cpg islands

Summary

Summary: Areas of increased density of the dinucleotide sequence cytosine--phosphate diester--guanine. They form stretches of DNA several hundred to several thousand base pairs long. In humans there are about 45,000 CpG islands, mostly found at the 5' ends of genes. They are unmethylated except for those on the inactive X chromosome and some associated with imprinted genes.

Top Publications

  1. ncbi Initial sequencing and analysis of the human genome
    E S Lander
    Whitehead Institute for Biomedical Research, Center for Genome Research, Cambridge, Massachusetts 02142, USA
    Nature 409:860-921. 2001
  2. pmc Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
    Tarjei S Mikkelsen
    Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
    Nature 448:553-60. 2007
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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

Detail Information

Publications368 found, 100 shown here

  1. ncbi Initial sequencing and analysis of the human genome
    E S Lander
    Whitehead Institute for Biomedical Research, Center for Genome Research, Cambridge, Massachusetts 02142, USA
    Nature 409:860-921. 2001
    ..We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence...
  2. pmc Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
    Tarjei S Mikkelsen
    Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
    Nature 448:553-60. 2007
    ..This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations...
  3. 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
    ..bisulphite sequencing and single-molecule-based sequencing, we generated DNA methylation maps covering most CpG islands, and a representative sampling of conserved non-coding elements, transposons and other genomic features, for ..
  4. 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
    Vertebrate CpG islands (CGIs) are short interspersed DNA sequences that deviate significantly from the average genomic pattern by being GC-rich, CpG-rich, and predominantly nonmethylated...
  5. 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
    ..assumed that functionally important DNAm will occur in promoters, and that most DNAm changes in cancer occur in CpG islands. Here we show that most methylation alterations in colon cancer occur not in promoters, and also not in CpG ..
  6. 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...
  7. 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
    ..sequencing shows these variable cDMRs are related to loss of sharply delimited methylation boundaries at CpG islands. Furthermore, we find hypomethylation of discrete blocks encompassing half the genome, with extreme gene ..
  8. 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
  9. 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
    ..7 million of the 28 million CpG sites. From the dense, high-resolution coverage of CpG islands, the majority of methylated CpG islands were shown to be in intragenic and intergenic regions, whereas less ..
  10. 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
    ..This Review discusses the different approaches and their relative merits and introduces considerations for data analysis...
  11. 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
    ..Drawing on insights from both plants and animals should deepen our understanding of the regulation and biological significance of DNA methylation...
  12. 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
    ..Our data provide a genome-scale, base-resolution timeline of DNA methylation in the pre-specified embryo, when this epigenetic modification is most dynamic, before returning to the canonical somatic pattern...
  13. 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
    ..Our data demonstrate that extant DNA methylation systems are mosaics of conserved and derived features, and indicate that gene body methylation is an ancient property of eukaryotic genomes...
  14. 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 believe these data, which we have made publicly available, will provide a critical step toward understanding the biological effects of genetic variation...
  15. 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
    ..The innovative content includes coverage of 99% of RefSeq genes with multiple probes per gene, 96% of CpG islands from the UCSC database, CpG island shores and additional content selected from whole-genome bisulfite ..
  16. 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
    ..Therefore, the present study was designed to develop a program for such applications...
  17. ncbi Initial sequencing and comparative analysis of the mouse genome
    Robert H Waterston
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 420:520-62. 2002
    ....
  18. 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
    ..that 5hmC is mostly associated with euchromatin and that whereas 5mC is under-represented at gene promoters and CpG islands, 5hmC is enriched and is associated with increased transcriptional levels...
  19. pmc Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains
    Manching Ku
    Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
    PLoS Genet 4:e1000242. 2008
    ..locations of PRC2 and PRC1 can be largely predicted from the locations, sizes, and underlying motif contents of CpG islands. We propose that large CpG islands depleted of activating motifs confer epigenetic memory by recruiting the ..
  20. 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...
  21. 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
    ..The 450K microarray includes CpG and CNG sites, CpG islands/shores/shelves/open sea, non-coding RNA (microRNAs and long non-coding RNAs) and sites surrounding the ..
  22. 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...
  23. 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
    ..We demonstrate the utility of oxBS-Seq to map and quantify 5hmC at CpG islands (CGIs) in mouse embryonic stem (ES) cells and identify 800 5hmC-containing CGIs that have on average 3...
  24. 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
    A striking feature of the human genome is the dearth of CpG dinucleotides (CpGs) interrupted occasionally by CpG islands (CGIs), regions with relatively high content of the dinucleotide...
  25. 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
    ....
  26. pmc Genetic control of individual differences in gene-specific methylation in human brain
    Dandan Zhang
    Department of Psychiatry and Behavioral Neuroscience, The University of Chicago, Chicago, IL 60637, USA
    Am J Hum Genet 86:411-9. 2010
    ..6229 genes in 153 human adult cerebellum samples, enriched in CpG island "shores" and at further distances from CpG islands. To search for genetic factors that regulate this variation, we performed a genome-wide association study (GWAS)..
  27. ncbi Genome-wide DNA methylation profiling using Infinium® assay
    Marina Bibikova
    Illumina Inc, 9885 Towne Centre Dr, San Diego, CA 92121, USA
    Epigenomics 1:177-200. 2009
    ....
  28. ncbi The role of DNA methylation in mammalian epigenetics
    P A Jones
    USC Norris Comprehensive Cancer Center, Departments of Biochemistry and Molecular Biology, Keck School of Medicine of the University of Southern California, 1441 Eastlake Avenue, MS 8302L, Los Angeles, CA 90089 9181, USA
    Science 293:1068-70. 2001
    ....
  29. pmc Transposable elements: targets for early nutritional effects on epigenetic gene regulation
    Robert A Waterland
    Department of Radiation Oncology, Duke University Medical Center, Durham, NC 27710, USA
    Mol Cell Biol 23:5293-300. 2003
    ..These findings suggest that dietary supplementation, long presumed to be purely beneficial, may have unintended deleterious influences on the establishment of epigenetic gene regulation in humans...
  30. ncbi CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer
    Daniel J Weisenberger
    Department of Surgery, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90089 9176, USA
    Nat Genet 38:787-93. 2006
    Aberrant DNA methylation of CpG islands has been widely observed in human colorectal tumors and is associated with gene silencing when it occurs in promoter areas...
  31. pmc Dynamic DNA methylation across diverse human cell lines and tissues
    Katherine E Varley
    HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
    Genome Res 23:555-67. 2013
    ..This study provides an atlas of DNA methylation across diverse and well-characterized samples and enables new discoveries about DNA methylation and its role in gene regulation and disease...
  32. pmc Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2
    Myunggon Ko
    Department of Pathology, Harvard Medical School, Immune Disease Institute and Program in Cellular and Molecular Medicine, Children s Hospital Boston, Boston, Massachusetts 02115, USA
    Nature 468:839-43. 2010
    ..Measurement of 5hmC levels in myeloid malignancies may prove valuable as a diagnostic and prognostic tool, to tailor therapies and assess responses to anticancer drugs...
  33. 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
    ..Finally, we identify nonimprinted genes that inherit promoter DNA methylation from parental gametes, suggesting that escape of post-fertilization DNA methylation reprogramming is prevalent in the mouse genome...
  34. pmc Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome
    Wei Xie
    Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA 92093 0653, USA
    Cell 148:816-31. 2012
    ..Our results provide a resource for understanding the mechanisms of imprinting and allele-specific gene expression in mammalian cells...
  35. pmc Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands
    J G Herman
    Oncology Center, Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
    Proc Natl Acad Sci U S A 93:9821-6. 1996
    Precise mapping of DNA methylation patterns in CpG islands has become essential for understanding diverse biological processes such as the regulation of imprinted genes, X chromosome inactivation, and tumor suppressor gene silencing in ..
  36. pmc Genome-scale analysis of aberrant DNA methylation in colorectal cancer
    Toshinori Hinoue
    Department of Surgery and Department of Biochemistry and Molecular Biology, University of Southern California, USC Epigenome Center, Los Angeles, California 90089 9601, USA
    Genome Res 22:271-82. 2012
    ..characterized by DNA hypermethylation of a subset of CIMP-H-associated markers rather than a unique group of CpG islands. Non-CIMP tumors are separated into two distinct clusters...
  37. pmc The DNA methylome of human peripheral blood mononuclear cells
    Yingrui Li
    BGI Shenzhen, Shenzhen, Guangdong, China
    PLoS Biol 8:e1000533. 2010
    ..Together with recently reported similar studies, our study provides a comprehensive resource for future epigenomic research and confirms new sequencing technology as a paradigm for large-scale epigenomics studies...
  38. 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
    ..Moreover, we observe that inactive unmethylated CpG island promoters show elevated levels of dimethylation of Lys4 of histone H3, suggesting that this chromatin mark may protect DNA from methylation...
  39. pmc SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips
    Jovana Maksimovic
    Murdoch Childrens Research Institute, Parkville, Australia
    Genome Biol 13:R44. 2012
    ..SWAN is available in the minfi Bioconductor package...
  40. 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
    ..Differential DNA methylation correlated with gene expression more strongly at CpG island shores than CpG islands. Many examples of genes and pathways not previously known to be involved in choice between lymphoid/myeloid ..
  41. pmc Dynamic CpG island methylation landscape in oocytes and preimplantation embryos
    Sebastien A Smallwood
    Epigenetics Programme, The Babraham Institute, Cambridge, UK
    Nat Genet 43:811-4. 2011
    Elucidating how and to what extent CpG islands (CGIs) are methylated in germ cells is essential to understand genomic imprinting and epigenetic reprogramming...
  42. 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...
  43. pmc Epigenome-wide scans identify differentially methylated regions for age and age-related phenotypes in a healthy ageing population
    Jordana T Bell
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
    PLoS Genet 8:e1002629. 2012
    ..Our results suggest that in a small set of genes DNA methylation may be a candidate mechanism of mediating not only environmental, but also genetic effects on age-related phenotypes...
  44. 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
    b>CpG islands (CGIs) are prominent in the mammalian genome owing to their GC-rich base composition and high density of CpG dinucleotides...
  45. pmc QUMA: quantification tool for methylation analysis
    Yuichi Kumaki
    Laboratory for Mammalian Epigenetic Studies, Center for Developmental Biology, RIKEN, 2 2 3 Minatojima minamimachi, Chuo Ku, Kobe 650 0047, Japan
    Nucleic Acids Res 36:W170-5. 2008
    ..It also provides a platform for consistent quality control of the analysis. The QUMA web server is available at http://quma.cdb.riken.jp/...
  46. ncbi CpG motifs in bacterial DNA and their immune effects
    Arthur M Krieg
    Department of Veterans Affairs Medical Center, Iowa City, Iowa 52246, USA
    Annu Rev Immunol 20:709-60. 2002
    ..CpG ODN also enhance the development of acquired immune responses for prophylactic and therapeutic vaccination...
  47. 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...
  48. 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
    ....
  49. pmc Comprehensive high-throughput arrays for relative methylation (CHARM)
    Rafael A Irizarry
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
    Genome Res 18:780-90. 2008
    ..three methods provide useful information, there were significant limitations to each, specifically bias toward CpG islands in MeDIP, relatively incomplete coverage in HELP, and location imprecision in McrBC...
  50. pmc Contribution of intragenic DNA methylation in mouse gametic DNA methylomes to establish oocyte-specific heritable marks
    Hisato Kobayashi
    Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
    PLoS Genet 8:e1002440. 2012
    ..Furthermore, a comparison of oocyte and sperm methylomes identified more than 1,600 CpG islands differentially methylated in oocytes and sperm (germline differentially methylated regions, gDMRs), in addition ..
  51. pmc Changes in the pattern of DNA methylation associate with twin discordance in systemic lupus erythematosus
    Biola M Javierre
    Chromatin and Disease Group, Cancer Epigenetics and Biology Programme PEBC, Bellvitge Biomedical Research Institute IDIBELL, L Hospitalet de Llobregat, Barcelona 08907, Spain
    Genome Res 20:170-9. 2010
    ....
  52. ncbi Classification of colorectal cancer based on correlation of clinical, morphological and molecular features
    J R Jass
    Department of Pathology, McGill University, Montreal, Canada
    Histopathology 50:113-30. 2007
    ..This approach to the classification of CRC should accelerate understanding of causation and will impact on clinical management in the areas of both prevention and treatment...
  53. pmc Highly integrated single-base resolution maps of the epigenome in Arabidopsis
    Ryan Lister
    Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
    Cell 133:523-36. 2008
    ..Finally, strand-specific mRNA-seq revealed altered transcript abundance of hundreds of genes, transposons, and unannotated intergenic transcripts upon modification of the DNA methylation state...
  54. pmc Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia
    Altuna Akalin
    Department of Physiology and Biophysics and the HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, United States of America
    PLoS Genet 8:e1002781. 2012
    ..which resulted in greater capture of DNA methylation information of regions lying outside of traditional CpG islands. Applying this method to primary human bone marrow specimens from patients with Acute Myelogeneous Leukemia (..
  55. ncbi DNA methylation in cancer: too much, but also too little
    Melanie Ehrlich
    Human Genetics Program SL31, Department of Biochemistry, Tulane Medical School, New Orleans, Louisiana, LA 70122, USA
    Oncogene 21:5400-13. 2002
    ..Genomic hypermethylation in cancer has been observed most often in CpG islands in gene regions...
  56. ncbi DNA methylation analysis by pyrosequencing
    Jorg Tost
    Laboratory for Epigenetics, CEA Institut de Génomique, Centre National de Genotypage, Evry Cedex, France
    Nat Protoc 2:2265-75. 2007
    ..Quantitative epigenotypes are obtained using this protocol in approximately 4 h for up to 96 DNA samples when bisulfite-treated DNA is already available as the starting material...
  57. ncbi DNA methylation and cancer
    Marta Kulis
    The Bellvitge Institute forBiomedical Research, L Hospitalet de Llobregat, Barcelona, Catalonia, Spain
    Adv Genet 70:27-56. 2010
    ..group occurs generally in cytosine within CpG dinucleotides which are concentrated in large clusters called CpG islands. DNA methyltransferases are responsible for establishing and maintenance of methylation pattern...
  58. ncbi Identification of genetic elements that autonomously determine DNA methylation states
    Florian Lienert
    Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
    Nat Genet 43:1091-7. 2011
    ..These results demonstrate that proximal sequence elements are both necessary and sufficient for regulating DNA methylation and reveal basic constraints of this regulation...
  59. pmc Disease-associated epigenetic changes in monozygotic twins discordant for schizophrenia and bipolar disorder
    Emma L Dempster
    MRC Social, Genetic and Developmental Psychiatry Centre, King s College London, De Crespigny Park, Denmark Hill, London SE5 8AF, UK
    Hum Mol Genet 20:4786-96. 2011
    ..Overall, our data provide further evidence to support a role for DNA methylation differences in mediating phenotypic differences between MZ twins and in the etiology of both SZ and BD...
  60. pmc Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells
    Hao Wu
    Department of Molecular and Medical Pharmacology, UCLA David Geffen School of Medicine, Los Angeles, California 90095, USA
    Nature 473:389-93. 2011
    ....
  61. ncbi The sequence of the human genome
    J C Venter
    Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA
    Science 291:1304-51. 2001
    ..Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge...
  62. ncbi Epigenetic silencing of microRNA-34b/c and B-cell translocation gene 4 is associated with CpG island methylation in colorectal cancer
    Minoru Toyota
    First Department of Internal Medicine, Cancer Research Institute, Sapporo Medical University, Sapporo, Japan
    Cancer Res 68:4123-32. 2008
    ..Our results suggest that miR-34b/c and BTG4 are novel tumor suppressors in CRC and that the miR-34b/c CpG island, which bidirectionally regulates miR-34b/c and BTG4, is a frequent target of epigenetic silencing in CRC...
  63. ncbi Epigenetic reprogramming in mouse primordial germ cells
    Petra Hajkova
    Universitat des Saarlandes, FR 8 2 Genetik, Postfach 151150, 66041 Saarbrucken, Germany
    Mech Dev 117:15-23. 2002
    ..Aberrant epigenetic reprogramming in the germ line would cause the inheritance of epimutations that may have consequences for human diseases as suggested by studies on mouse models...
  64. ncbi Prenatal exposure to maternal depression, neonatal methylation of human glucocorticoid receptor gene (NR3C1) and infant cortisol stress responses
    Tim F Oberlander
    Department of Pediatrics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
    Epigenetics 3:97-106. 2008
    ....
  65. 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
    Mammalian genomes are punctuated by DNA sequences containing an atypically high frequency of CpG sites termed CpG islands (CGIs). CGIs generally lack DNA methylation and associate with the majority of annotated gene promoters...
  66. pmc Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation
    Jason Gertz
    HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
    PLoS Genet 7:e1002228. 2011
    ..These events are under-represented in CpG islands, enriched in intergenic regions, and located in regions of low evolutionary conservation...
  67. ncbi 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
    ..Cyclical changes in the methylation status of promoter CpGs may thus represent a critical event in transcriptional achievement...
  68. pmc DNA methylation: TET proteins-guardians of CpG islands?
    Kristine Williams
    Biotech Research and Innovation Centre BRIC, and Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
    EMBO Rep 13:28-35. 2012
    ..We propose that the TET proteins have an important role in regulating DNA methylation fidelity, and that their inactivation contributes to the DNA hypermethylation phenotype often observed in cancer...
  69. pmc A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling
    Vladimir R Ramirez-Carrozzi
    Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
    Cell 138:114-28. 2009
    ..The low nucleosome occupancy at promoters in this class can be attributed to the assembly of CpG islands into unstable nucleosomes, which may lead to SWI/SNF independence...
  70. pmc DNA methylation differences after exposure to prenatal famine are common and timing- and sex-specific
    Elmar W Tobi
    Molecular Epidemiology, Leiden University Medical Center, Leiden 2300 RC, The Netherlands
    Hum Mol Genet 18:4046-53. 2009
    ..017). Our data indicate that persistent changes in DNA methylation may be a common consequence of prenatal famine exposure and that these changes depend on the sex of the exposed individual and the gestational timing of the exposure...
  71. ncbi Deficiency of methyl-CpG binding protein-2 in CNS neurons results in a Rett-like phenotype in mice
    R Z Chen
    The Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    Nat Genet 27:327-31. 2001
    ..Mecp2 deficiency in these neurons is sufficient to cause neuronal dysfunction with symptomatic manifestation similar to Rett syndrome...
  72. pmc Tobacco-smoking-related differential DNA methylation: 27K discovery and replication
    Lutz P Breitling
    Division C070 Clinical Epidemiology and Aging Research, German Cancer Research Center, D 69120 Heidelberg, Germany
    Am J Hum Genet 88:450-7. 2011
    ..To date, this gene had not attracted attention in the literature on smoking...
  73. pmc Maternal nutrient supplementation counteracts bisphenol A-induced DNA hypomethylation in early development
    Dana C Dolinoy
    Department of Radiation Oncology and University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
    Proc Natl Acad Sci U S A 104:13056-61. 2007
    ..Thus, we present compelling evidence that early developmental exposure to BPA can change offspring phenotype by stably altering the epigenome, an effect that can be counteracted by maternal dietary supplements...
  74. pmc Cell type-specific DNA methylation at intragenic CpG islands in the immune system
    Aimée M Deaton
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
    Genome Res 21:1074-86. 2011
    Human and mouse genomes contain a similar number of CpG islands (CGIs), which are discrete CpG-rich DNA sequences associated with transcription start sites...
  75. pmc Feeding pregnant rats a protein-restricted diet persistently alters the methylation of specific cytosines in the hepatic PPAR alpha promoter of the offspring
    Karen A Lillycrop
    Development and Cell Biology, Biomedical Sciences Building, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK
    Br J Nutr 100:278-82. 2008
    ..These data show for the first time that prenatal nutrition induces differential changes to the methylation of individual CpG dinucleotides in juvenile rats which persist in adults...
  76. ncbi Gene silencing in cancer by histone H3 lysine 27 trimethylation independent of promoter DNA methylation
    Yutaka Kondo
    Department of Leukemia, University of Texas M D Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA
    Nat Genet 40:741-50. 2008
    ..ChIP-chip) in prostate cancer cells compared to normal prostate, we found that up to 5% of promoters (16% CpG islands and 84% non-CpG islands) were enriched with H3K27triM...
  77. ncbi The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA
    Jafar Sharif
    Tohoku University Biomedical Engineering Research Organization TUBERO, 2 1 Seiryo machi, Aoba ku, Sendai 980 8575, Japan
    Nature 450:908-12. 2007
    ..The link between hemi-methylated DNA, Np95 and Dnmt1 thus establishes key steps of the mechanism for epigenetic inheritance of DNA methylation...
  78. pmc Genomic distribution and inter-sample variation of non-CpG methylation across human cell types
    Michael J Ziller
    Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
    PLoS Genet 7:e1002389. 2011
    ..In summary these results contribute further to our understanding of cytosine methylation patterns in human cells using a large representative sample set...
  79. ncbi Variation, patterns, and temporal stability of DNA methylation: considerations for epigenetic epidemiology
    Rudolf P Talens
    Department of Molecular Epidemiology, Leiden University Medical Center, Postal Zone S 05 P, PO Box 9600, 2300RC, Leiden, The Nethelands
    FASEB J 24:3135-44. 2010
    ..75). Our data suggest that epigenetic studies on complex diseases may be feasible for a proportion of genomic loci provided that they are carefully designed...
  80. ncbi Genomic DNA methylation: the mark and its mediators
    Robert J Klose
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Mayfield Road, Edinburgh EH9 3JR, UK
    Trends Biochem Sci 31:89-97. 2006
    ..Recent studies have illuminated the role of DNA methylation in controlling gene expression and have strengthened its links with histone modification and chromatin remodelling...
  81. pmc Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome
    Robert Shoemaker
    Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, USA
    Genome Res 20:883-9. 2010
    ..This study identified distinct types of ASM across many cell types and suggests a potential role for CpG-SNP in connecting genetic variation with the epigenome...
  82. pmc DNA methylation profiling identifies epigenetic dysregulation in pancreatic islets from type 2 diabetic patients
    Michael Volkmar
    Laboratory of Cancer Epigenetics, Faculty of Medicine, Universite Libre de Bruxelles, Brussels, Belgium
    EMBO J 31:1405-26. 2012
    ..Together, our findings offer new insights into the intricate mechanisms of T2D pathogenesis, underscore the important involvement of epigenetic dysregulation in diabetic islets and may advance our understanding of T2D aetiology...
  83. ncbi Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling
    Hongcang Gu
    Broad Institute, Cambridge, Massachusetts, USA
    Nat Protoc 6:468-81. 2011
    ..The entire process of RRBS library construction takes ∼9 d...
  84. 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
    ..Our data suggest DNA methylation to be ontogenetically more stable than previously thought...
  85. ncbi Epigenetic inactivation of microRNA gene hsa-mir-9-1 in human breast cancer
    U Lehmann
    Institute of Pathology, Medizinische Hochschule Hannover, Carl Neuberg Strasse 1, D 30625, Hannover, Germany
    J Pathol 214:17-24. 2008
    ..8). In conclusion, this study demonstrates that various microRNA genes are also affected by epigenetic inactivation due to aberrant hypermethylation and that this is an early and frequent event in breast cancer development...
  86. ncbi Transient cyclical methylation of promoter DNA
    Sara Kangaspeska
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Nature 452:112-5. 2008
    ..This coincides with a low-level re-expression of ERalpha and of pS2 transcripts...
  87. pmc Neuronal activity modifies the DNA methylation landscape in the adult brain
    Junjie U Guo
    Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
    Nat Neurosci 14:1345-51. 2011
    ..Our study implicates modification of the neuronal DNA methylome as a previously underappreciated mechanism for activity-dependent epigenetic regulation in the adult nervous system...
  88. 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...
  89. pmc Comprehensive analysis of CpG islands in human chromosomes 21 and 22
    Daiya Takai
    Department of Biochemistry and Molecular Biology, University of Southern California Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
    Proc Natl Acad Sci U S A 99:3740-5. 2002
    b>CpG islands are useful markers for genes in organisms containing 5-methylcytosine in their genomes...
  90. ncbi MeCP2 binding to DNA depends upon hydration at methyl-CpG
    Kok Lian Ho
    School of Biological Sciences, University of Edinburgh, King s Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
    Mol Cell 29:525-31. 2008
    ..The MeCP2-DNA complex also identifies a unique structural role for T158, the residue most commonly mutated in Rett syndrome...
  91. pmc Aging and environmental exposures alter tissue-specific DNA methylation dependent upon CpG island context
    Brock C Christensen
    Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
    PLoS Genet 5:e1000602. 2009
    ..we found striking, highly significant CpG island-dependent correlations between age and methylation; loci in CpG islands gained methylation with age, loci not in CpG islands lost methylation with age (P<0...
  92. pmc Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver
    Alayne L Brunner
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
    Genome Res 19:1044-56. 2009
    ..Taken together, our results indicate that hESC differentiation has a unique DNA methylation signature that may not be indicative of in vivo differentiation...
  93. pmc Epigenomic profiling reveals DNA-methylation changes associated with major psychosis
    Jonathan Mill
    Krembil Family Epigenetic Laboratory, Centre for Addiction and Mental Health, 250 College Street, Toronto, Ontario, M5T 1R8, Canada
    Am J Hum Genet 82:696-711. 2008
    ..Our data are consistent with the epigenetic theory of major psychosis and suggest that DNA-methylation changes are important to the etiology of schizophrenia and bipolar disorder...
  94. pmc Selective anchoring of DNA methyltransferases 3A and 3B to nucleosomes containing methylated DNA
    ShinWu Jeong
    Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center Keck School of Medicine, University of Southern California, NOR 8302L, 9181, Los Angeles, CA 90089 9181, USA
    Mol Cell Biol 29:5366-76. 2009
    ..We also show that nucleosomes containing methylated SINE and LINE elements and CpG islands are the main sites of DNMT3A/3B binding...
  95. ncbi DNA methylation regulates MicroRNA expression
    Liangfeng Han
    Predoctoral Training Program in Human Genetics, McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
    Cancer Biol Ther 6:1284-8. 2007
    ..We also found that HOXA3 and HOXD10 were putative targets of mir-10a, one of the differentially expressed miRNAs that is located in HOX gene cluster...
  96. pmc Chromatin and sequence features that define the fine and gross structure of genomic methylation patterns
    John R Edwards
    Center for Pharmacogenomics, Department of Medicine, Washington University School of Medicine, St Louis, Missouri 63110, USA
    Genome Res 20:972-80. 2010
    ....
  97. pmc A human B cell methylome at 100-base pair resolution
    Tibor A Rauch
    Department of Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
    Proc Natl Acad Sci U S A 106:671-8. 2009
    ..Our data provide a valuable resource for the analysis of CpG methylation patterns in a differentiated human cell type and provide new clues regarding the function of mammalian DNA methylation...
  98. ncbi Characterizing DNA methylation patterns in pancreatic cancer genome
    Aik Choon Tan
    The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
    Mol Oncol 3:425-38. 2009
    ....
  99. ncbi Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism
    Kyohei Arita
    Graduate School of Engineering, Kyoto University, Kyoto 615 8510, Japan
    Nature 455:818-21. 2008
    ..The complex structure suggests that the successive flip out of the pre-existing methylated cytosine and the target cytosine to be methylated is associated with the coordinated transfer of the hemi-methylated CpG site from UHRF1 to Dnmt1...
  100. ncbi Structural basis for recognition of hemi-methylated DNA by the SRA domain of human UHRF1
    George V Avvakumov
    Structural Genomics Consortium, University of Toronto, 100 College Street, Toronto, Ontario M5G 1L5, Canada
    Nature 455:822-5. 2008
    ..The structure, along with mutagenesis data, suggests how UHRF1 acts as a key factor for DNMT1 maintenance methylation through recognition of a fundamental unit of epigenetic inheritance, mCpG...
  101. ncbi EBV transformation and cell culturing destabilizes DNA methylation in human lymphoblastoid cell lines
    D Grafodatskaya
    Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
    Genomics 95:73-83. 2010
    ..HumanMethylation27 platform containing 27,578 CpG sites and Agilent Human CpG island Array containing 27,800 CpG islands. Comparison of genome-wide methylation profiles between white blood cells and lymphoblastoid cell lines ..

Research Grants72

  1. DNA methylation of extracellular superoxide dismutase in pulmonary hypertension
    EVA NOZIK GRAYCK; Fiscal Year: 2012
    ..cytosine methylation within the promoter region, specifically cytosines adjacent to guanosine nucleotides (CpG islands)...
  2. Genistein, microRNAs and kidney cancer
    Rajvir Dahiya; Fiscal Year: 2013
    ..We will treat kidney cancer cells with genistein and then analyze hypomethylation of CpG Islands in putative promoter regions of miRNAs using sodium bisulfite methylation techniques and direct DNA sequencing...
  3. Regulation of Airway Mucin Gene Expression by Epigenetic Mechanism
    Reen Wu; Fiscal Year: 2013
    ..Preliminary studies have shown the presence of CpG islands in the upstream promoter region of human MUC5AC (at -4,396 bp - 4,541bp), which is not present in the mouse ..
  4. CPG METHYLATION AND MUTATION
    Gerd P Pfeifer; Fiscal Year: 2013
    Transcriptional gene silencing by hypermethylation of CpG islands spanning the promoter regions of genes is a common and important mechanism in carcinogenesis...
  5. Folate Status, Genomic Uracil, and the Balance of Base Excision Repair Activity
    Michael D Wyatt; Fiscal Year: 2011
    ..Thus, several questions arise. During folate deprivation, what happens when BER is initiated at CpG islands when BER cannot be completed accurately? What is the balance between mutagenic consequences if BER is not ..
  6. Epigenetic Alterations in IPF Fibroblastic Foci
    YAN SANDERS; Fiscal Year: 2010
    ..DNA methylation at gene promoter regions rich in cytosine-guanine (CpG islands) and histone modifications both play important roles in gene silencing;these paradigms are important in ..
  7. Aberrant DNA Methylation of MicroRNA Genes in Hepatocellular Carcinoma (HCC)
    Jing Shen; Fiscal Year: 2012
    ..PHS 398/2590 (Rev. 06/09) Page Continuation Format Page ..
  8. The role of NLRP7 and related genes in hydatidiform moles and reproductive failur
    Ignatia Van den Veyver; Fiscal Year: 2009
    ..and their molar trophoblast tissues show abnormal expression of imprinted genes and abnormal methylation of CpG islands at imprinting control regions (ICRs)...
  9. Regulators of Cancer-Specific DNA Hypermethylation.
    Jean Pierre J Issa; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): In normal cells, DNA methylation is rare in promoter-associated CpG islands but important to X-inactivation, genomic imprinting and repression of repetitive elements...
  10. Inducible Dysplastic Nephropathy in B2-Deficient Mice
    Samir S El-Dahr; Fiscal Year: 2013
    ..H3 deacetylation and lysine 4 (H3K4) demethylation and H3K9/27 methylation, followed by hypermethylation of CpG islands. We postulate that these modifications in the histone code inhibit transcription factor binding to the Pax2 ..
  11. MECHANISMS OF FETAL MEMBRANE RUPTURE
    Jerome F Strauss; Fiscal Year: 2010
    ..The hypotheses to be tested are: 1) that variation in methylation of CpG islands in the promoters of MMP and collagen synthesis genes regulate gene expression;2) that certain metyhylation ..
  12. Transition State Analogues as Modulators of DNA Methylation
    Vern L Schramm; Fiscal Year: 2012
    ..leading to cancer are governed, in part, by DNA methylation at regions of the genome rich in CpG bases, called CpG islands. The hypothesis for this research is that MTAP inhibitors alter metabolite levels in cancer tissues to inhibit ..
  13. Regulation of Genomic Instability in Early Breast Cancer
    Thea D Tlsty; Fiscal Year: 2013
    ..transformation, including dynamic epigenetic remodeling resulting in the targeted methylation of selected CpG islands. Repression of p16INK4a activity in HMEC increases expression of the E2F1 transcription factor and, ..
  14. GENESIS AND CONSEQUENCES OF ABERRANT DNA METHYLATION
    Paula M Vertino; Fiscal Year: 2013
    ..several years points to local chromatin environment as a critical factor in determining the epigenetic fate of CpG islands during development and transformation...
  15. Detection of Tumor DNA in Plasma from Carolina Breast Cancer Study Patients
    KATHLEEN CONWAY DORSEY; Fiscal Year: 2013
    ..cancer through regulation of gene transcription and genome stability, and methylation of cytosine residues in CpG islands of gene promoters can silence tumor suppressor genes critical to breast cancer development and progression...
  16. Epigenetic regulation of HIV latency
    ERIC M VERDIN; Fiscal Year: 2013
    ..To test the hypothesis that HIV integration in or near hypermethylated CpG islands leads to latency, we propose to compare the state of DNA methylation in resting and activated lymphocytes at ..
  17. Prostate Cancer Detection by Molecular Urinalysis
    Christian P Pavlovich; Fiscal Year: 2010
    ..Three urinary analyses will form the cornerstones of this study: methylation of DNA at CpG islands of the pi-class glutathione-s transferase (GSTP1) promoter, a noncoding RNA "differential display 3" (DD3), and ..
  18. Aging and brain 5-lipoxygenase
    Hari Manev; Fiscal Year: 2010
    ..data indicate that neuronal 5-LOX expression increases following changes in the methylation state of CpG islands in 5-LOX promoter (e.g...
  19. Cigarette Smoking Alters the Genomic Tone of Alveolar Macrophages
    Martha M Monick; Fiscal Year: 2013
    ..Differentially expressed microRNAs and altered methylated CpG islands in promoter regions will be correlated with exon-specific mRNA expression via bioinformatics analysis...
  20. Epigenetic Changes in Retinoid Signaling in Oral Cavity Carcinogenesis
    KATARZYNA MARIA MARCINKIEWICZ; Fiscal Year: 2013
    ..Methylation of the promoter of the RA-inducible gene retinoic receptor beta 2 (RARBeta2) at CpG islands is one of the first events that occurs as normal oral cavity epithelial cells become malignantly transformed...
  21. Wnt antagonist genes in kidney tumor progression and metastasis
    Rajvir Dahiya; Fiscal Year: 2012
    ..Under this aim, we will analyze hypermethylation of CpG Islands in promoter regions of Wnt antagonist genes using sodium bisulfite methylation techniques and confirm by direct ..
  22. Epigenetic regulation of vascular smooth muscle cell phenotype
    Christopher P Mack; Fiscal Year: 2013
    ..methylation, and interestingly, the SRF binding regions within the SMC-specific promoters are embedded within CpG islands. Based on our preliminary data indicating that the SMC-specific promoters are regulated by methylation, the ..
  23. Identification and Classification of Epigenetic Changes in Head and Neck Cancer
    Thomas J Belbin; Fiscal Year: 2010
    In many cancers, aberrant DNA methylation of so called "CpG islands", CpG-rich sequences frequently associated with promoters or first exons, is associated with the inappropriate transcriptional silencing of critical genes...
  24. Genome-scale anaylsis of DNA methylation in CpG Islands with bisulfite sequencing
    Kun Zhang; Fiscal Year: 2011
    ..The goal of this proposal is to enable digital quantification of DNA methylation status of non-repetitive CpG islands on the genome scale efficiently and inexpensively...
  25. Environmental Epigenetics and Stem/Progenitor Cell Injury
    Tim H M Huang; Fiscal Year: 2010
    ..apos;Global analysis is expected to identify altered methylation status in 1-2% of ~29,000 CpG islands analyzed. These epigenetic events can be the direct results of exposing stem/progenitor cells to xenoestrogens...
  26. GENE THERAPY WITH SOCS-3 IN INTIMAL HYPERPLASIA AND IN-STENT RESTENOSIS
    Devendra K Agrawal; Fiscal Year: 2013
    ..We will determine whether or not aberrant hypermethylation of promoter regions in CpG islands is associated with transcriptional silencing of the SOCS3 gene and up- regulation of active NF-kB and STAT3 in ..
  27. Promoter Specific Hypermethylation Sensors for Early Cancer Detection
    Indraneel Ghosh; Fiscal Year: 2011
    ..On the other hand CpG islands, defined as short sequences with statistically high CpG content, present in the promoter region of many genes (..
  28. Characterization of the role of CpA methylation in neuronal plasticity
    Stavros Lomvardas; Fiscal Year: 2009
    ..DNA methylation on CpG islands is a well established mechanism of gene silencing...
  29. Role of TWEAK in Skeletal Muscle Metabolism
    Ashok Kumar; Fiscal Year: 2013
    ..Hypothesis 3: Demethylation of CpG islands in Fn14 promoter followed by binding of SP1 transcription factor triggers the expression of Fn14 in skeletal ..
  30. Cancer Genome Characterization Center at Johns Hopkins
    Stephen Baylin; Fiscal Year: 2009
    ..will again use the Illumina technology for high-throughput and accurate assay of functionally selected 5'CpG islands across the genome, as well as all CpG islands located on chromosomes 21 and 22, and a random selection of non- ..
  31. Reduced Levels of 5-alpha Reductase 2 in Adult Prostate Tissue and BPH Therapy
    Aria F Olumi; Fiscal Year: 2013
    ..of genes has been associated with regulation of genes, we investigated whether the 5-1 reductase gene contains CpG islands. We found that the 5-1 reductase 2 promoters contains a rich CpG island and in fact the CpG island is ..
  32. Genetic and Epigenetic Regulation of Addiction Genes
    Wolfgang Sadee; Fiscal Year: 2010
    ..A large portion of suspected addiction susceptibility genes harbors CpG islands, methylation of which represents a main epigenetic mechanism...
  33. Interaction of HIV-Tat and methamphetamine: Role of ion channels and epigenetics
    Marilou A Andres; Fiscal Year: 2013
    ..We will determine how methamphetamine use changes the DNA methylation patterns of the APOE promoter and exon 4 CpG islands in HIV-individuals who are ?4+ and ?4-...
  34. Investigating CpG islands in mammalian genomes
    Zhongming Zhao; Fiscal Year: 2010
    b>CpG islands, clusters of CpG dinucleotides in GC-rich regions, are often located in the 5'end of genes and are considered gene markers in mammalian genomes...
  35. Epigenetic Drivers of Cancer Progression
    Andrew P Feinberg; Fiscal Year: 2013
    ..The first of these discoveries is that most altered DNA methylation in cancer is not at CpG islands but at nearby regions we termed "CpG island shores," and that most of the disrupted methylation in cancer ..
  36. Gene-Specific Epigenetic Programming of WNT Signaling Pathway by Dietary Soy
    Hong Chen; Fiscal Year: 2009
    ..Using techniques including methylation analysis of CpG islands and chromatin immunoprecipitation coupled to a pathway-specific microarray, specific aims in this proposal ..
  37. Combinational Environmental Chemicals Altering Susceptibility for Mammary Cancer
    Jose Russo; Fiscal Year: 2013
    ..affected signaling pathways;3) using the information from the gene array data and MIRA-seq (methylated CpG islands recovery assay coupled with massively parallel sequencing), the investigators will identify candidate DNA ..
  38. Familial and Early Onset Colorectal Cancer
    CLEMENT R BOLAND; Fiscal Year: 2013
    ..We will also look for evidence of methylation-induced silencing of the MSH2 and MSH6 genes, which also have CpG islands in their promoters, and should be susceptible to the same perturbation...
  39. Glucose Metabolism in Adults Prenatally Exposed to Diabetogenic Pollutants
    PHILIPPE ADAM GRANDJEAN; Fiscal Year: 2013
    ..We will examine CpG islands and shores, CpG outside islands, non-CpG methylated sites identified in human cancer stem cells, miRNA promoter ..
  40. Epigenetic Basis for Prostate Carcinogenesis following Early Estrogenic Exposures
    Gail S Prins; Fiscal Year: 2012
    ..MSRP and methylation arrays will be used to expand our prostatic screen to identify a full panel of candidate genes and a stringent algorithm will be followed to identify candidates with regulatory CpG islands.
  41. Loss of miR-29s as predictor of response to demethylating agents
    Carlo M Croce; Fiscal Year: 2010
    ..This leads to silencing of tumor suppressors through methylation of CpG islands of their promoters that can be reversed by transfection with miR-29s...
  42. Defining Genomic Signatures for Aberrant DNA Methylation in Human Cancers
    Paula M Vertino; Fiscal Year: 2013
    ..Epigenetic silencing involving alterations in DNA methylation and chromatin structure at promoter region CpG islands is a common mechanism of tumor suppressor gene inactivation in human cancers...
  43. CpG Island Methylator Phenotypes in Breast Cancer
    Tim H M Huang; Fiscal Year: 2011
    ..Tumors possessing a CIMP usually display concurrent hypermethylation of multiple promoter CpG islands. The causes of CIMP are unknown...
  44. Clonal evolution
    Brian J Reid; Fiscal Year: 2011
    ..We hypothesize that i) epigenetic abnormalities arise as early events in a limited number of CpG islands before widespread genomic instability;ii) early chromosomal instability in BE progression is characterized by ..
  45. Environmental obesogens reduce Thy1 expression and promote obesity
    Richard P Phipps; Fiscal Year: 2013
    ..The Thy1 locus contains multiple CpG islands that can be controlled epigenetically and may be key targets of obesogens...
  46. "R-loop formation protects CpG islands against epigenetic silencing".
    FREDERIC LOUIS CHEDIN; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Project Summary: CpG islands (CGIs) function as promoters for greater than 60% of human genes...
  47. Epigenomics of Bisphenol A Exposure and Disease Risk
    Tim H M Huang; Fiscal Year: 2013
    ..heritably transmitted to the differentiated progeny, and DNA methylation is progressively accumulated in target CpG islands. Epigenomic mapping of these CpG islands may identify potential biomarkers that are used as environmental ..
  48. In utero exposure to arsenic, links to epigenetic alterations and disease
    REBECCA FRY; Fiscal Year: 2013
    ..sequencing to establish that arsenicosis may be associated with altered DNA methylation patterns in CpG islands of genes of the NF-:B pathway...
  49. Identify and validate novel epigenetic molecular markers for colorectal neoplasm
    Sanford D Markowitz; Fiscal Year: 2013
    ..These epigenetic alterations include the aberrant methylation of the 5'promoter region of genes with CpG islands, which can silence the expression of tumor suppressor genes...
  50. Center for the Epigenetics of Common Human Disease
    Andrew P Feinberg; Fiscal Year: 2013
    ..Using these tools, we discovered that most variable DNAm is in neither CpG islands nor proelationship between epigenetic variation, genetic variation, environment and phenotype...
  51. The role of epigenetics and miRNAs in IPF
    Melissa G Piper; Fiscal Year: 2013
    ..Moreover, we believe that the cluster itself is also regulated by DNA methylation of CpG islands in its promoter, forming a negative feedback loop between DNMT1 and miRs-19b and - 20a expression...
  52. Epigenetic markers involved in colorectal cancer recurrence and metastases
    Nita Ahuja; Fiscal Year: 2012
    ..Epigenetic gene silencing involving aberrant DNA methylation of promoter-associated CpG islands functions as a central mechanism of inactivation of tumor-suppressor genes in colorectal cancer...
  53. HudsonAlpha Cancer Genome Characterization Center
    Richard Myers; Fiscal Year: 2009
    ..Genome Atlas Project, the Stanford CGCC proposes to: 1) characterize comprehensive DNA methylation changes at CpG Islands and other CpG-rich regions of the human genome in normal and malignant tissues by using a new microarray based ..
  54. Large-Scale Methylation Profiling in Metabolic Syndrome Phenotypes
    Melanie Carless; Fiscal Year: 2013
    ..Genomic methylation of CpG islands within the promoter and 5'region of a gene typically causes silencing of that gene, which is a reversible ..
  55. 5-hydroxymethylcytosine in human cancer
    Gerd P Pfeifer; Fiscal Year: 2013
    ..in cancer affecting predominantly repetitive DNA sequences, and (ii) gene-specific hypermethylation of CpG islands affecting hundreds of genes...
  56. Massively Parallel Sequencing Technology for Cancer Epigenome.
    Lanlan Shen; Fiscal Year: 2010
    ..methylated CpG rich regions throughout the whole genome, covering 76% of all genes and 70% of all bona fide CpG islands. When coupled with microarrays, this technique has proven to be highly specific and very useful for the high-..
  57. (PQA-5) DNA methylation and cancer prevention: duration and intensity of exercise
    Angela D Bryan; Fiscal Year: 2013
    ..this application on sedentary women, a group at higher risk for the development of breast cancer than regularly exercising women, and on DNA methylation on the CpG islands of genes associated with breast cancer, as in our previous work.
  58. Impact of PAH carcinogen-DNA adducts on DNA methylation
    Nicholas Geacintov; Fiscal Year: 2003
    ..In different types of tumors, aberrant or accidental methylation of CpG islands in the promoter region has been observed for many cancer-related genes resulting in the silencing of their ..
  59. Mouse models for GABA epigenetic dysfunction
    Alessandro Guidotti; Fiscal Year: 2009
    ..2002a), and a hypermethylation of the reelin promoter CpG islands (Grayson, personal communication) encouraged us to consider that hypermethylation of promoter CpG islands is a ..
  60. Development Modulation of Mouse Uterine Tumorigenesis
    Shuk Mei Ho; Fiscal Year: 2006
    ..test the hypothesis that neonatal exposure to estrogenic compounds induces 1) aberrant methylation of 5'CpG islands of specific genes, and 2) that these changes persist in adult uterine tissues leading to "permanent" changes in ..
  61. SBIR TOPIC 264 (PHASE 1) - THE OBJECTIVE OF THIS PROJECT IS TO DEVELOP KITS THAT
    MICHELLE M HANNA; Fiscal Year: 2009
    ..project is to develop a sensitive, bisulfite-free assay for detecting methylation of Individual or multiple CpG islands. The assay will use 2 ng or less of genomic DNA, allow detection of 50 or fewer copies of a methylated island, ..
  62. SIGNIFICANCE OF AGE DEPENDENT CHANGES IN DNA METHYLATION
    Bruce Richardson; Fiscal Year: 2002
    ..for genome scanning has been implemented by our group that allows detection of methylation changes in CpG islands which occur close to gene coding sequences...
  63. DNA Methylation as a Risk Factor for Cervical Neoplasia
    Long Fu Xi; Fiscal Year: 2009
    ..A loss of function of certain critical genes by methylation of CpG islands in promoter region has been found in a variety of cancers, including cancer of the cervix...
  64. Reactivation of GSTP1 Gene by Green Tea Polyphenols
    Sanjay Gupta; Fiscal Year: 2005
    ..GSTP1), a critical enzyme of carcinogen defense, through methylation of deoxycytidine residue in CpG islands in the 5'- regulating region...
  65. DNA methylation patterns as biomarker for breast cancer
    Kristin Skinner; Fiscal Year: 2003
    ..We hypothesize that methylation changes in the CpG islands of tumor suppressor genes represent some of the earliest changes in the progression to malignancy in breast ..
  66. Epigenetic Targeting in Non-Hodgkin's Lymphoma
    Huidong Shi; Fiscal Year: 2007
    unreadable] DESCRIPTION (provided by applicant): Hypermethylation of promoter CpG islands plays a prominent role in cancer...
  67. DNA Methylation in Non-Hodgkin's Lymphomas
    Charles Caldwell; Fiscal Year: 2006
    ..is studies of DNA methylation in tumorigenesis, a process commonly observed in GC-rich sequences called CpG islands in many types of human cancers and is often associated with transcriptional silencing...
  68. TRIGGERING OF ABERRANT CPG ISLAND METHYLATION
    Russ Pieper; Fiscal Year: 2002
    ..b>CpG islands are regions of DNA associated with promoters of approximately 50 percent of human genes...
  69. HIGH THROUGHPUT METHYLATION ANALYSIS IN CANCER
    Tim Huang; Fiscal Year: 2002
    Aberrant DNA methylation frequently occurs in CpG islands, which are 0.2 to 2-kb GC-rich sequences located in the 5 ends of approximately 60 percent of all genes, in neoplasia...
  70. CpG island methylation in glioblastoma cancer stem cells
    KRISTOPHER MOOREFIELD; Fiscal Year: 2007
    ..The Costello laboratory has developed a novel technique to assess the methylation status of CpG islands on a genome-wide scale using existing BAG array technology...
  71. Technology to Detect Genome wide DNA Methylation Changes
    Fumiichiro Yamamoto; Fiscal Year: 2002
    ..For instance, hypermethylation of CpG islands in promoter regions has been increasingly associated with transcriptional inactivation of tumor suppressor ..
  72. DNA METHYLATION AND GENE EXPRESSION IN CANCER CELLS
    Samson Jacob; Fiscal Year: 2004
    ..Although methylation at CpG islands is known to occur in several genes that leads to suppression of their expression, the molecular mechanism of ..