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. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. ncbi 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
  8. 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
  9. 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
  10. 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

Detail Information

Publications294 found, 100 shown here

  1. 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 ..
  2. 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...
  3. 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...
  4. 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
    ....
  5. 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...
  6. 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...
  7. ncbi 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...
  8. 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...
  9. 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...
  10. 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
  11. 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...
  12. 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...
  13. 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...
  14. 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...
  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. 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...
  17. 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
    ....
  18. 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...
  19. ncbi 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.
  20. 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...
  21. 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...
  22. 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...
  23. 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...
  24. 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...
  25. 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)...
  26. ncbi 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...
  27. pmc Germline DNA demethylation dynamics and imprint erasure through 5-hydroxymethylcytosine
    Jamie A Hackett
    Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
    Science 339:448-52. 2013
    ..Nonetheless, we identify rare regulatory elements that escape systematic DNA demethylation in PGCs, providing a potential mechanistic basis for transgenerational epigenetic inheritance...
  28. doi Epigenetics in cancer
    Manel Esteller
    Cancer Epigenetics Laboratory, Spanish National Cancer Research Center, Madrid, Spain
    N Engl J Med 358:1148-59. 2008
  29. ncbi Gene silencing in cancer in association with promoter hypermethylation
    James G Herman
    Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins Medical Institutions, Baltimore, USA
    N Engl J Med 349:2042-54. 2003
  30. 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...
  31. ncbi DNA methylation profiling in the clinic: applications and challenges
    Holger Heyn
    Cancer Epigenetics and Biology Program PEBC, Bellvitge Biomedical Research Institute IDIBELL, 08908 L Hospitalet de Llobregat, Barcelona, Catalonia, Spain
    Nat Rev Genet 13:679-92. 2012
    ..epigenetic alterations in disease emphasizes the crucial role of these epigenetic alterations - particularly DNA methylation - for future diagnosis, prognosis and prediction of response to therapies...
  32. ncbi 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...
  33. 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...
  34. 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...
  35. 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...
  36. 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...
  37. 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.
  38. 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...
  39. pmc IDH1 mutation is sufficient to establish the glioma hypermethylator phenotype
    Sevin Turcan
    Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
    Nature 483:479-83. 2012
    ....
  40. 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...
  41. 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, ..
  42. 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...
  43. 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)...
  44. ncbi 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...
  45. ncbi High density DNA methylation array with single CpG site resolution
    Marina Bibikova
    Illumina, Inc 9885 Towne Centre Drive, San Diego, CA 92121, USA
    Genomics 98:288-95. 2011
    We have developed a new generation of genome-wide DNA methylation BeadChip which allows high-throughput methylation profiling of the human genome...
  46. ncbi 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 ..
  47. 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...
  48. 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...
  49. ncbi 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...
  50. 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...
  51. pmc DNMT3A mutations in acute myeloid leukemia
    Timothy J Ley
    Department of Genetics, Genome Center, Washington University, St Louis, MO 63110, USA
    N Engl J Med 363:2424-33. 2010
    ..The genetic alterations responsible for an adverse outcome in most patients with acute myeloid leukemia (AML) are unknown...
  52. 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...
  53. pmc Differential DNA methylation in purified human blood cells: implications for cell lineage and studies on disease susceptibility
    Lovisa E Reinius
    Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
    PLoS ONE 7:e41361. 2012
    ..The application of DNA methylation analysis is becoming widely popular in complex disorders, for example, to understand part of the "missing ..
  54. 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...
  55. 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 ..
  56. ncbi 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...
  57. 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...
  58. pmc Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome
    Hume Stroud
    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
    Cell 152:352-64. 2013
    ..Multiple pathways regulate DNA methylation in different sequence contexts, but the factors that regulate DNA methylation at a given site in the genome ..
  59. pmc The dynamics of genome-wide DNA methylation reprogramming in mouse primordial germ cells
    Stefanie Seisenberger
    Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
    Mol Cell 48:849-62. 2012
    Genome-wide DNA methylation reprogramming occurs in mouse primordial germ cells (PGCs) and preimplantation embryos, but the precise dynamics and biological outcomes are largely unknown...
  60. ncbi DNA methylation: roles in mammalian development
    Zachary D Smith
    Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Nat Rev Genet 14:204-20. 2013
    b>DNA methylation is among the best studied epigenetic modifications and is essential to mammalian development...
  61. pmc Charting a dynamic DNA methylation landscape of the human genome
    Michael J Ziller
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Nature 500:477-81. 2013
    b>DNA methylation is a defining feature of mammalian cellular identity and is essential for normal development...
  62. 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 ..
  63. 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...
  64. ncbi 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...
  65. 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.
  66. 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...
  67. 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...
  68. pmc Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis
    Yun Liu
    Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
    Nat Biotechnol 31:142-7. 2013
    ..01), with the rest showing suggestive association, in monocyte cell fractions in an independent cohort of 12 cases and 12 controls. Thus, DNA methylation is a potential mediator of genetic risk.
  69. pmc DNA methylation arrays as surrogate measures of cell mixture distribution
    Eugene Andres Houseman
    College of Public Health and Human Sciences, Oregon State University, Corvallis, OR 97331, USA
    BMC Bioinformatics 13:86. 2012
    ..Emerging research demonstrates that DNA methylation is responsible for cellular differentiation, and when measured in whole peripheral blood, serves to ..
  70. 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...
  71. 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...
  72. ncbi Mobile elements: drivers of genome evolution
    Haig H Kazazian
    Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
    Science 303:1626-32. 2004
    ..Although the host can often control their numbers, massive expansions of retrotransposons have been tolerated during evolution. Now mobile elements are becoming useful tools for learning more about genome evolution and gene function...
  73. 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...
  74. ncbi 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...
  75. ncbi Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis
    Xiaoyu Zhang
    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
    Cell 126:1189-201. 2006
    ..Here we report the first comprehensive DNA methylation map of an entire genome, at 35 base pair resolution, using the flowering plant Arabidopsis thaliana as a ..
  76. ncbi 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...
  77. ncbi Cancer epigenetics: from mechanism to therapy
    Mark A Dawson
    Gurdon Institute and Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
    Cell 150:12-27. 2012
    The epigenetic regulation of DNA-templated processes has been intensely studied over the last 15 years. DNA methylation, histone modification, nucleosome remodeling, and RNA-mediated targeting regulate many biological processes that are ..
  78. 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
    ....
  79. 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...
  80. 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...
  81. 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...
  82. ncbi 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...
  83. 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 ..
  84. 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 ..
  85. ncbi 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
    ....
  86. 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.
  87. 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...
  88. 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...
  89. 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...
  90. 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...
  91. ncbi 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...
  92. 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...
  93. ncbi 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...
  94. 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.
  95. 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...
  96. 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...
  97. 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...
  98. 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...
  99. 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
    ....
  100. 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...

Research Grants74

  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. 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. ..
  3. High Throughput Genotyping and DNA Sequencing for Studying the Genetic Contributi
    Sonia Dua; Fiscal Year: 2013
    ..3) A [unreadable]genotyping[unreadable] platform capable of measuring DNA methylation in human samples using arrays that cover 10,000 to 250,000 potential sites of methylation in the human genome...
  4. Role of the Y-Located TSPY Gene in Human Oncogenesis
    Yun Fai Chris Lau; Fiscal Year: 2013
    ..oncogenesis in the TSPY-LADY bi-transgenic mice, in terms of tumor pathogenesis, transgene expression, DNA methylation status of the TSPY promoter and exon 1, and identification of transcription factors and repressors affected ..
  5. MECHANISMS IN THE REGULATION OF SP-A GENE EXPRESSION
    Carole R Mendelson; Fiscal Year: 2013
    ..This will be correlated with local changes in histone modification, DNA methylation, and DNaseI hypersensitive sites, to assess changes in chromatin structure...
  6. Prospective studies of cancer etiology and prevention in Shanghai and Singapore
    Jian Min Yuan; Fiscal Year: 2013
    ..studies within the two cohorts to elucidate the role of environmental exposure, genetic variants and DNA methylation in the development of lung or liver cancer...
  7. DNA methylation of extracellular superoxide dismutase in pulmonary hypertension
    EVA NOZIK GRAYCK; Fiscal Year: 2012
    ..Based on these data, we hypothesize that DNA methylation of the EC-SOD promoter mediates silencing of this protective gene and contributes to the pathogenesis of ..
  8. Epigenetics of Sex Differences in Brain and Behavior
    BRIDGET NUGENT; Fiscal Year: 2012
    ..b>DNA methylation is the epigenetic process by which a DNA methyltransferase (DNMT) enzyme covalently modifies cytosine ..
  9. Hepatic Steatosis Modulation by Apo B Gene Transcription
    JANET DEHOFF SPARKS; Fiscal Year: 2010
    ..Aim 3 examines the role of DNA methylation in regulating apob gene expression as a potential mechanism of betaine action by assessment of global and ..
  10. Regulation of Airway Mucin Gene Expression by Epigenetic Mechanism
    Reen Wu; Fiscal Year: 2013
    ..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 ..
  11. Chronic Stress and Abdominal Pain: Novel Mechanisms
    John W Wiley; Fiscal Year: 2013
    ..refers to stable and/or heritable changes in gene function without changes in the DNA sequence via DNA methylation, histone modification and chromatin remodeling...
  12. DNA Methylation in Ethanol Drinking Behavior
    David P Gavin; Fiscal Year: 2013
    ..b>DNA methylation is one component of epigenetic gene regulation...
  13. 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...
  14. CPG METHYLATION AND MUTATION
    Gerd P Pfeifer; Fiscal Year: 2013
    ..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...
  15. Transgenerational effects of endocrine disruptors: epigenetics and physiology
    Rebecca A Simmons; Fiscal Year: 2013
    ..In addition to testing the expression and DNA methylation of imprinted genes, we will assay genome-wide DNA methylation changes and key histone modifications in F1-F3 ..
  16. Epigenetic effects of developmental endocrine disruptor exposure in the ovary
    Mehmet Uzumcu; Fiscal Year: 2010
    ..Epigenetic mechanisms (e.g., DNA methylation) may play a role as a link between environmental EDC exposures during development and the adult diseases...
  17. Genistein and Prostate Cancer
    Rajvir Dahiya; Fiscal Year: 2010
    ..hypothesize that genistein inhibits prostate cancer growth through modulation of epigenetic events, such as DNA methylation and histone acetylation...
  18. Signaling Mechanisms in Alcohol Drinking Behaviors
    Subhash C Pandey; Fiscal Year: 2013
    ..epigenetic regulatory mechanism which has been shown to play a role in the regulation of gene expression is DNA methylation. DNA methyltransferases (DNMT) catalyze DNA methylation allowing for the binding of methyl-CpG-binding ..
  19. MECHANISMS OF EUKARYOTIC TRANSCRIPTIONAL REGULATION
    Michael R Green; Fiscal Year: 2013
    ..activity of many genes is controlled by epigenetic mechanisms that involve histone modifications and DNA methylation. The detailed mechanisms and pathways by which epigenetic repression is established and maintained on ..
  20. Transplacental Arsenic Induced Hepatic Dysfunction and Vascular Disease
    J Christopher States; Fiscal Year: 2010
    ..Transplacental arsenic exposure can disrupt liver DNA methylation patterns and thus alter liver gene expression...
  21. Regulation of Genomic and Epigenomic Stability at CpG Sites
    Alfonso Bellacosa; Fiscal Year: 2013
    ..b>DNA methylation is an important epigenetic modification of the mammalian genome consisting in the formation of 5-..
  22. Roles of RNA Polymerases IV and V in siRNA-mediated gene silencing
    CRAIG STUART PIKAARD; Fiscal Year: 2013
    ..These novel RNA polymerases play non- redundant roles in RNA-directed DNA methylation, silencing of transposable elements, large-scale heterochromatin organization, long-distance spreading of ..
  23. Role of ALDH7A1 in Ethanol-Induced Oxidative Damage
    CHAD NICHOLAS BROCKER; Fiscal Year: 2011
    ..SAM is the principle biological methyl donor and required for protein, phospholipid and DNA methylation. In the liver, chronic ethanol consumption both dramatically elevates LPO-derived aldehyde production and ..
  24. Epigenetic downregulation of the antibody response and inhibition of autoimmunity
    Paolo Casali; Fiscal Year: 2013
    ..of the antibody response and inhibition of autoimmunity Epigenetic marks (including histone modifications, DNA methylation and microRNAs) "interact" with genetic programs to regulate B cell functions, such as class switch DNA ..
  25. Analysis of epigenetic regulation in early mammalian embryos via RNA interference
    Charles R Long; Fiscal Year: 2010
    ..Two major mechanisms appear to be responsible for establishing and maintaining the epigenome, DNA methylation and histone modifications...
  26. 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 ..
  27. Interrelationships among nutrients involved in one-carbon metabolism in Banglades
    MEGAN NINA HALL; Fiscal Year: 2011
    ..nutrients involved in methylation pathways, which have not previously been considered in relation to As and DNA methylation, will be examined...
  28. B Cell Development in Aging
    John C Cambier; Fiscal Year: 2010
    ..Little is known regarding the patterns of histone modification and DNA methylation that impact early steps in hematopoiesis, and how these patterns might be altered during aging...
  29. Transgenerational effects of maternal high fat diet during pregnancy on breast ca
    Leena A Hilakivi-Clarke; Fiscal Year: 2013
    ..In addition, we will investigate whether these transgenerational effects involve changes in DNA methylation. Our preliminary analysis performed using massively parallel sequencing identified 144 "named" genes which ..
  30. SATB1-dependent epigenetic regulation of leukemia initiating cells
    Britta Will; Fiscal Year: 2011
    ..will utilize global chromatin immunoprecipitation analysis (ChIP-seq) in combination with gene expression and DNA methylation pattern analysis...
  31. Adiponectin and fetal programming
    Jianhua Shao; Fiscal Year: 2013
    ..Adiponectin treatment increased C/EBP2 gene expression while reduced its DNA methylation in MEFs...
  32. Adult and Transgenerational Toxicity Due to Developmental TCDD Exposure
    Tracie R Baker; Fiscal Year: 2013
    ..tissues from each generation and will use both gene- specific and global techniques to examine alterations in DNA methylation and chromatin structure induced by TCDD exposure and transmitted into F1 and F2 fish...
  33. Early social stress, novelty seeking, and impulsive behavior
    David M Lyons; Fiscal Year: 2013
    ..e., increased DNA methylation) and thereby increases anticipatory impulsivity. Specifically, we address the following three aims. Aim 1...
  34. Regulation of Rhox5 Transcriptional Elongation
    Marcy E Richardson; Fiscal Year: 2013
    ..A strong candidate to control AR recruitment is DNA methylation, as many of the AR- binding sites in the Pp are methylated in tissues and developmental stages that exhibit ..
  35. Regulated Accessibility of a cytokine gene locus.
    Anjana Rao; Fiscal Year: 2013
    ..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 ..
  36. Genome-wide DNA Methylation Profiles Associated with Abnormal Intrauterine Growth
    Cristina Montagna; Fiscal Year: 2013
    ..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 ..
  37. Aberrant DNA Methylation of MicroRNA Genes in Hepatocellular Carcinoma (HCC)
    Jing Shen; Fiscal Year: 2012
    DESCRIPTION (provided by applicant): Tumor suppressor gene silencing by promoter DNA methylation is an important mechanism of tumorigenesis, including in hepatocellular carcinoma (HCC)...
  38. Role of natural indoles in experimental autoimmune encephalomyelitis
    Mitzi Nagarkatti; Fiscal Year: 2013
    ..proinflammatory Th1/Th17cells and induction of T regs/Th2 cells via epigenetic regulatory mechanisms such as DNA methylation and miRNA dysregulation that block neuroinflammation...
  39. Epigenetic Alterations in IPF Fibroblastic Foci
    YAN SANDERS; Fiscal Year: 2010
    ..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 ..
  40. DNA Methylation Control Hematopoietic Stem Cell Lineage Differentiation
    GRANT ANTHONY CHALLEN; Fiscal Year: 2013
    ..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...
  41. Epigenetic Regulation of Serotonin:Relevance to HIV and Methamphetamine Abuse
    GREGORY MICHAEL MILLER; Fiscal Year: 2012
    ..We will also assess the involvement of DNA methylation and CCCTC-binding factor (CTCF) in the regulation of TPH2 gene expression...
  42. 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...
  43. Low level exposure to PBDEs: testing the hormetic and epigenetic hypotheses
    Lucio G Costa; Fiscal Year: 2013
    ..that exposure of neurons in vitro to low levels of BDE-47 would result in epigenetic changes, at the level of DNA methylation and of miRNA homeostasis, which may be relevant for brain development and may result in specific changes in ..
  44. Functional Analysis of the Embryonic Epigenome in a Non-rodent Model
    Mark E Westhusin; Fiscal Year: 2013
    ..Two key factors are associated with the epigenetic control of gene expression 1) DNA methylation and 2) histone modifications...
  45. EFFECT OF DRUGS OF ABUSE ON NEURONAL REDOX AND METHYLATION STATUS
    Richard C Deth; Fiscal Year: 2012
    ..only partially understood, there is increasing evidence for the involvement of epigenetic mechanisms such as DNA methylation. Studies our lab have identified a critical role for the cysteine/glutamate uptake transporter EAAT3 (..
  46. Interaction of fetal growth and bisphenol A in obesity
    Frederick S vom Saal; Fiscal Year: 2013
    ..glucose homeostasis, adipocyte number and size, gene expression by qPCR and Next Generation sequencing and DNA methylation in adulthood and on PND 21-28...
  47. The Role of the Nuclear Lamina in Chromatin Organization and Gene Expression in N
    Marcos Estecio; Fiscal Year: 2012
    ..we will profile genome-nuclear lamina interactions, histone tail posttranslational modifications and DNA methylation in primary normal and cancer cells...
  48. 2011 Epigenetics Gordon Research Conference
    Marisa S Bartolomei; Fiscal Year: 2011
    ..Modification of the chromatin by DNA methylation, post- translational modification of the histones that wrap the DNA, use of alternative histone variants and ..
  49. 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...
  50. Epigenomic Regulation of Gene Expression in Diet Induced Obesity
    Donald K Scott; Fiscal Year: 2012
    ..of epigenetics, a spectrum of largely sequence-independent regulatory influences on gene expression including DNA methylation. Epigenetic influences on phenotype are perhaps best exemplified by recent studies demonstrating that the ..
  51. The Toxic Environment and the Epigenetics of Fetal Growth
    HEATHER HERSON BURRIS; Fiscal Year: 2013
    ..goals: (1) assess the role that arsenic plays in fetal growth;(2) assess the role arsenic plays in the DNA methylation of genes involved in fetal growth such as inflammatory cytokine genes and the glucocorticoid receptor gene, ..
  52. In utero programming of the dopamine system: behavior, neuroanatomy &epigenetics
    Teresa M Reyes; Fiscal Year: 2013
    ..manner, as well as significant increases in the expression of genes that play an important role in DNA methylation, including DNA methyltransferase 1 (DNMT1) and methyl CpG binding protein 2 (MeCP2)...
  53. Epigenetic Changes in the Glucocorticoid Receptor Gene Due to Arsenic Exposure
    Andrea M Allan; Fiscal Year: 2013
    ..Epigenetic mechanisms, including DNA methylation, histone modification, and noncoding RNA-mediated processes, are known to play significant roles in ..
  54. SPLENIC TOXICITY OF ANILINE
    M Firoze Khan; Fiscal Year: 2010
    ..Aim 2 will examine the role of oxidative DNA damage and repair, malondialdehyde-DNA adducts, DNA methylation, and mutations in the tumor suppressor gene p53 in aniline-induced splenic toxicity...
  55. Effect of preimplantation embryo culture on adult glucose homeostasis
    Paolo Rinaudo; Fiscal Year: 2013
    ..The aberrant txnip gene expression is associated with altered expression of several genes that control DNA methylation, suggesting an epigenetic regulation...
  56. Prenatal stress and epigenetic programming of the HPA axis and autonomic balance
    Rosalind J Wright; Fiscal Year: 2013
    ..We will investigate methylation in two complementary ways, i.e., DNA methylation of selected candidate genes and genome-wide discovery...
  57. Epigenetic programming of brain development by choline nutrition
    Jan Krzysztof Blusztajn; Fiscal Year: 2011
    ..embryonic day 16 and postnatal day 30 we will determine: 1) global transcriptome profile using microarrays;2) DNA methylation patterns with methylated DNA immunoprecipitation (MeDIP) followed by microarray analysis and 3) chromatin ..
  58. FASEB SRC on Hematopoietic Malignancies
    MICHELLE ALICE KELLIHER; Fiscal Year: 2011
    ..of altered transcriptional regulation in hematopoietic neoplasms, with a particular focus on changes in DNA methylation as well as histone acetylation, methylation and chromatin structure;4) Role of microRNAs in CLL pathogenesis ..
  59. Generation of Human iPS Cells via Non-integrating Vectors
    Wen Shu Wu; Fiscal Year: 2010
    ..mainly from mouse somatic cells, and these cells are similar to ES cells in terms of gene expression profile, DNA methylation, and perhaps most significantly self-renewal and differentiation potential...
  60. Molecular Analysis of Alcohol Effects on Human Oral Epithelium Cells'Epigenome
    Alison Urvalek; Fiscal Year: 2013
    ..of this application is to understand whether alcohol regulates genome-wide epigenetic changes, such as DNA methylation and histone modifications in intergenic regions and at the promoters of genes whose expression is changed ..
  61. Cytosine DNA Methylation and Transcriptional Repression in African Trypanosomes
    KEVIN MILITELLO; Fiscal Year: 2012
    ..Our studies of cytosine DNA methylation in Trypanosoma brucei may reveal the mechanism by which the parasites regulate expression of surface antigens ..
  62. INTERNATIONAL GENETIC EPIDEMIOLOGY OF ORAL CLEFTS
    Terri H Beaty; Fiscal Year: 2013
    ..serum samples from mothers of cleft cases to evaluate biological models relevant to one carbon metabolism and DNA methylation. 3) To further investigate genes showing evidence of parent- of-origin effects (which may reflect genetic ..
  63. PTIP as an epigenetic regulator in male meiosis
    Guo Zhang Zhu; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): It is becoming evident that epigenetic mechanisms, including DNA methylation, histone modification and non-coding RNAs, play significant roles in spermatogenesis...
  64. 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 ..
  65. 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 ..
  66. 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 ..
  67. 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...
  68. 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 ..
  69. 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...
  70. 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-..
  71. 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...
  72. 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 ..
  73. 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...
  74. 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. ..