
    Peter Jones; Fiscal Year: 2009
    ..funded for almost 30 years, have been to understand the mechanisms for the establishment and inheritance of DNA methylation patterns and to develop drugs which can interfere with cytosine methylation and reactivate silenced genes...
  80. MECHANISMS OF DE NOVO METHYLATION IN CANCER
    Peter A Jones; Fiscal Year: 2010
    ..funded for almost 30 years, have been to understand the mechanisms for the establishment and inheritance of DNA methylation patterns and to develop drugs which can interfere with cytosine methylation and reactivate silenced genes...
  81. De Novo Methyltransferase Function in Chromatin and Cancer
    Keith D Robertson; Fiscal Year: 2010
    b>DNA methylation is an essential regulator of transcription, chromatin structure, development, and genomic stability in mammalian cells that is mediated by a family of DNA methyltransferases (DNMTs): DNMT1, DNMT3A, and DNMT3B...
  82. De Novo Methyltransferase Function in Chromatin and Cancer
    KEITH ROBERTSON; Fiscal Year: 2009
    b>DNA methylation is an essential regulator of transcription, chromatin structure, development, and genomic stability in mammalian cells that is mediated by a family of DNA methyltransferases (DNMTs): DNMT1, DNMT3A, and DNMT3B...
  83. ROLE OF DNA METHYLTRANSFERASE 3B IN LUNG TUMORIGENESIS
    Li Mao; Fiscal Year: 2009
    ..Epigenetic alterations, particularly aberrant DNA methylation, play as important a role as genetic alterations in lung tumorigenesis...
  84. DNA Methylation and Ovarian Cancer
    Kenneth P Nephew; Fiscal Year: 2010
    ..During the initial funding period, we demonstrated that increased DNA methylation and alterations in histone methylation are strongly associated with ovarian cancer chemoresistance...
  85. DNA Methylation and Ovarian Cancer
    Kenneth Nephew; Fiscal Year: 2009
    ..During the initial funding period, we demonstrated that increased DNA methylation and alterations in histone methylation are strongly associated with ovarian cancer chemoresistance...
  86. Cancer prevention by indole-3-carbinol via modulation of the epigenome
    Abby Benninghoff; Fiscal Year: 2009
    ..I3C is capable of donating to the methyl donor pool, thus increasing available methyl groups for DNA methylation. In contrast, 3,3'-diindolylmethane (DIM), which is not protective against DBP-induced lymphoma, is not ..
  87. DNA METHYLOME STUDY IN TYPE 1 DIABETES
    ART PETRONIS; Fiscal Year: 2009
    ..More specifically, we will investigate DNA methylation, which is one of the key epigenetic mechanisms...
  88. Cancer prevention by indole-3-carbinol via modulation of the epigenome
    Abby D Benninghoff; Fiscal Year: 2010
    ..I3C is capable of donating to the methyl donor pool, thus increasing available methyl groups for DNA methylation. In contrast, 3,3'-diindolylmethane (DIM), which is not protective against DBP-induced lymphoma, is not ..
  89. Targeting aberrant epigenetics by nanomedicine
    Shujun Liu; Fiscal Year: 2012
    ..Inhibition of aberrant DNA methylation by decitabine or 5-azacitidine restores normal patterns of cell proliferation, differentiation and apoptosis, ..
  90. GENETIC ASPECTS OF DNA METHYLATION
    ERIC SELKER; Fiscal Year: 2009
    We exploit the fungus Neurospora crassa to elucidate the control and function of DNA methylation, an pigenetic process required for X chromosome-inactivation, genomic imprinting and normal development in mammals...
  91. DNA-Methylation Profiling from Fixed Melanocytic Tissues
    Nancy Thomas; Fiscal Year: 2009
    ..The central hypothesis of our proposal is that DNA methylation patterns exist that can discriminate melanomas from benign moles with high sensitivity, specificity, and ..
  92. NIH Director's Pioneer Award
    Vicki Chandler; Fiscal Year: 2009
    ..In New Research Direction, I briefly describe the new approaches I am proposing, explain how this builds on my past work, and discuss why the NDPA process provides a unique opportunity to pursue this work. ..
  93. METHYLATION OF THE CALCITONIN GENE IN HUMAN TUMORS
    Stephen Baylin; Fiscal Year: 2009
    ..related to the above two, links vulnerability of genes in adult tumorigenesis to acquire abnormal promoter DNA methylation, with key histone modifications, and proteins establishing and interpreting them, in embryonic stem/..
  94. RNAi and DNA Methylation Control Genomic Stability and Transcriptional Silencing
    John Frazer; Fiscal Year: 2009
    ..RNA Interference (RNAi) and DNA methylation are two chromatin-modifying activities that regulate eukaryotic genomes...
  95. RNAi and DNA Methylation Control Genomic Stability and Transcriptional Silencing
    John Frazer; Fiscal Year: 2007
    ..RNA Interference (RNAi) and DNA methylation are two chromatin-modifying activities that regulate eukaryotic genomes...
  96. RNAi and DNA Methylation Control Genomic Stability and Transcriptional Silencing
    John Frazer; Fiscal Year: 2006
    ..RNA Interference (RNAi) and DNA methylation are two chromatin-modifying activities that regulate eukaryotic genomes...
  97. Epigenetics Landscape of Chronic Kidney Disease
    Katalin Susztak; Fiscal Year: 2009
    ..We propose to use the HELP assay to determine DNA methylation patterns of microdissected glomerular and tubulointerstitial samples. 2...