5 methylcytosine

Summary

Summary: A methylated nucleotide base found in eukaryotic DNA. In ANIMALS, the DNA METHYLATION of CYTOSINE to form 5-methylcytosine is found primarily in the palindromic sequence CpG. In PLANTS, the methylated sequence is CpNpGp, where N can be any base.

Top Publications

  1. pmc RNA cytosine methylation analysis by bisulfite sequencing
    Matthias Schaefer
    Division of Epigenetics, German Cancer Research Center, Heidelberg, Germany
    Nucleic Acids Res 37:e12. 2009
  2. pmc DEMETER and REPRESSOR OF SILENCING 1 encode 5-methylcytosine DNA glycosylases
    Teresa Morales-Ruiz
    Departamento de Genetica, Universidad de Cordoba, 14071 Cordoba, Spain
    Proc Natl Acad Sci U S A 103:6853-8. 2006
  3. pmc Bisulfite genomic sequencing: systematic investigation of critical experimental parameters
    C Grunau
    Institute of Molecular Biotechnology, Department of Genome Analysis, Beutenbergstrasse 11, 07745 Jena, Germany
    Nucleic Acids Res 29:E65-5. 2001
  4. ncbi Identification and resolution of artifacts in bisulfite sequencing
    Peter M Warnecke
    Sydney Cancer Centre, Kanematsu Laboratories, Royal Prince Alfred Hospital, Missenden Road, Camperdown, New South Wales 2050, Australia
    Methods 27:101-7. 2002
  5. ncbi Atomic model of the 5-methylcytosine-specific restriction enzyme McrA reveals an atypical zinc finger and structural similarity to betabetaalphaMe endonucleases
    J M Bujnicki
    Mol Microbiol 37:1280-1. 2000
  6. doi Genome-scale relationships between cytosine methylation and dinucleotide abundances in animals
    Martin W Simmen
    School of Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
    Genomics 92:33-40. 2008
  7. ncbi Changes in DNA methylation in neoplasia: pathophysiology and therapeutic implications
    V Santini
    Department of Hematology, University of Florence, Viale Morgagni 85, Florence, Italy
    Ann Intern Med 134:573-86. 2001
  8. pmc Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a
    B H Ramsahoye
    Department of Hematology, Western General Hospital, EH4 2XU Edinburgh, United Kingdom
    Proc Natl Acad Sci U S A 97:5237-42. 2000
  9. pmc The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix
    Hideharu Hashimoto
    Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, Georgia 30322, USA
    Nature 455:826-9. 2008
  10. ncbi Identification of the 16S rRNA m5C967 methyltransferase from Escherichia coli
    X R Gu
    Department of Biochemistry and Biophysics, University of California, San Francisco 94143 0448, USA
    Biochemistry 38:4053-7. 1999

Detail Information

Publications245 found, 100 shown here

  1. pmc RNA cytosine methylation analysis by bisulfite sequencing
    Matthias Schaefer
    Division of Epigenetics, German Cancer Research Center, Heidelberg, Germany
    Nucleic Acids Res 37:e12. 2009
    ..These results establish a versatile method for the identification and characterization of RNA methylation patterns, which will be useful for defining the biological function of RNA methylation...
  2. pmc DEMETER and REPRESSOR OF SILENCING 1 encode 5-methylcytosine DNA glycosylases
    Teresa Morales-Ruiz
    Departamento de Genetica, Universidad de Cordoba, 14071 Cordoba, Spain
    Proc Natl Acad Sci U S A 103:6853-8. 2006
    ..These findings suggest that a function of ROS1 and DME is to initiate erasure of 5-meC through a base excision repair process and provide strong biochemical evidence for the existence of an active DNA demethylation pathway in plants...
  3. pmc Bisulfite genomic sequencing: systematic investigation of critical experimental parameters
    C Grunau
    Institute of Molecular Biotechnology, Department of Genome Analysis, Beutenbergstrasse 11, 07745 Jena, Germany
    Nucleic Acids Res 29:E65-5. 2001
    ..The recognition rates for cytosine (>/=97%) and 5-methylcytosine (>/=94%) were found to be identical for both templates...
  4. ncbi Identification and resolution of artifacts in bisulfite sequencing
    Peter M Warnecke
    Sydney Cancer Centre, Kanematsu Laboratories, Royal Prince Alfred Hospital, Missenden Road, Camperdown, New South Wales 2050, Australia
    Methods 27:101-7. 2002
    ..We also include a brief summary of the experimental protocol for bisulfite treatment and tips for designing polymerase chain reaction (PCR) primers to amplify from bisulfite-treated DNA...
  5. ncbi Atomic model of the 5-methylcytosine-specific restriction enzyme McrA reveals an atypical zinc finger and structural similarity to betabetaalphaMe endonucleases
    J M Bujnicki
    Mol Microbiol 37:1280-1. 2000
  6. doi Genome-scale relationships between cytosine methylation and dinucleotide abundances in animals
    Martin W Simmen
    School of Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
    Genomics 92:33-40. 2008
    ..CpG deficit also correlates with CpT excess in mammals, which may reflect enhanced cytosine mutation in the context 5'-YCG-3'. Analyses with repeat-masked sequences show that the results are not attributable to repetitive elements...
  7. ncbi Changes in DNA methylation in neoplasia: pathophysiology and therapeutic implications
    V Santini
    Department of Hematology, University of Florence, Viale Morgagni 85, Florence, Italy
    Ann Intern Med 134:573-86. 2001
    ....
  8. pmc Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a
    B H Ramsahoye
    Department of Hematology, Western General Hospital, EH4 2XU Edinburgh, United Kingdom
    Proc Natl Acad Sci U S A 97:5237-42. 2000
    ..Analysis of genomic methylation in transgenic Drosophila expressing Dnmt3a reveals that Dnmt3a is predominantly a CpG methylase but also is able to induce methylation at CpA and at CpT...
  9. pmc The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix
    Hideharu Hashimoto
    Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, Georgia 30322, USA
    Nature 455:826-9. 2008
    ..Hence, UHRF1 contains a previously unknown DNA-binding module and is the first example of a non-enzymatic, sequence-specific DNA-binding protein domain to use the base flipping mechanism to interact with DNA...
  10. ncbi Identification of the 16S rRNA m5C967 methyltransferase from Escherichia coli
    X R Gu
    Department of Biochemistry and Biophysics, University of California, San Francisco 94143 0448, USA
    Biochemistry 38:4053-7. 1999
    ..Further, fmu disruption did not significantly alter the growth rate of E. coli in rich or minimal media. We propose renaming this ORF "rrmB" and the enzyme "RrmB" for rRNA methyltransferase...
  11. ncbi Purification, cloning, and characterization of the 16S RNA m5C967 methyltransferase from Escherichia coli
    J S Tscherne
    Department of Biochemistry and Molecular Biology, University of Miami School of Medicine, Florida 33101, USA
    Biochemistry 38:1884-92. 1999
    ..30S ribosomal subunits were not a substrate. There was no requirement for added magnesium, suggesting that extensive secondary or tertiary structure in the RNA substrate may not be a requirement for recognition...
  12. doi 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...
  13. pmc Oxidative damage to methyl-CpG sequences inhibits the binding of the methyl-CpG binding domain (MBD) of methyl-CpG binding protein 2 (MeCP2)
    Victoria Valinluck
    Department of Biochemistry and Microbiology, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
    Nucleic Acids Res 32:4100-8. 2004
    ..Oxidative damage to DNA could therefore result in heritable, epigenetic changes in chromatin organization...
  14. pmc DNA demethylation in the Arabidopsis genome
    Jon Penterman
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 104:6752-7. 2007
    ..Our results show that demethylation by DML DNA glycosylases edits the patterns of DNA methylation within the Arabidopsis genome to protect genes from potentially deleterious methylation...
  15. pmc Escherichia coli K-12 restricts DNA containing 5-methylcytosine
    E A Raleigh
    Proc Natl Acad Sci U S A 83:9070-4. 1986
    ..Mcr restriction may seriously interfere with molecular cloning of 5-methylcytosine-containing foreign DNAs. The Mcr phenotypes of some commonly used strains of E. coli K-12 are reported...
  16. pmc A novel activity in Escherichia coli K-12 that directs restriction of DNA modified at CG dinucleotides
    J E Kelleher
    New England Biolabs, Beverly, Massachusetts 01915
    J Bacteriol 173:5220-3. 1991
    ..A. Raleigh, R. Trimarchi, and H. Revel, Genetics 122:279-296, 1989)...
  17. ncbi RNA methyltransferases utilize two cysteine residues in the formation of 5-methylcytosine
    Michelle Y King
    Indiana University School of Medicine, Fort Wayne Center, 2101 Coliseum Boulevard East, Fort Wayne, Indiana 46805, USA
    Biochemistry 41:11218-25. 2002
    ..Evidence for the predicted accumulation of protein-RNA complexes following mutation of the assisting cysteine has been obtained with Nop2p and a known tRNA m(5)C methyltransferase called Ncl1p (Trm4)...
  18. pmc Site-specific methylases induce the SOS DNA repair response in Escherichia coli
    J Heitman
    J Bacteriol 169:3243-50. 1987
    ..SOS induction by cytosine methylation required the rglB locus, which encodes an endonuclease that cleaves DNA containing 5-hydroxymethyl- or 5-methylcytosine (E. A. Raleigh and G. Wilson, Proc. Natl. Acad. Sci. USA 83:9070-9074, 1986)...
  19. ncbi DNA methylation: bisulphite modification and analysis
    Susan J Clark
    Cancer Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, NSW 2010, Australia
    Nat Protoc 1:2353-64. 2006
    ..Bisulphite conversion of DNA, in either single tubes or in a 96-well format, can be performed in a minimum of 8 h and a maximum of 18 h, depending on the amount and quality of starting DNA...
  20. ncbi A candidate mammalian DNA methyltransferase related to pmt1p of fission yeast
    J A Yoder
    Department of Genetics and Development, College of Physicians and Surgeons of Columbia University, 701 West 168 Street, New York, NY 10032, USA
    Hum Mol Genet 7:279-84. 1998
    ..Dnmt2 is a candidate for the activity that methylates newly integrated retroviral DNA and maintains trace levels of 5-methylcytosine in the DNA of embryonic stem cells homozygous for null mutations in Dnmt1...
  21. doi Arabidopsis DEMETER-LIKE proteins DML2 and DML3 are required for appropriate distribution of DNA methylation marks
    Ana Pilar Ortega-Galisteo
    Departamento de Genetica, Universidad de Cordoba, Edificio Gregor Mendel, Campus de Rabanales s n, 14071, Cordoba, Spain
    Plant Mol Biol 67:671-81. 2008
    ..These results suggest that DML2 and DML3 are required not only for removing DNA methylation marks from improperly-methylated cytosines, but also for maintenance of high methylation levels in properly targeted sites...
  22. doi Genome-wide high throughput analysis of DNA methylation in eukaryotes
    Kyle R Pomraning
    Center for Genome Research and Biocomputing and Department of Biochemistry and Biophysics, Oregon State University, 2011 ALS Building, Corvallis, OR 97331 7305, USA
    Methods 47:142-50. 2009
    ....
  23. pmc Identification of human tRNA:m5C methyltransferase catalysing intron-dependent m5C formation in the first position of the anticodon of the pre-tRNA Leu (CAA)
    Bartosz Brzezicha
    Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Miedzychodzka 5, 60 371 Poznan, Poland
    Nucleic Acids Res 34:6034-43. 2006
    ..To our knowledge, this is the first report showing intron-dependent methylation of humanpre-tRNA Leu (CAA) and identification of human gene encoding tRNA methylase responsible for this reaction...
  24. pmc Depletion of Saccharomyces cerevisiae tRNA(His) guanylyltransferase Thg1p leads to uncharged tRNAHis with additional m(5)C
    Weifeng Gu
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine, 601 Elmwood Avenue, Rochester, NY 14642, USA
    Mol Cell Biol 25:8191-201. 2005
    ..We developed a new method to map m(5)C residues in RNA and localized the additional m(5)C to positions 48 and 50. This is the first documented example of the accumulation of additional modifications in a eukaryotic tRNA species...
  25. ncbi DNA methylation in insects
    L M Field
    BCH Division, Rothamsted Research, Harpenden, Herts, UK
    Insect Mol Biol 13:109-15. 2004
    ....
  26. ncbi A systematic profile of DNA methylation in human cancer cell lines
    Maria F Paz
    Cancer Epigenetics Laboratory, Molecular Pathology Program, Spanish National Cancer Center, Carlos III Institute of Health, 28029 Madrid, Spain
    Cancer Res 63:1114-21. 2003
    ..Our data provide a basis for a better use of human cancer cell lines in basic and translational research with respect to their DNA methylation environment...
  27. pmc Both hypomethylation and hypermethylation in a 0.2-kb region of a DNA repeat in cancer
    Rie Nishiyama
    Human Genetics Program, Department of Biochemistry, and Tulane Cancer Center, Tulane Medical School, New Orleans, LA 70112, USA
    Mol Cancer Res 3:617-26. 2005
    ..NBL2 is an attractive candidate for an epigenetic cancer marker and for elucidating the nature of epigenetic changes in cancer...
  28. pmc Cloning, purification and initial characterization of E. coli McrA, a putative 5-methylcytosine-specific nuclease
    Elizabeth A Mulligan
    Department of Molecular Genetics and Microbiology, School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
    Protein Expr Purif 62:98-103. 2008
    ....
  29. ncbi p53 mutational spectra and the role of methylated CpG sequences
    G P Pfeifer
    Department of Biology, Beckman Research Institute of the City of Hope, 1450 East Duarte Road, Duarte, CA 91010, USA
    Mutat Res 450:155-66. 2000
    ..These sequences are particularly prone to mutagenesis involving endogenous events as well as modification by exogenous carcinogens...
  30. doi Oxygenase catalyzed 5-methylcytosine hydroxylation
    Christoph Loenarz
    Chemistry Research Laboratory and the Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
    Chem Biol 16:580-3. 2009
    ..2009). This discovery has potential far-reaching implications for epigenetic regulation and will stimulate efforts to identify new nucleic acid modifications...
  31. doi Phylogenetic analysis of the eukaryotic RNA (cytosine-5)-methyltransferases
    Athanasia Pavlopoulou
    Biomedical Research Foundation of the Academy of Athens, Department of Biotechnology, Bioinformatics and Medical Informatics Team, Soranou Efesiou 4, 11527 Athens, Greece
    Genomics 93:350-7. 2009
    ..Furthermore, the results of this study add further support to a previous hypothesis that RCMTs represent evolutionary intermediates of RNA (uridine-5)-methyltransferases and DNA (cytosine-5)-methyltransferases...
  32. pmc McrA and McrB restriction phenotypes of some E. coli strains and implications for gene cloning
    E A Raleigh
    New England Biolabs, Beverly, MA 01915
    Nucleic Acids Res 16:1563-75. 1988
    ..coli K12, are tabulated here. We briefly review some evidence suggesting that McrB restriction of mouse-modified DNA does occur in vivo and does in fact interfere with cloning of specific mouse sequences...
  33. ncbi The CpG dinucleotide and human genetic disease
    D N Cooper
    Haematology Department, King s College School of Medicine and Dentistry, London, UK
    Hum Genet 78:151-5. 1988
    ..These findings are consistent with methylation-induced deamination of 5-methyl cytosine and suggest that methylation of DNA within coding regions may contribute significantly to the incidence of human genetic disease...
  34. ncbi RecA protein promotes strand exchange with DNA substrates containing isoguanine and 5-methyl isocytosine
    K P Rice
    Department of Biochemistry, University of Wisconsin Madison, 53706, USA
    Biochemistry 39:10177-88. 2000
    ..This observation provides an expanded experimental basis for discussions of potential roles for iG and MiC in a genetic code. Experiments of this type also provide another avenue for exploring RecA-facilitated DNA pairing mechanisms...
  35. ncbi Determination of 5-methyl-cytosine and cytosine in tumor DNA of cancer patients
    Karina Sandoval Guerrero
    Lab de Desarrollo de Métodos Analíticos, FES Cuautitlan, UNAM, Cuautitlan Izcalli, Estado de Mexico, Mexico
    Electrophoresis 26:1057-62. 2005
    ..5 cm effective length, 20 mM carbonate buffer (pH 9.6) plus 80 mM sodium dodecyl sulfate, a separation voltage of 20 kV, and detection at 223 nm...
  36. ncbi Miscoding properties of isoguanine (2-oxoadenine) studied in an AMV reverse transcriptase in vitro system
    A M Bukowska
    Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
    Acta Biochim Pol 43:247-54. 1996
    ..Our results indicate also that formation of the reverse transcriptase catalyzed base pairs between iG and A, G or C can occur only at a low frequency, comparable to the frequency, of mismatches of.(ABSTRACT TRUNCATED)..
  37. ncbi DNA methylation and the regulation of gene transcription
    J T Attwood
    Department of Internal Medicine, University of Michigan, Taubman Center, Ann Arbor 48109, USA
    Cell Mol Life Sci 59:241-57. 2002
    ....
  38. pmc MethylQuant: a sensitive method for quantifying methylation of specific cytosines within the genome
    Helene Thomassin
    Institut Jacques Monod du CNRS, Universites Paris 6 7, Tour 43, 2 place Jussieu, 75251 Paris Cedex 05, France
    Nucleic Acids Res 32:e168. 2004
    ..The method is high-throughput, cost-effective, relatively simple and does not require any specific equipment other than a real-time PCR instrument...
  39. pmc A phase I study of hydralazine to demethylate and reactivate the expression of tumor suppressor genes
    Pilar Zambrano
    Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología Instituto de Investigaciones Biomédicas, UNAM, Mexico
    BMC Cancer 5:44. 2005
    ..The antihypertensive compound hydralazine is a known demethylating agent. This phase I study evaluated the tolerability and its effects upon DNA methylation and gene reactivation in patients with untreated cervical cancer...
  40. ncbi Chromatin remodeling in plant cell culture: patterns of DNA methylation and histone H3 and H4 acetylation vary during growth of asynchronous potato cell suspensions
    R David Law
    United States Department of Agriculture, Agricultural Research Service, Northern Crop Science Laboratory, Sugarbeet and Potato Research, Post Office Box 5677, State University Station, Fargo, ND 58105 5677, USA
    Plant Physiol Biochem 43:527-34. 2005
    ....
  41. ncbi Differential patterns of methylation of the IFN-gamma promoter at CpG and non-CpG sites underlie differences in IFN-gamma gene expression between human neonatal and adult CD45RO- T cells
    Gregory P White
    TVW Telethon Institute for Child Health Research and Centre for Child Health Research, University of Western Australia, Perth, Western Australia, Australia
    J Immunol 168:2820-7. 2002
    ..We additionally demonstrate that overexpression of DNA methyltransferase 3a in embryonic kidney carcinoma cells is accompanied by CpA methylation of the IFN-gamma promoter...
  42. ncbi Methylation in the core-promoter region of the chondromodulin-I gene determines the cell-specific expression by regulating the binding of transcriptional activator Sp3
    Tomoki Aoyama
    Institute for Frontier Medical Sciences, Kyoto University, 53 Kawahara cho, Shogoin, Sakyo ku, Kyoto 606 8507, Japan
    J Biol Chem 279:28789-97. 2004
    ..These results suggest that the methylation status of the core-promoter region is one of the mechanisms to determine the cell-specific expression of the ChM-I gene through the regulation of the binding of Sp3...
  43. ncbi Altered global methylation of DNA: an epigenetic difference in susceptibility for lung cancer is associated with its progression
    C J Piyathilake
    Department of Nutrition Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA
    Hum Pathol 32:856-62. 2001
    ..If these results are confirmed, the status of DNA methylation in early lesions such as epithelial hyperplasia could be used to identify smokers who are at risk for the development of SCC...
  44. ncbi Hypomethylation of DNA and the insulin-like growth factor-II gene in dichloroacetic and trichloroacetic acid-promoted mouse liver tumors
    Lianhui Tao
    Department of Pathology, Medical College of Ohio, 3055 Arlington Avenue, Toledo, OH 43614 5806, USA
    Toxicology 196:127-36. 2004
    ..The results support the hypothesis that DNA hypomethylation is involved in the mechanism for the tumorigenicity of DCA and TCA...
  45. pmc Cytosine methylation by the SuaI restriction-modification system: implications for genetic fidelity in a hyperthermophilic archaeon
    Dennis W Grogan
    New England Biolabs, Inc, Beverly, Massachusetts 01915, USA
    J Bacteriol 185:4657-61. 2003
    ..The results show that the SuaI system uses N(4) methylation to block cleavage of its recognition site, thereby avoiding the creation of G. T mismatches by spontaneous deamination at extremely high temperature...
  46. ncbi DNA methylation: a profile of methods and applications
    Mario F Fraga
    Spanish National Cancer Research Center CNIO, Madrid
    Biotechniques 33:632, 634, 636-49. 2002
    ..We hope this review will be a valuable tool in selecting the best techniques to address particular questions concerning the cytosine methylation status of genomic DNA...
  47. ncbi Measuring DNA demethylase activity in vitro
    Moshe Szyf
    Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
    Methods Mol Biol 200:155-61. 2002
  48. ncbi Specific methylation of the CpG-rich domains in the promoter of the human tissue transglutaminase gene
    Tiziana Cacciamani
    Institute of Biochemistry, University of Ancona, Ancona, Italy
    Gene 297:103-12. 2002
    ....
  49. ncbi Absence of global genomic cytosine methylation pattern erasure during medaka (Oryzias latipes) early embryo development
    Ronald B Walter
    Department of Chemistry and Biochemistry, Southwest Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX 78666 4616, USA
    Comp Biochem Physiol B Biochem Mol Biol 133:597-607. 2002
    ..From a comparative viewpoint, these data may indicate that mammals and fishes methylate and demethylate their genomes in very different manners during development...
  50. ncbi Distribution of 5-methylcytosine residues in 5S rRNA genes in Arabidopsis thaliana and Secale cereale
    J Fulnecek
    Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, CZ 612 65 Brno, Czech Republic
    Mol Genet Genomics 268:510-7. 2002
    ..The differences in methylation levels in different sequence contexts might be of phylogenetic significance, but further species in related and different taxa need to be studied before firm conclusions can be drawn...
  51. ncbi Cellular vitamins, DNA methylation and cancer risk
    Chandrika J Piyathilake
    Department of Nutrition Sciences, The University of Alabama at Birmingham, 35294, USA
    J Nutr 132:2340S-2344S. 2002
    ....
  52. ncbi Methylation of a euchromatin-heterochromatin transition region in Arabidopsis thaliana chromosome 5 left arm
    Olivier Mathieu
    U M R CNRS 6547 BIOMOVE, Universite Blaise Pascal, 24 avenue des Landais, 63177 Aubiere Cedex, France
    Chromosome Res 10:455-66. 2002
    ..The most methylated repeated family at CpG, CpNpG and asymmetrical sites is the 5S ribosomal DNA, highly methylated even though it is transcribed...
  53. ncbi Germ-line variants in methyl-group metabolism genes and susceptibility to DNA methylation in normal tissues and human primary tumors
    Maria F Paz
    Cancer Epigenetics Laboratory, Molecular Pathology Program, Spanish National Cancer Research Center CNIO, 28029 Madrid, Spain
    Cancer Res 62:4519-24. 2002
    ..029). The existence of these associations may provide another example of the interplay between genetic and epigenetic factors in the cancer cell...
  54. ncbi Enhanced CpG mutability and tumorigenesis in MBD4-deficient mice
    Catherine B Millar
    Wellcome Trust Centre for Cell Biology, The King s Buildings, Edinburgh University, Edinburgh EH9 3JR, UK
    Science 297:403-5. 2002
    ..On a cancer-susceptible Apc(Min/+) background, Mbd4-/- mice showed accelerated tumor formation with CpG --> TpG mutations in the Apc gene. Thus MBD4 suppresses CpG mutability and tumorigenesis in vivo...
  55. ncbi Parental 5-methylcytosine methylation patterns are stable upon inter-species hybridization of Xiphophorus (Teleostei: Poeciliidae) fish
    Hai Ying Li
    Department of Chemistry and Biochemistry, Southwest Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX 78666 4616, USA
    Comp Biochem Physiol B Biochem Mol Biol 133:581-95. 2002
    ..Through F(1) inter-species hybridization and succeeding meiosises leading to first generation (BC(1)) and second generation (BC(2)) backcross hybrid progeny, we demonstrate that parental species methylation patterns are stable...
  56. ncbi Profiling DNA methylation by melting analysis
    Per Guldberg
    Institute of Cancer Biology, Danish Cancer Society, Strandboulevarden 49, DK 2100 Copenhagen, Denmark
    Methods 27:121-7. 2002
    ..Both methods allow resolution of "heterogeneous" methylation, i.e., the situation where the content and distribution of 5-methylcytosine in a target gene differ between different molecules in the same sample...
  57. ncbi Cytosine methylation and CpG, TpG (CpA) and TpA frequencies
    Kamel Jabbari
    Laboratoire de Genetique Moleculaire, Institut Jacques Monod, 2 place Jussieu, F 75005 Paris, France
    Gene 333:143-9. 2004
    ..The implications of these results are discussed...
  58. ncbi Transient decreases in methylation at 5'-cCGG-3' sequences in potato (Solanum tuberosum L.) meristem DNA during progression of tubers through dormancy precede the resumption of sprout growth
    R David Law
    United States Department of Agriculture, Agricultural Research Service, Northern Crop Science Laboratory, Post Office Box 5677, State University Station, Fargo, ND 58105 5677, USA
    Plant Mol Biol 51:437-47. 2003
    ....
  59. ncbi De novo methylation of MMLV provirus in embryonic stem cells: CpG versus non-CpG methylation
    Jonathan E Dodge
    Department of Medicine, Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA
    Gene 289:41-8. 2002
    ..These results demonstrate that the Dnmt3 enzymes methylate predominantly CpG sites and at a low frequency CpA sites with no apparent sequence preferences...
  60. ncbi The activity of the murine DNA methyltransferase Dnmt1 is controlled by interaction of the catalytic domain with the N-terminal part of the enzyme leading to an allosteric activation of the enzyme after binding to methylated DNA
    M Fatemi
    Institut für Biochemie Fachbereich 8, Justus Liebig Universitat, Heinrich Buff Ring 58, Giessen, 35392, Germany
    J Mol Biol 309:1189-99. 2001
    ..It suggests that Dnmt1 might be responsible for spreading of methylation, a process that is observed during aging and carcenogenesis but may be important for de novo methylation of DNA...
  61. ncbi Principal causes of hot spots for cytosine to thymine mutations at sites of cytosine methylation in growing cells. A model, its experimental support and implications
    E Lutsenko
    463 Chemistry Building, Department of Chemistry, Wayne State University, Detroit, MI 48202 3489, USA
    Mutat Res 437:11-20. 1999
    ..G mismatches can be quantitatively modeled to explain the occurrence of the hot spot at 5meC. This model has implications for mutational hot and cold spots in all organisms...
  62. ncbi Epigenetic inactivation of a RAS association domain family protein from the lung tumour suppressor locus 3p21.3
    R Dammann
    Department of Biology, Beckman Research Institute, City of Hope Medical Center, Duarte, California, USA
    Nat Genet 25:315-9. 2000
    ..These characteristics indicate a potential role for RASSF1A as a lung tumour suppressor gene...
  63. ncbi Methyl-specific DNA binding by McrBC, a modification-dependent restriction enzyme
    F J Stewart
    New England Biolabs, Inc, Beverly, MA 01915, USA
    J Mol Biol 298:611-22. 2000
    ..The addition of McrC did not affect the footprint obtained. We propose that McrC effects a conformational change in the complex rather than a reorganization of the DNA:protein interface...
  64. pmc Single-molecule and population probing of chromatin structure using DNA methyltransferases
    Jessica A Kilgore
    Department of Biochemistry and Biophysics, Texas A and M University, 2128 TAMU, College Station, TX 77843 2128, USA
    Methods 41:320-32. 2007
    ..This application of MAP-IT provides the first means to simultaneously determine CpG methylation of mammalian genes and their overlying chromatin structure in the same single DNA molecule...
  65. ncbi Direct labeling of 5-methylcytosine and its applications
    Kazuo Tanaka
    Frontier Research System, RIKEN, The Institute of Physical and Chemical Research, Wako, Saitama 351 0198, Japan
    J Am Chem Soc 129:5612-20. 2007
    ..This direct labeling of methylcytosine is a conceptually new methylation detection assay with many merits different from conventional assays...
  66. doi 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...
  67. ncbi Genome-wide epigenetic alterations in cloned bovine fetuses
    Gabriela Gebrin Cezar
    Infigen, Inc, DeForest, Wisconsin 53532, USA
    Biol Reprod 68:1009-14. 2003
    ..This is the first report to indicate that global methylation losses may contribute to the developmental failure of cloned bovine fetuses...
  68. 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
    ....
  69. doi Bisulfite modification for analysis of DNA methylation
    Hikoya Hayatsu
    Faculty of Pharmaceutical Sciences, Okayama University, Tsushima, Okayama, Japan
    Curr Protoc Nucleic Acid Chem . 2008
    ..This unit describes an efficient procedure utilizing a newly developed high-concentration bisulfite solution. Protocols for this methodology are supplemented with discussions focused on chemical aspects of the bisulfite treatment...
  70. ncbi Role of DNA 5-methylcytosine transferase in cell transformation by fos
    A V Bakin
    Department of Developmental Neurobiology, St Jude Children s Research Hospital, Memphis, TN 38105, USA
    Science 283:387-90. 1999
    ..Inhibition of histone deacetylase, which associates with methylated DNA, also caused reversion. These results suggest that fos may transform cells through alterations in DNA methylation and in histone deacetylation...
  71. ncbi Endogenous cytosine damage products alter the site selectivity of human DNA maintenance methyltransferase DNMT1
    Victoria Valinluck
    Department of Biochemistry and Microbiology, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
    Cancer Res 67:946-50. 2007
    ..These data may provide a mechanistic link for the associations documented between inflammation and cancer...
  72. doi Photocurrent response after enzymatic treatment of DNA duplexes immobilized on gold electrodes: electrochemical discrimination of 5-methylcytosine modification in DNA
    Hisatsugu Yamada
    Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura Campus, Kyoto 615 8510, Japan
    Org Biomol Chem 6:272-7. 2008
    ..This significant difference in the photocurrent response between mC and normal C residues in DNA on the gold electrodes is potentially applicable to the detection of mC modification in DNA...
  73. ncbi Genome-wide hypomethylation in hepatocellular carcinogenesis
    C H Lin
    Liver Research Unit, Chang Gung Memorial Hospital, 199 Tung-Hua North Road, Taipei, Taiwan 155
    Cancer Res 61:4238-43. 2001
    ..In addition, our results did not support the hypothesis of activation of transposable elements in HCC via genome-wide hypomethylation...
  74. pmc Glucocorticoid-induced DNA demethylation and gene memory during development
    H Thomassin
    Institut Jacques Monod du CNRS, , Tour 43, 2 place Jussieu, 75251 Paris Cedex 05, France
    EMBO J 20:1974-83. 2001
    ..There fore, demethylation appears to contribute to the fine-tuning of the enhancer and to the memorization of a regulatory event during development...
  75. ncbi DNA methylation learns to fly
    F Lyko
    Trends Genet 17:169-72. 2001
  76. pmc A link between DNA methylation and epigenetic silencing in transgenic Volvox carteri
    P Babinger
    , , D-93040 Regensburg, Germany
    Nucleic Acids Res 29:1261-71. 2001
    ..The observed correlation of CpG methylation and transgene inactivation in a green alga will be discussed in the light of transcriptional silencing...
  77. pmc Very-short-patch repair in Escherichia coli requires the dam adenine methylase
    D C Bell
    Biology Department, Concordia University, Montreal, Quebec H3G 1M8, Canada
    J Bacteriol 183:3631-5. 2001
    ..We also show that production of the dcm-encoded cytosine methylase is unaffected in Dam(-) strains. Since the dcm and vsr genes are cotranscribed, the regulation of Vsr by Dam is probably posttranscriptional...
  78. pmc Lowering S-adenosylmethionine levels in Escherichia coli modulates C-to-T transition mutations
    G Macintyre
    Biology Department, Concordia University, Montreal, Quebec H3G 1M8, Canada
    J Bacteriol 183:921-7. 2001
    ..However, increased mutagenesis was not observed until extremely high arabinose concentrations were used, and genome methylation at Dcm sites was negligible...
  79. ncbi Similarities in sunlight-induced mutational spectra of CpG-methylated transgenes and the p53 gene in skin cancer point to an important role of 5-methylcytosine residues in solar UV mutagenesis
    Y H You
    Department of Biology, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
    J Mol Biol 305:389-99. 2001
    ....
  80. ncbi Cytosine methylation and DNA repair
    C P Walsh
    Centre for Molecular Biosciences, School of Biomedical Sciences, University of Ulster, Northern Ireland
    Curr Top Microbiol Immunol 301:283-315. 2006
    ..We also look at the possible role of specific cytosine deaminases such as Aid and Apobec in accelerating deamination of methylcytosine and consequent DNA demethylation...
  81. doi The bisulfite genomic sequencing used in the analysis of epigenetic states, a technique in the emerging environmental genotoxicology research
    Hikoya Hayatsu
    Faculty of Pharmaceutical Sciences, Okayama University, Tsushima, Okayama 700 8530, Japan
    Mutat Res 659:77-82. 2008
    ..A laboratory protocol for quantifying bisulfite, suitably simple for routine practice to ensure valid experiments, is described...
  82. doi Carba-LNA-5MeC/A/G/T modified oligos show nucleobase-specific modulation of 3'-exonuclease activity, thermodynamic stability, RNA selectivity, and RNase H elicitation: synthesis and biochemistry
    RamShankar Upadhayaya
    Institute of Molecular Medicine, International Biotech Park, Tal Mulshi, Hinjewadi, Pune, India
    J Org Chem 76:4408-31. 2011
    ....
  83. ncbi DNA methylation in plants
    B F Vanyushin
    Belozersky Institute of Physical and Chemical Biology, Lomonosov Moscow State University, Russia
    Curr Top Microbiol Immunol 301:67-122. 2006
    ..Cytoplasmic viral RNA can affect methylation of homologous nuclear sequences and it maybe one of the feedback mechanisms between the cytoplasm and the nucleus to control gene expression...
  84. ncbi Repair of deaminated bases in DNA
    Yoke W Kow
    Department of Radiation Oncology, Laughlin Radiation Center, Emory University School of Medicine, 145 Edgewood Avenue, Atlanta, GA 30335, USA
    Free Radic Biol Med 33:886-93. 2002
    ..Endonuclease V sequence homologs are present in all kingdoms, and it is conceivable that endonuclease V might also be a major enzyme that initiates the repair of hypoxanthine and xanthine in mammalian cells...
  85. doi Different types of plant chromatin associated with modified histones H3 and H4 and methylated DNA
    Lidiane Feitoza
    Laboratory of Plant Cytogenetics, Department of Botany, Federal University of Pernambuco, Recife, Brazil
    Genetica 139:305-14. 2011
    ..Notably, none of these marks distinguished classical heterochromatin from the early condensing euchromatin. It is suggested that the early condensing chromatin is an intermediate type between classical heterochromatin and euchromatin...
  86. ncbi Enzymatic DNA methylation is an epigenetic control for genetic functions of the cell
    B F Vanyushin
    Belozersky Institute of Physico Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
    Biochemistry (Mosc) 70:488-99. 2005
    ..Revelation of an essential role of DNA methylation in the regulation of genetic processes has laid a foundation for and materialized epigenetics and epigenomics...
  87. pmc Dependence of substrate binding and catalysis on pH, ionic strength, and temperature for thymine DNA glycosylase: Insights into recognition and processing of G·T mispairs
    Atanu Maiti
    Department of Biochemistry and Molecular Biology, Greenebaum Cancer Center, School of Medicine, University of Maryland, Baltimore, 21201, USA
    DNA Repair (Amst) 10:545-53. 2011
    ..Our findings provide important insight into catalysis by TDG, particularly for mutagenic G·T mispairs...
  88. pmc Characterization of a thermostable DNA glycosylase specific for U/G and T/G mismatches from the hyperthermophilic archaeon Pyrobaculum aerophilum
    H Yang
    Department of Microbiology and Molecular Genetics and the Molecular Biology Institute, University of California, Los Angeles, California 90095, USA
    J Bacteriol 182:1272-9. 2000
    ..The unique conserved amino acid motifs of MIG proteins are proposed to distinguish MIG proteins from the closely related Nth/MutY DNA glycosylases...
  89. pmc Efficient removal of uracil from G.U mispairs by the mismatch-specific thymine DNA glycosylase from HeLa cells
    P Neddermann
    Department of Biochemistry, Istituto di Richerche di Biologia Molecolare P Angeletti, Pomezia, Italy
    Proc Natl Acad Sci U S A 91:1642-6. 1994
    ..U mispairs inefficiently removed by the more abundant ubiquitous uracil glycosylases, such as those arising from cytosine deamination in G+C-rich regions of the genome...
  90. ncbi H1 histone modulates DNA hydrolysis with WEN1 and WEN2 endonucleases from wheat coleoptiles
    L I Fedoreyeva
    Belozersky Institute of Physico Chemical Biology, Lomonosov Moscow State University, Russia
    Biochemistry (Mosc) 74:145-52. 2009
    ..We suggest that H1 histone changes site specificity of endonucleases or it might be responsible for formation of new or masking of old sites available for these enzymes due to changes in DNA structure induced in a DNA-histone complex...
  91. pmc Role of two strictly conserved residues in nucleotide flipping and N-glycosylic bond cleavage by human thymine DNA glycosylase
    Atanu Maiti
    Department of Biochemistry and Molecular Biology, Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
    J Biol Chem 284:36680-8. 2009
    ..Arg(275) does not contribute substantially to the binding of TDG to abasic DNA product, and it cannot account for the slow product release exhibited by TDG...
  92. doi Embryonic lethal phenotype reveals a function of TDG in maintaining epigenetic stability
    Daniel Cortázar
    Department of Biomedicine, Institute of Biochemistry and Genetics, University of Basel, 4048 Basel, Switzerland
    Nature 470:419-23. 2011
    ..We thus conclude that TDG-dependent DNA repair has evolved to provide epigenetic stability in lineage committed cells...
  93. pmc Methylation-mediated deamination of 5-methylcytosine appears to give rise to mutations causing human inherited disease in CpNpG trinucleotides, as well as in CpG dinucleotides
    David N Cooper
    Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF144XN, UK
    Hum Genomics 4:406-10. 2010
    ..We therefore estimate that ∼5 per cent of missense/nonsense mutations causing human inherited disease may be attributable to methylation-mediated deamination of 5mC within a CpHpG context...
  94. pmc The RNA moiety of chick embryo 5-methylcytosine- DNA glycosylase targets DNA demethylation
    J P Jost
    Friedrich Miescher Institute, PO Box 2543, CH 4002 Basel, Switzerland
    Nucleic Acids Res 25:4545-50. 1997
    ..An excess of targeting oligoribonucleotides cannot change the preferential substrate specificity of the enzyme for hemimethylated double-stranded DNA...
  95. ncbi Characterization of DNA demethylation in normal and cancerous cell lines and the regulatory role of cell cycle proteins in human DNA demethylase activity
    Mariappan Vairapandi
    The Fels Institute for Cancer Research and Molecular Biology, School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, USA
    J Cell Biochem 91:572-83. 2004
    ....
  96. ncbi Immunohistochemical evaluation of global DNA methylation and histone acetylation in papillary urothelial neoplasm of low malignant potential
    F Barbisan
    Section of Pathological Anatomy, Polytechnic University of the Marche Region, School of Medicine, United Hospitals, Ancona, Italy
    Int J Immunopathol Pharmacol 21:615-23. 2008
    ..Further studies are needed to elucidate the complex interplay between chromatin structure, its modifications and recurrence of PUNLMP...
  97. ncbi Deregulation of DNA methyltransferases and loss of parental methylation at the insulin-like growth factor II (Igf2)/H19 loci in p53 knockout mice prior to tumor development
    In Young Park
    Department of Biological Sciences, 373 1 Gusung Dong, Korea Advanced Institute of Science and Technology, Yusung Gu, Taejon 305 701, Republic of Korea
    J Cell Biochem 94:585-96. 2005
    ..Our results suggest that p53 is required for the maintenance of DNA methylation patterns in vivo...
  98. ncbi DNA sequence determinants for binding of the Escherichia coli catabolite gene activator protein
    A Gunasekera
    Department of Chemistry, Rutgers University, New Brunswick, New Jersey 08855
    J Biol Chem 267:14713-20. 1992
    ..The quantitative data in this report provide base-line thermodynamic data required for detailed investigations of amino acid-base pair and amino acid-phosphate contacts in this protein-DNA complex...
  99. pmc A 5-methylcytosine DNA glycosylase/lyase demethylates the retrotransposon Tos17 and promotes its transposition in rice
    Honggui La
    Department of Plant Pathology, Ohio State University, Columbus, OH 43210, USA
    Proc Natl Acad Sci U S A 108:15498-503. 2011
    ..Our results demonstrate that rice DNG701 is a 5-meC DNA glycosylase/lyase responsible for the demethylation of Tos17 and this DNA demethylase plays a critical role in promoting Tos17 transposition in rice calli...
  100. pmc Structure of pvu II DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment
    W Gong
    W M Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 25:2702-15. 1997
    ..Pvu II, M. Taq I and M. Hha I reveals that catalytic amino acids essential for cytosine N4 and adenine N6 methylation coincide spatially with those for cytosine C5 methylation, suggesting a mechanism for amino methylation...
  101. ncbi Thymine DNA glycosylase
    U Hardeland
    Institute of Medical Radiobiology, University of Zurich, Paul Scherrer Institute, August Forel Strasse 7, Ch 8008 Zurich, Switzerland
    Prog Nucleic Acid Res Mol Biol 68:235-53. 2001
    ....

Research Grants64

  1. DNA Methylation in Ethanol Drinking Behavior
    David P Gavin; Fiscal Year: 2013
    ..Ultimately, these studies will identify novel molecular targets in the actions of ethanol and ethanol drinking behavior, and promote the development of pharmacotherapy for alcoholism. ..
  2. Chemical modulators of Tet-family proteins
    Anjana Rao; Fiscal Year: 2010
    ..These molecules will be useful for further investigations into the biological functions of TET proteins, and may eventually be used in the clinic to treat Rett syndrome and other diseases of DNA methylation. ..
  3. Ferritin: Protein/mRNA/DNA in Fe/O Regulation/Metabolism
    ELIZABETH C contact THEIL; Fiscal Year: 2010
    ....
  4. Folate Status, Genomic Uracil, and the Balance of Base Excision Repair Activity
    Michael D Wyatt; Fiscal Year: 2011
    ..We will investigate the links between BER and folic acid that define the seemingly contradictory pro- and anticancer effects of each. ..
  5. Regulation of Genomic and Epigenomic Stability at CpG Sites
    Alfonso Bellacosa; Fiscal Year: 2013
    ..These studies may lead to novel strategies for the diagnosis and treatment of cancer. ..
  6. Biomarkers to Assess Selenium Chemoprevention for NSCLC
    Steven A Belinsky; Fiscal Year: 2012
    ..Studies will also assess whether these same biomarkers can predict cancer recurrence. Finally, a cocktail of agents with minimal side effects is being evaluated that could ultimately be used in the prevention of lung cancer in humans. ..
  7. Regulated Accessibility of a cytokine gene locus.
    Anjana Rao; Fiscal Year: 2013
    ..In this proposal we plan to investigate the role of TET proteins in T cells, a major class of cells in the immune system that protect the organism from attack by bacteria, viruses and other pathogens including cancer cells. ..
  8. Cytosine DNA Methylation and Transcriptional Repression in African Trypanosomes
    KEVIN MILITELLO; Fiscal Year: 2012
    ..Engineered parasites lacking DNA methylation may over-express surface antigens and serve as a vaccine. ..
  9. Epigenetic Effects of Prenatal Ethanol Exposure
    Thomas P Yang; Fiscal Year: 2010
    ..An understanding of the underlying mechanisms of FAS may permit the development of novel therapies for treatment of FAS. ..
  10. INFIDELITY OF CYTOSINE METHYLATION AND HUMAN CANCER
    Lawrence C Sowers; Fiscal Year: 2013
    ..We present for the first time, the measurement of 5ClC and 5BrC in human surgical tissues. Completion of the aims proposed here will allow an in- depth examination of the connection between inflammation, DNA damage and cancer etiology. ..
  11. Epigenetic Dysregulation by Oxidative Stress from Environmental Insults
    Suresh Cuddapah; Fiscal Year: 2013
    ....
  12. Sequence Distribution of Tobacco Carcinogen-DNA Adducts
    Natalia Y Tretyakova; Fiscal Year: 2012
    ....
  13. DNA Demethylation and Transcriptional Gene Silencing
    Jian Kang Zhu; Fiscal Year: 2013
    ..The proposed work will advance new concepts and fill major gaps in our understanding of the dynamic control of DNA methylation, and thus will contribute significantly to elucidating the molecular basis of epigenetic regulation. ..
  14. Molecular Mechanisms of IDH1-mediated Gliomagenesis
    Ingo K Mellinghoff; Fiscal Year: 2013
    ..Results of our studies will shed light on mechanisms through which an "oncometabolite" can regulate the molecular pathogenesis of cancer and refine our view of mutant IDH1 as a potential therapeutic target in human glioma. ..
  15. TILLING Wheat for Reduced Celiac Disease Causing Proteins
    CHARLES PAUL MOEHS; Fiscal Year: 2010
    ..5-1%, and currently the only treatment for patients is the complete exclusion of cereal proteins from the diet. Developing wheat that is acceptable for celiac patients thus addresses an urgent, unmet need. ..
  16. Epigenetic Regulation of Neuronal Cell Death
    Lee J Martin; Fiscal Year: 2013
    ..By studying the DNA methylation and gene silencing in ALS, we could identify novel cell-based, genome-based, and physiology-based mechanisms of ALS pathogenesis that could lead to novel strategies for treating ALS. ..
  17. 5-Hydroxymethylcytosine and Globin Gene Switching
    Donald Lavelle; Fiscal Year: 2013
    ....
  18. Structure and mechanism of CpG specific DNA glycosylases
    ALEX C DROHAT; Fiscal Year: 2013
    ....
  19. FUNCTIONALLY TETHERED OLIGONUCLEOTIDES
    Gregory L Verdine; Fiscal Year: 2011
    ..Our studies will focus on understanding how DNA cytosine methyltransferases (DCMTases) target particular cytosine residues in DNA for extrusion from the DNA helix and insert them into the extrahelical active site on the enzyme. ..
  20. 5-Hydroxymethylcytosine in Neurodevelopment
    Peng Jin; Fiscal Year: 2013
    ..3) To determine the role of Tet proteins in learning and memory. The success of our planned work will define the fundamental role of 5-hmC in neurodevelopment as well as learning and memory. ..
  21. Effects of a Maternal Obesogenic Environment on DNA Methylation in the Placenta
    Leslie Myatt; Fiscal Year: 2013
    ....
  22. Epigenomics of T cells and innate immune cells in human asthma
    Pandurangan Vijayanand; Fiscal Year: 2013
    ..They will have a broad impact on our understanding of asthma, and set an important precedent for investigating the role of epigenetic mechanisms in other immune-mediated disorders. ) ..
  23. UV damage, repair, and mutagenesis
    Gerd P Pfeifer; Fiscal Year: 2013
    ..abstract_text> ..
  24. Role of TET Proteins in ES Cell Pluripotency and Function
    Anjana Rao; Fiscal Year: 2013
    ..In this proposal we plan to investigate the role of TET1 and TET2 proteins in ES and iPS cells. ..
  25. Activation-induced Deaminase and Antibody Maturation
    Ashok S Bhagwat; Fiscal Year: 2013
    ....
  26. 5-hydroxymethylcytosine in human cancer
    Gerd P Pfeifer; Fiscal Year: 2013
    ..The third Aim will focus on functional studies of TET and TET-associated proteins and their aberrations in cancer. ..
  27. FINDING NOVEL REAGENTS BY BIOINFORMATICS AND BIOCHEMISTRY
    Richard J Roberts; Fiscal Year: 2013
    ..Thus, the results of this research will have immediate implications for the fields of epigenetics, pathogenesis and genome annotation. ..
  28. NOVEL 5-HYDROXYMETHYLCYTOSINE SPECIFIC ENZYMES FOR EPIGENETIC STUDIES.
    Zhenyu Zhu; Fiscal Year: 2013
    ....
  29. Methylation Landscape of the Human Genome
    Timothy Bestor; Fiscal Year: 2003
    ..The impending completion of the sequence of the human genome presents a unique opportunity to gain understanding of the shape of genomic methylation patterns and their role in human development and disease. ..
  30. Impact of PAH carcinogen-DNA adducts on DNA methylation
    Nicholas Geacintov; Fiscal Year: 2003
    ..The results should provide novel insights into the mechanisms of carcinogenesis associated with the formation of the stereoisomeric PAR diol epoxide-DNA lesions and their impact on biological methylation. ..
  31. Sequence Distribution of Tabacco Carcinogen-DNA Adducts
    Natalia Tretyakova; Fiscal Year: 2007
    ..The proposed research is significant because of the widespread human exposure to tobacco products and because of their central role in the initiation of lung cancer in humans. ..
  32. Extended Thermodynamic Database for Modified Oligonucleotides
    WILLIAM J KENNELLY; Fiscal Year: 2010
    ....
  33. Role of TET2 mutations in malignant transformation and acute myeloid leukemia
    Ross L Levine; Fiscal Year: 2013
    ....
  34. Chemical Pathology of 5-aza-2'-deoxycytidine
    Lawrence Sowers; Fiscal Year: 2007
    ..The results of the studies proposed here should shed significant light on the chemical properties of DAC that could be responsible for the array of biochemical effects induced by this compound in human cells. ..
  35. Novel 5-methylcytosine Oxidases
    Yu Zheng; Fiscal Year: 2013
    ..In summary, our studies will bring a number of novel enzymatic reagents to the research market and generate scientific insights on epigenetic regulation involving 5hmC. ..
  36. Direct Single Base-Pair Real-Time DNA Methylation Sequencing
    STEPHEN WHITFIELD TURNER; Fiscal Year: 2010
    ..The ability to directly determine genomic DNA methylation patterns will dramatically speed up and reduce the cost of projects aiming to illuminate its role in human health. ..
  37. MED1 MUTATIONS IN COLORECTAL CANCER
    Alfonso Bellacosa; Fiscal Year: 2002
    ..Experiments are proposed to address: 1) the nature and frequency of MED1 mutations in colorectal cancer; 2) whether MED1 mutations are a prognostic factor and influence response to treatment. ..
  38. MUTATIONAL HOT SPOTS AND DEAMINATION OF 5 METHYLCYTOSINE
    ASHOK BHAGWAT; Fiscal Year: 1999
    ..Together these studies should help one evaluate the role of cytosine methyltransferases in creating C to T mutations and the relative merits of competing hypotheses regarding the mechanism of mutations at sites of cytosine methylation. ..
  39. ANTIHIV OLIGONUCLEOTIDES WITH REACTIVE FUNCTIONAL GROUPS
    Paul Miller; Fiscal Year: 2006
    ..The antiviral activities of the antisense and TFO mr-OMPs will be investigated in collaboration with Dr. Jeffrey Laurence, Cornell Medical Center. ..
  40. FORMATION, MUTAGENICITY & REPAIR OF PHOTOHYDRATES IN DNA
    George Teebor; Fiscal Year: 1999
    ....
  41. DIET CANCER AND ONCOGENE EXPRESSION IN INBRED MICE
    ELSIE WAINFAN; Fiscal Year: 1990
    ....
  42. ENVIRONMENTAL HYDRAZINES AND METHYLATION OF DNA GUANINE
    RONALD SHANK; Fiscal Year: 1992
    ....
  43. HYPERTHERMIA AND THE FUNCTION OF HSP70
    Gloria Li; Fiscal Year: 2007
    ..abstract_text> ..
  44. A Genetic System Able to Screen for Active DNA Demethylation
    Shuang yong Xu; Fiscal Year: 2006
    ..In addition, knowledge of the mechanism of demethylation could be crucial in converting fully differentiated adult stem cells into totipotent stem cells. [unreadable] [unreadable] [unreadable]..
  45. Array-based methylation analysis using anti-5mC antibody
    Fumiichiro Yamamoto; Fiscal Year: 2007
    ..We will evaluate the sensitivity, specificity, and reproducibility of the method, using BAG clone microarrays, DNA fragment microarrays, and oligonucleotide microarrays. [unreadable] [unreadable] [unreadable]..
  46. STUDIES OF THE FOS ONCOGENE
    Tom Curran; Fiscal Year: 2004
    ..These cells will be used to generate mutant mice and cell lines that will be used to analyze the role of Ref-1 in modulating AP1 activity and cell growth. ..
  47. EPIGENETIC CHANGES AND VITAMIN STATUS IN BREAST CANCER
    GARY JOHANNING; Fiscal Year: 2001
    ..We propose to fill this gap in knowledge by investigating the association between gene-specific and global DNA methylation patterns and breast cancer. ..
  48. DNA CYTOSINE C5 METHYLTRANSFERASE
    Norbert Reich; Fiscal Year: 2000
    ..Others have proposed that this mutagenic reaction may account for many human genetic diseases including cancer. However, the reaction has only been demonstrated with bacterial DCMTases. ..
  49. GENOMIC METHYLATION--A MECHANISM TO ALTER PHENOTYPES
    Bernard Futscher; Fiscal Year: 2000
    ....
  50. X CHROMOSOME INACTIVATION AND DNA METHYLATION
    ARTHUR RIGGS; Fiscal Year: 2002
    ..DNA methylation is becoming increasingly recognized as a significant factor for many cancers. ..
  51. X-CHROMOSOME INACTIVATION AND DNA METHYLATION
    ARTHUR RIGGS; Fiscal Year: 1992
    ....
  52. FSHD: Chromatin Structure, Looping, & Expression
    Melanie Ehrlich; Fiscal Year: 2009
    ..The proposed research should elucidate new aspects of long-distance control of gene expression as well as lending clinically useful insights into this currently intractable disease. ..
  53. FSHD Syndrome: DNA Repeats, Methylation, & Chromatin
    Melanie Ehrlich; Fiscal Year: 2003
    ..The proposed research should help elucidate the molecular etiology of the enigmatic FSHD syndrome. ..
  54. DNA methylation in cancer genomes
    GERD PFEIFER; Fiscal Year: 2008
    ..unreadable] [unreadable] [unreadable]..
  55. Prognostic Significance of Altered DNA Methylation
    Chandrika Piyathilake; Fiscal Year: 2002
    ..A newly developed and tested immunohistochemical technique, which measures the degree of global methylation in intact and specific types of cells, will be used to evaluate global DNA methylation in the proposed study. ..
  56. UV DAMAGE, REPAIR AND MUTAGENESIS
    GERD PFEIFER; Fiscal Year: 2003
    ..abstract_text> ..
  57. Characterization of MBD3L1 and MBD3L2
    GERD PFEIFER; Fiscal Year: 2008
    ..Since both proteins are likely functioning as transcriptional regulators, it will be important to determine if there are changes in gene expression patterns in Mbd311 and Mbd312 (-/-) cells. ..
  58. RASSF1 Tumor Suppressor Gene
    GERD PFEIFER; Fiscal Year: 2005
    ..The effect of RASSF1 expression on RAS signaling pathways will be studied. We will examine if RASSF1A, alone or in combination with activated RAS, induces cell death (apoptosis). ..
  59. Effects of Folate Fortification on Cancer Prevention an*
    Chandrika Piyathilake; Fiscal Year: 2005
    ....
  60. Prognostic Significance of DNA and Histone Methylation
    Chandrika Piyathilake; Fiscal Year: 2007
    ..Investigator talent, equipment, facilities and access to study subjects at UAB are ideal for conducting this study. ..
  61. HPV Clearance by Folic Acid Supplementation
    Chandrika J Piyathilake; Fiscal Year: 2010
    ..Because this study will be conducted among women positive for HPV 16, the most prevalent and powerful causative agent of CC, the public health significance of this study could be enormous and will complement HPV vaccine studies. ..