Genomes and Genes
Summary: Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.
Publications278 found, 100 shown here
- Human DNA methylomes at base resolution show widespread epigenomic differencesRyan Lister
Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
Nature 462:315-22. 2009..These reference epigenomes provide a foundation for future studies exploring this key epigenetic modification in human disease and development...
- DNA methylation patterns and epigenetic memoryAdrian Bird
Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK
Genes Dev 16:6-21. 2002
- Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1Mamta Tahiliani
Department of Pathology, Harvard Medical School and Immune Disease Institute, 200 Longwood Avenue, Boston, MA 02115, USA
Science 324:930-5. 2009..hmC is present in the genome of mouse embryonic stem cells, and hmC levels decrease upon RNA interference-mediated depletion of TET1. Thus, TET proteins have potential roles in epigenetic regulation through modification of 5mC to hmC...
- The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shoresRafael A Irizarry
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
Nat Genet 41:178-86. 2009For the past 25 years, it has been known that alterations in DNA methylation (DNAm) occur in cancer, including hypomethylation of oncogenes and hypermethylation of tumor suppressor genes...
- Epigenetics in cancerManel Esteller
Cancer Epigenetics Laboratory, Spanish National Cancer Research Center, Madrid, Spain
N Engl J Med 358:1148-59. 2008
- MGMT gene silencing and benefit from temozolomide in glioblastomaMonika E Hegi
Laboratory of Tumor Biology and Genetics, Department of Neurosurgery, University Hospital Lausanne, Lausanne, Switzerland
N Engl J Med 352:997-1003. 2005....
- Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAsJohn L Rinn
Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
Cell 129:1311-23. 2007..Thus, transcription of ncRNA may demarcate chromosomal domains of gene silencing at a distance; these results have broad implications for gene regulation in development and disease states...
- Increased methylation variation in epigenetic domains across cancer typesKasper Daniel Hansen
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
Nat Genet 43:768-75. 2011..We suggest a model for cancer involving loss of epigenetic stability of well-defined genomic domains that underlies increased methylation variability in cancer that may contribute to tumor heterogeneity...
- Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNAYu Fei He
Group of DNA Metabolism, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
Science 333:1303-7. 2011..These data suggest that oxidation of 5mC by Tet proteins followed by TDG-mediated base excision of 5caC constitutes a pathway for active DNA demethylation...
- Identification of a CpG island methylator phenotype that defines a distinct subgroup of gliomaHoutan Noushmehr
USC Epigenome Center, University of Southern California, Los Angeles, CA 90033, USA
Cancer Cell 17:510-22. 2010We have profiled promoter DNA methylation alterations in 272 glioblastoma tumors in the context of The Cancer Genome Atlas (TCGA)...
- CpG islands and the regulation of transcriptionAimée M Deaton
The Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
Genes Dev 25:1010-22. 2011..CGIs are therefore generically equipped to influence local chromatin structure and simplify regulation of gene activity...
- Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cellsRyan Lister
Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
Nature 471:68-73. 2011..However, it remains unknown how complete the reestablishment of ES-cell-like DNA methylation patterns is throughout the genome...
- Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genomeMichael Weber
Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH 4058 Basel, Switzerland
Nat Genet 39:457-66. 2007To gain insight into the function of DNA methylation at cis-regulatory regions and its impact on gene expression, we measured methylation, RNA polymerase occupancy and histone modifications at 16,000 promoters in primary human somatic ..
- Generation of germline-competent induced pluripotent stem cellsKeisuke Okita
Department of Stem Cell Biology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606 8507, Japan
Nature 448:313-7. 2007..proliferation and teratoma formation; however, they are different with regards to gene expression and DNA methylation patterns, and fail to produce adult chimaeras...
- Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosineShinsuke Ito
Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 7295, USA
Science 333:1300-3. 2011..Thus, we identify two previously unknown cytosine derivatives in genomic DNA as the products of Tet proteins. Our study raises the possibility that DNA demethylation may occur through Tet-catalyzed oxidation followed by decarboxylation...
- Functions of DNA methylation: islands, start sites, gene bodies and beyondPeter A Jones
USC Norris Comprehensive Cancer Center, Keck School of Medicine of University of Southern California, Los Angeles, California 90089 99176, USA
Nat Rev Genet 13:484-92. 2012b>DNA methylation is frequently described as a 'silencing' epigenetic mark, and indeed this function of 5-methylcytosine was originally proposed in the 1970s...
- Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiationGabriella Ficz
Laboratory of Developmental Genetics and Imprinting, The Babraham Institute, Cambridge CB22 3AT, UK
Nature 473:398-402. 2011..We propose that the balance between hydroxymethylation and methylation in the genome is inextricably linked with the balance between pluripotency and lineage commitment...
- DNA methylation landscapes: provocative insights from epigenomicsMiho M Suzuki
The Wellcome Trust Centre for Cell Biology, The University of Edinburgh, Michael Swann Building, The King s Buildings, Edinburgh EH9 3JR, UK
Nat Rev Genet 9:465-76. 2008..New techniques are making it easier to map DNA methylation patterns on a large scale and the results have already provided surprises...
- Reprogramming of human somatic cells to pluripotency with defined factorsIn Hyun Park
Division of Pediatric Hematology Oncology, Children s Hospital Boston and Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
Nature 451:141-6. 2008..These data demonstrate that defined factors can reprogramme human cells to pluripotency, and establish a method whereby patient-specific cells might be established in culture...
- DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian developmentM Okano
Cardiovascular Research Center, Massachusetts General Hospital, Department of Medicine, Harvard Medical School, Charlestown 02129, USA
Cell 99:247-57. 1999The establishment of DNA methylation patterns requires de novo methylation that occurs predominantly during early development and gametogenesis in mice...
- DNA demethylation dynamicsNidhi Bhutani
Baxter Laboratory for Stem Cell Biology, Institute for Stem Cell Biology and Regenerative Medicine, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305 5175, USA
Cell 146:866-72. 2011..These reports highlight that in certain contexts, DNA methylation is not fixed but dynamic, requiring continuous regulation.
- Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblastsAkiko Doi
Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
Nat Genet 41:1350-3. 2009Induced pluripotent stem (iPS) cells are derived by epigenetic reprogramming, but their DNA methylation patterns have not yet been analyzed on a genome-wide scale...
- Conserved role of intragenic DNA methylation in regulating alternative promotersAlika 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. 2010Although it is known that the methylation of DNA in 5' promoters suppresses gene expression, the role of DNA methylation in gene bodies is unclear...
- Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiationMaria E Figueroa
Weill Cornell Medical College, New York, NY 10065, USA
Cancer Cell 18:553-67. 2010..Finally, either expression of mutant IDH1/2 or Tet2 depletion impaired hematopoietic differentiation and increased stem/progenitor cell marker expression, suggesting a shared proleukemogenic effect...
- Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brainJunjie U Guo
Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
Cell 145:423-34. 2011..Our study suggests a TET1-induced oxidation-deamination mechanism for active DNA demethylation in mammals...
- Principles and challenges of genomewide DNA methylation analysisPeter W Laird
USC Epigenome Center, University of Southern California, Keck School of Medicine, Los Angeles, 90089 9601, USA
Nat Rev Genet 11:191-203. 2010..Therefore, profiling DNA methylation across the genome is vital to understanding the influence of epigenetics...
- Genome-scale DNA methylation maps of pluripotent and differentiated cellsAlexander Meissner
Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
Nature 454:766-70. 2008b>DNA methylation is essential for normal development and has been implicated in many pathologies including cancer...
- TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelityKristine 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.
- Cancer epigenetics reaches mainstream oncologyManuel Rodríguez-Paredes
Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L Hospitalet, and Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Spain
Nat Med 17:330-9. 2011..The field has moved from just one recognized marker, DNA methylation, to a variety of others, including a wide spectrum of histone modifications...
- DNA methylation patterns associate with genetic and gene expression variation in HapMap cell linesJordana T Bell
Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
Genome Biol 12:R10. 2011b>DNA methylation is an essential epigenetic mechanism involved in gene regulation and disease, but little is known about the mechanisms underlying inter-individual variation in methylation profiles...
- Epigenome-wide association studies for common human diseasesVardhman K Rakyan
Blizard Institute of Cell and Molecular Science, Barts and the London School of Medicine and Dentistry, Queen Mary, University of London, London, UK
Nat Rev Genet 12:529-41. 2011..to initiate large-scale studies of human disease-associated epigenetic variation, specifically variation in DNA methylation. Such epigenome-wide association studies (EWASs) present novel opportunities but also create new challenges ..
- Epigenetic reprogramming in mammalian developmentW Reik
Laboratory of Developmental Genetics and Imprinting, The Babraham Institute, Cambridge CB2 4AT, UK
Science 293:1089-93. 2001b>DNA methylation is a major epigenetic modification of the genome that regulates crucial aspects of its function. Genomic methylation patterns in somatic differentiated cells are generally stable and heritable...
- Genome-wide evolutionary analysis of eukaryotic DNA methylationAssaf Zemach
Department of Plant and Microbial Biology, 211 Koshland Hall, University of California, Berkeley, CA 94720, USA
Science 328:916-9. 2010..We quantified DNA methylation in 17 eukaryotic genomes and found that gene body methylation is conserved between plants and animals, ..
- Linking DNA methylation and histone modification: patterns and paradigmsHoward Cedar
Department of Developmental Biology and Cancer Research, Hebrew University Medical School, Ein Kerem, Jerusalem 91120, Israel
Nat Rev Genet 10:295-304. 2009Both DNA methylation and histone modification are involved in establishing patterns of gene repression during development...
- Establishing, maintaining and modifying DNA methylation patterns in plants and animalsJulie A Law
Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, 90095 1606, USA
Nat Rev Genet 11:204-20. 2010Cytosine DNA methylation is a stable epigenetic mark that is crucial for diverse biological processes, including gene and transposon silencing, imprinting and X chromosome inactivation...
- Thymine DNA glycosylase is essential for active DNA demethylation by linked deamination-base excision repairSalvatore Cortellino
Cancer Biology Program and Epigenetics and Progenitor Cells Keystone Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
Cell 146:67-79. 2011b>DNA methylation is a major epigenetic mechanism for gene silencing...
- MethPrimer: designing primers for methylation PCRsLong Cheng Li
Department of Urology, Veterans Affairs Medical Center, and University of California San Francisco, San Francisco, CA 94121, USA
Bioinformatics 18:1427-31. 2002b>DNA methylation is an epigenetic mechanism of gene regulation...
- Persistent epigenetic differences associated with prenatal exposure to famine in humansBastiaan T Heijmans
Departments of Molecular Epidemiology, Medical Statistics, and Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
Proc Natl Acad Sci U S A 105:17046-9. 2008..who were prenatally exposed to famine during the Dutch Hunger Winter in 1944-45 had, 6 decades later, less DNA methylation of the imprinted IGF2 gene compared with their unexposed, same-sex siblings...
- CTCF-promoted RNA polymerase II pausing links DNA methylation to splicingSanjeev Shukla
Center for Cancer Research, Mouse Cancer Genetics Program, National Cancer Institute at Frederick, Frederick, Maryland 21702, USA
Nature 479:74-9. 2011..reports have identified distinct histone methylation patterns, elevated nucleosome occupancy and enriched DNA methylation at exons relative to introns...
- DNA-binding factors shape the mouse methylome at distal regulatory regionsMichael 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.
- Mechanisms of polycomb gene silencing: knowns and unknownsJeffrey A Simon
Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis 55455, USA
Nat Rev Mol Cell Biol 10:697-708. 2009..These findings have an impact on the epigenetic programming of gene expression in many biological systems...
- Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signalsRudolf Jaenisch
Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
Nat Genet 33:245-54. 2003..Research over the past few years has focused on two molecular mechanisms that mediate epigenetic phenomena: DNA methylation and histone modifications...
- Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiencyChristian Popp
Laboratory of Developmental Genetics and Imprinting, The Babraham Institute, Cambridge, UK
Nature 463:1101-5. 2010..Here we profiled DNA methylation throughout the genome by unbiased bisulphite next generation sequencing in wild-type and AID-deficient mouse ..
- Epigenetic programming by maternal behaviorIan C G Weaver
Douglas Hospital Research Center, 6875 LaSalle Blvd, Montreal, Quebec H4H 1R3, Canada
Nat Neurosci 7:847-54. 2004..Offspring of mothers that showed high levels of LG and ABN were found to have differences in DNA methylation, as compared to offspring of 'low-LG-ABN' mothers...
- A unique regulatory phase of DNA methylation in the early mammalian embryoZachary D Smith
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
Nature 484:339-44. 2012b>DNA methylation is highly dynamic during mammalian embryogenesis...
- Environmental epigenomics and disease susceptibilityRandy L Jirtle
Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina 27710, USA
Nat Rev Genet 8:253-62. 2007..Methods are now becoming available to investigate the relevance of these phenomena to human disease...
- Epigenetic differences arise during the lifetime of monozygotic twinsMario F Fraga
Epigenetics Laboratory, Spanish National Cancer Centre CNIO, Melchor Fernandez Almagro 3, 28029 Madrid, Spain
Proc Natl Acad Sci U S A 102:10604-9. 2005..To address this issue, we examined the global and locus-specific differences in DNA methylation and histone acetylation of a large cohort of monozygotic twins...
- Validation of a DNA methylation microarray for 450,000 CpG sites in the human genomeJuan Sandoval
Cancer Epigenetics and Biology Program PEBC, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute IDIBELL, Spain
Epigenetics 6:692-702. 2011b>DNA methylation is the most studied epigenetic mark and CpG methylation is central to many biological processes and human diseases...
- Evaluation of the Infinium Methylation 450K technologySarah Dedeurwaerder
Laboratory of Cancer Epigenetics, Universite Libre de Bruxelles, Faculty of Medicine, Brussels, Belgium
Epigenomics 3:771-84. 2011..In particular, we compare the methylation values of the Infinium I and Infinium II assays...
- Epigenetic modifications and human diseaseAnna Portela
Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, Barcelona, Catalonia, Spain
Nat Biotechnol 28:1057-68. 2010..These allow the mapping of epigenetic marks, such as DNA methylation, histone modifications and nucleosome positioning, which are critical for regulating gene and noncoding RNA ..
- Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applicationsFelix Krueger
Bioinformatics Group, The Babraham Institute, CB22 3AT, Cambridge, UK
Bioinformatics 27:1571-2. 2011..Availability and implementation: Bismark is released under the GNU GPLv3+ licence. The source code is freely available from www.bioinformatics.bbsrc.ac.uk/projects/bismark/...
- A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promotersSerge Saxonov
Biomedical Informatics Program, Stanford University, Stanford, CA 94305, USA
Proc Natl Acad Sci U S A 103:1412-7. 2006....
- Epigenetic regulation of the glucocorticoid receptor in human brain associates with childhood abusePatrick O McGowan
Douglas Mental Health University Institute, 6875 LaSalle Boulevard, Montreal, Quebec, H4H 1R3, Canada
Nat Neurosci 12:342-8. 2009..These findings translate previous results from rat to humans and suggest a common effect of parental care on the epigenetic regulation of hippocampal glucocorticoid receptor expression...
- Dynamic changes in the human methylome during differentiationLouise Laurent
UCSD Medical Center, Department of Reproductive Medicine, San Diego, California 92103, USA
Genome Res 20:320-31. 2010b>DNA methylation is a critical epigenetic regulator in mammalian development...
- Abundant quantitative trait loci exist for DNA methylation and gene expression in human brainJ Raphael Gibbs
Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
PLoS Genet 6:e1000952. 2010..We present a set of integrated experiments that investigate the effects of common genetic variability on DNA methylation and mRNA expression in four human brain regions each from 150 individuals (600 samples total)...
- DNA methylation profiling of human chromosomes 6, 20 and 22Florian Eckhardt
Epigenomics AG, Kleine Präsidentstrasse 1, 10178 Berlin, Germany
Nat Genet 38:1378-85. 2006b>DNA methylation is the most stable type of epigenetic modification modulating the transcriptional plasticity of mammalian genomes...
- Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterningShawn J Cokus
Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California 90095, USA
Nature 452:215-9. 2008Cytosine DNA methylation is important in regulating gene expression and in silencing transposons and other repetitive sequences...
- Epigenetic reprogramming in plant and animal developmentSuhua Feng
Howard Hughes Medical Institute and Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
Science 330:622-7. 2010..The mechanisms of genome-wide erasure of DNA methylation, which involve modifications to 5-methylcytosine and DNA repair, are being unraveled...
- Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cellsWilliam A Pastor
Harvard Medical School, Immune Disease Institute and Program in Cellular and Molecular Medicine, Children s Hospital Boston, Boston, Massachusetts 02115, USA
Nature 473:394-7. 2011..Our results indicate that 5hmC has a probable role in transcriptional regulation, and suggest a model in which 5hmC contributes to the 'poised' chromatin signature found at developmentally-regulated genes in ES cells...
- Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysisPan Du
Northwestern University Biomedical Informatics Center NUBIC, NUCATS, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
BMC Bioinformatics 11:587. 2010High-throughput profiling of DNA methylation status of CpG islands is crucial to understand the epigenetic regulation of genes...
- The mammalian epigenomeBradley 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...
- The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytesTian Peng Gu
Group of DNA Metabolism, The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
Nature 477:606-10. 2011..Therefore, Tet3-mediated DNA hydroxylation is involved in epigenetic reprogramming of the zygotic paternal DNA following natural fertilization and may also contribute to somatic cell nuclear reprogramming during animal cloning...
- DNA methylation and human diseaseKeith D Robertson
Department of Biochemistry and Molecular Biology, Shands Cancer Center, University of Florida, Gainesville, Florida 32610, USA
Nat Rev Genet 6:597-610. 2005b>DNA methylation is a crucial epigenetic modification of the genome that is involved in regulating many cellular processes...
- Distinct epigenomic landscapes of pluripotent and lineage-committed human cellsR David Hawkins
Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
Cell Stem Cell 6:479-91. 2010..of potential regulatory sequences also exhibit a high degree of dynamics in chromatin modifications and DNA methylation. Additionally, we observe novel, context-dependent relationships between DNA methylation and chromatin ..
- Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell linesChristoph Bock
Broad Institute, Cambridge, MA 02142, USA
Cell 144:439-52. 2011..Toward this goal we have established genome-wide reference maps of DNA methylation and gene expression for 20 previously derived human ES lines and 12 human iPS cell lines, and we have ..
- Directly reprogrammed fibroblasts show global epigenetic remodeling and widespread tissue contributionNimet Maherali
Massachusetts General Hospital Cancer Center and Center for Regenerative Medicine, Harvard Stem Cell Institute, 185 Cambridge Street, Boston, MA 02114, USA
Cell Stem Cell 1:55-70. 2007....
- A microRNA DNA methylation signature for human cancer metastasisAmaia 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.
- MicroRNA-29 family reverts aberrant methylation in lung cancer by targeting DNA methyltransferases 3A and 3BMuller Fabbri
Department of Molecular Virology, Immunology, and Medical Genetics, Comprehensive Cancer Center, and College of Pharmacy, Ohio State University, Columbus, OH 43210, USA
Proc Natl Acad Sci U S A 104:15805-10. 2007..3'-UTRs of DNA methyltransferase (DNMT)3A and -3B (de novo methyltransferases), two key enzymes involved in DNA methylation, that are frequently up-regulated in lung cancer and associated with poor prognosis...
- Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolutionMichael J Booth
Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
Science 336:934-7. 2012..Our results open new questions on 5hmC dynamics and sequence-specific targeting by TETs...
- Dissecting direct reprogramming through integrative genomic analysisTarjei S Mikkelsen
Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
Nature 454:49-55. 2008..We demonstrate that RNA inhibition of transcription factors can facilitate reprogramming, and that treatment with DNA methyltransferase inhibitors can improve the overall efficiency of the reprogramming process...
- Intra-individual change over time in DNA methylation with familial clusteringHans T Bjornsson
Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
JAMA 299:2877-83. 2008Changes over time in epigenetic marks, which are modifications of DNA such as by DNA methylation, may help explain the late onset of common human diseases...
- The fundamental role of epigenetic events in cancerPeter A Jones
USC Norris Comprehensive Cancer Center, Department of Urology, Keck School of Medicine, University of Southern California, 1441 Eastlake Avenue, MS 8302L, Los Angeles, California 90089 9181, USA
Nat Rev Genet 3:415-28. 2002Patterns of DNA methylation and chromatin structure are profoundly altered in neoplasia and include genome-wide losses of, and regional gains in, DNA methylation...
- Conservation and divergence of methylation patterning in plants and animalsSuhua Feng
Howard Hughes Medical Institute, Department of Molecular, Cell and Developmental Biology, and Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
Proc Natl Acad Sci U S A 107:8689-94. 2010Cytosine DNA methylation is a heritable epigenetic mark present in many eukaryotic organisms...
- CpG islands--'a rough guide'Robert S Illingworth
Wellcome Trust Centre for Cell Biology, Michael Swann Building, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JR, United Kingdom
FEBS Lett 583:1713-20. 2009..CGIs generally lack DNA methylation and associate with the majority of annotated gene promoters...
- Epigenetics in human disease and prospects for epigenetic therapyGerda Egger
Department of Biochemistry and Molecular Biology, USC Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, 1441 Eastlake Avenue, Room 8302L, Los Angeles, California 90089 9181, USA
Nature 429:457-63. 2004....
- Specific activation of microRNA-127 with downregulation of the proto-oncogene BCL6 by chromatin-modifying drugs in human cancer cellsYoshimasa 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...
- Targets and dynamics of promoter DNA methylation during early mouse developmentJulie 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. 2010b>DNA methylation is extensively reprogrammed during the early phases of mammalian development, yet genomic targets of this process are largely unknown...
- The relationship of DNA methylation with age, gender and genotype in twins and healthy controlsMarco P Boks
Rudolf Magnus Institute of Neuroscience, Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands
PLoS ONE 4:e6767. 2009..In addition to influences of age and gender, genetic control of DNA methylation levels has recently been described...
- Quantitative comparison of genome-wide DNA methylation mapping technologiesChristoph Bock
Broad Institute, Cambridge, Massachusetts, USA
Nat Biotechnol 28:1106-14. 2010b>DNA methylation plays a key role in regulating eukaryotic gene expression...
- Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complexX Nan
Institute of Cell and Molecular Biology, University of Edinburgh, UK
Nature 393:386-9. 1998..The data suggest that two global mechanisms of gene regulation, DNA methylation and histone deacetylation, can be linked by MeCP2.
- DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNASteen K T Ooi
Department of Genetics and Development, College of Physicians and Surgeons of Columbia University, New York, New York 10032, USA
Nature 448:714-7. 2007Mammals use DNA methylation for the heritable silencing of retrotransposons and imprinted genes and for the inactivation of the X chromosome in females...
- Targeted and genome-scale strategies reveal gene-body methylation signatures in human cellsMadeleine P Ball
Department of Genetics, Harvard Medical School, Cambridge, MA, USA
Nat Biotechnol 27:361-8. 2009..Our observations highlight the usefulness of techniques that are not inherently or intentionally biased towards particular subsets like CpG islands or promoter regions...
- Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domainsVardhman K Rakyan
Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
Genome Res 20:434-9. 2010....
- Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modificationsR Alan Harris
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
Nat Biotechnol 28:1097-105. 2010Analysis of DNA methylation patterns relies increasingly on sequencing-based profiling methods...
- Comprehensive methylome map of lineage commitment from haematopoietic progenitorsHong Ji
Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, 570 Rangos, 725 N Wolfe St, Baltimore, Maryland 21205, USA
Nature 467:338-42. 2010..Although DNA methylation is critical for myeloid versus lymphoid differentiation, as demonstrated by the myeloerythroid bias in Dnmt1 ..
- L1 retrotransposition in neurons is modulated by MeCP2Alysson R Muotri
University of California San Diego, School of Medicine, Department of Pediatrics Rady Children s Hospital San Diego, La Jolla, California 92093 0695, USA
Nature 468:443-6. 2010..in rodents are increased in the absence of methyl-CpG-binding protein 2 (MeCP2), a protein involved in global DNA methylation and human neurodevelopmental diseases...
- A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in miceAlexei A Aravin
Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
Mol Cell 31:785-99. 2008..The Piwi pathway lies upstream of known mediators of DNA methylation, since piRNAs are still produced in dnmt3L mutants, which fail to methylate transposons...
- Rethinking how DNA methylation patterns are maintainedPeter A Jones
Peter A Jones and Gangning Liang are at the Department of Urology, Biochemistry and Molecular Biology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089 9181, USA
Nat Rev Genet 10:805-11. 2009b>DNA methylation patterns are set up early in mammalian development and are then copied during the division of somatic cells...
- DNA methylation profiles in monozygotic and dizygotic twinsZachary A Kaminsky
Centre for Addiction and Mental Health, Toronto, Ontario M5T 1R8, Canada
Nat Genet 41:240-5. 2009..As epigenetic factors can contribute to phenotypic outcomes, we conducted a DNA methylation analysis in white blood cells (WBC), buccal epithelial cells and gut biopsies of 114 monozygotic (MZ) twins ..
- Dietary protein restriction of pregnant rats induces and folic acid supplementation prevents epigenetic modification of hepatic gene expression in the offspringKaren A Lillycrop
Development and Cell Biology, University of Southampton, UK
J Nutr 135:1382-6. 2005..This suggests persistent alteration of gene transcription. DNA methylation, which is largely established in utero, provides a causal mechanism by which unbalanced prenatal nutrition ..
- CpG islands influence chromatin structure via the CpG-binding protein Cfp1John P Thomson
Wellcome Trust Centre for Cell Biology, Michael Swann Building, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JR, UK
Nature 464:1082-6. 2010..Most human gene promoters are embedded within CGIs that lack DNA methylation and coincide with sites of histone H3 lysine 4 trimethylation (H3K4me3), irrespective of transcriptional ..
- Cyclical DNA methylation of a transcriptionally active promoterRaphaël Métivier
Universite de Rennes I, CNRS, UMR 6026 Equipe SPARTE, IFR 140 GFAS, Campus de Beaulieu, 35042 Rennes Cedex, France
Nature 452:45-50. 2008..b>DNA methylation on CpGs constitutes an epigenetic mark generally correlated with transcriptionally silent condensed chromatin...
- In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like stateMarius Wernig
Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
Nature 448:318-24. 2007..Here we show that DNA methylation, gene expression and chromatin state of such induced reprogrammed stem cells are similar to those of ES cells...
- Molecular pathogenesis of human hepatocellular carcinomaSnorri S Thorgeirsson
Laboratory of Experimental Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
Nat Genet 31:339-46. 2002..New strategies should enable these variants to be characterized...
- Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylationKristi Kerkel
Institute for Cancer Genetics, Columbia University Medical Center, New York, New York 10032, USA
Nat Genet 40:904-8. 2008Allele-specific DNA methylation (ASM) is a hallmark of imprinted genes, but ASM in the larger nonimprinted fraction of the genome is less well characterized...
- The Dnmt3a PWWP domain reads histone 3 lysine 36 trimethylation and guides DNA methylationArunkumar Dhayalan
Biochemistry Laboratory, School of Engineering and Science, Jacobs University Bremen, Bremen, Germany
J Biol Chem 285:26114-20. 2010..H3K36me3 is known to be a repressive modification correlated with DNA methylation in mammals and heterochromatin in Schizosaccharomyces pombe...
- Chromatin methylation activity of Dnmt3a and Dnmt3a/3L is guided by interaction of the ADD domain with the histone H3 tailYingying Zhang
Biochemistry Laboratory, School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
Nucleic Acids Res 38:4246-53. 2010..To establish a functional role of the ADD domain binding to unmodified H3 tails, we analyzed the DNA methylation of in vitro reconstituted chromatin with Dnmt3a2, the Dnmt3a2/Dnmt3L complex, and the catalytic domain of ..
- Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogrammingJie Deng
Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
Nat Biotechnol 27:353-60. 2009Current DNA methylation assays are limited in the flexibility and efficiency of characterizing a large number of genomic targets...
- Reprogramming towards pluripotency requires AID-dependent DNA demethylationNidhi Bhutani
Baxter Laboratory for Stem Cell Biology, Institute for Stem Cell Biology and Regenerative Medicine, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305 5175, USA
Nature 463:1042-7. 2010..These data provide new evidence that mammalian AID is required for active DNA demethylation and initiation of nuclear reprogramming towards pluripotency in human somatic cells...
- Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancerAndrew E Teschendorff
University College London, London WC1E 6BT, UK
Genome Res 20:440-6. 2010..These findings shed substantial novel insights into the epigenetic effects of aging and support the view that age may predispose to malignant transformation by irreversibly stabilizing stem cell features...
- DNA methylation in aging, race and prostate cancerRajvir Dahiya; Fiscal Year: 2006..Specific hypotheses: 1) The DNA methylation status of most frequently deleted genes [ERs, E-cadherin, CD44 and GSTPI (glutathione S-transferase pi)] will ..
- Dietary Methyl Score, Genomic DNA Methylation and Colorectal CancerEunyoung Cho; Fiscal Year: 2009..cancer risk in large prospective studies and expect that individuals with reduced levels of genomic DNA methylation are at increased risk of colorectal cancer...
- Targeting aberrant epigenetics by nanomedicineShujun Liu; Fiscal Year: 2010..Inhibition of aberrant DNA methylation by decitabine or 5-azacitidine restores normal patterns of cell proliferation, differentiation and apoptosis, ..
- Dietary Methyl Score, Genomic DNA Methylation and Colorectal CancerEunyoung Cho; Fiscal Year: 2010..cancer risk in large prospective studies and expect that individuals with reduced levels of genomic DNA methylation are at increased risk of colorectal cancer...
- Regulated Accessibility of a cytokine gene locus.Anjana Rao; Fiscal Year: 2011..in activated as well as silenced cytokine genes, as judged by changes in DNase I hypersensitive (DH) sites, DNA methylation and histone modification;explored the transcriptional and chromatin-based programs underlying CD8 T cell ..
- Regulated Accessibility of a cytokine gene locus.Anjana Rao; Fiscal Year: 2010..in activated as well as silenced cytokine genes, as judged by changes in DNase I hypersensitive (DH) sites, DNA methylation and histone modification;explored the transcriptional and chromatin-based programs underlying CD8 T cell ..
- Regulation of Airway Mucin Gene Expression by Epigenetic MechanismReen Wu; Fiscal Year: 2010..Based on these results, we hypothesize that epigenetic changes, especially changes in DNA methylation status, is one of the major mechanisms involved in the persistence of mucin gene expression, especially ..
- Exploring the Role of the Brain Epigenome: Cognitive Decline and Life ExperiencesDavid Bennett; Fiscal Year: 2009..Building on our prior work, we propose to conduct epigenome-wide DNA methylation scans on brain tissue from participants in an Exploratory Cohort consisting of the Rush Memory and Aging ..
- Carcinogenesis of Nickel and Epigenetic ControlMax Costa; Fiscal Year: 2007..region of genes is one of the most important chromatin marks and is commonly associated with nucleosomal DNA methylation and gene silencing...
- Genome-scale anaylsis of DNA methylation in CpG Islands with bisulfite sequencingKun Zhang; Fiscal Year: 2009..b>DNA methylation is the most stable form of epigenetic modification that leads to transcriptional silencing, X chromosome ..
- Genome-scale anaylsis of DNA methylation in CpG Islands with bisulfite sequencingKUN contact ZHANG; Fiscal Year: 2010..b>DNA methylation is the most stable form of epigenetic modification that leads to transcriptional silencing, X chromosome ..
- Genome-scale anaylsis of DNA methylation in CpG Islands with bisulfite sequencingKun Zhang; Fiscal Year: 2009..b>DNA methylation is the most stable form of epigenetic modification that leads to transcriptional silencing, X chromosome ..
- DNA Methyltransferase Inhibition by Intercalating AgentsKEITH ROBERTSON; Fiscal Year: 2006..Epigenetic genome modifications, in particular DNA methylation, have now been recognized as major regulators of gene activity and genomic stability...
- DNA Methyltransferase Inhibition by Intercalating AgentsKEITH ROBERTSON; Fiscal Year: 2007..Epigenetic genome modifications, in particular DNA methylation, have now been recognized as major regulators of gene activity and genomic stability...
- DNA METHYLATION AND PILI GENE REGULATIONDavid Low; Fiscal Year: 2006..This work will serve as a paradigm to understand how DNA methylation patterns control heritable gene expression states...
- Epigenetic Effects of Particles and Metals on Cardiac Health of an Aging CohortJoel Schwartz; Fiscal Year: 2009..and humans have shown that air particles and metals, which are constituents of particulate pollution, alter DNA methylation status...
- Epigenetic Effects of Particles and Metals on Cardiac Health of an Aging CohortJoel Schwartz; Fiscal Year: 2007..and humans have shown that air particles and metals, which are constituents of particulate pollution, alter DNA methylation status...
- Molecular Mechanisms of GSTP1 Reactivation by Green Tea PolyphenolsSanjay Gupta; Fiscal Year: 2007Aberrant DNA methylation and chromatin remodeling are common epigenetic changes that play critical role in gene silencing; implicated in the development and progression of prostate cancer...
- Molecular Mechanisms of GSTP1 Reactivation by Green Tea PolyphenolsSanjay Gupta; Fiscal Year: 2009Aberrant DNA methylation and chromatin remodeling are common epigenetic changes that play critical role in gene silencing; implicated in the development and progression of prostate cancer...
- CPG METHYLATION AND MUTATIONGerd P Pfeifer; Fiscal Year: 2010..This application will focus on mechanistic studies that will investigate the molecular pathways leading to DNA methylation changes in tumors with emphasis on DNA hypermethylation...
- DNA Methyltransferase Inhibition by Intercalating AgentsKeith D Robertson; Fiscal Year: 2010..Epigenetic genome modifications, in particular DNA methylation, have now been recognized as major regulators of gene activity and genomic stability...
- Regulation of Genomic and Epigenomic Stability at CpG SitesAlfonso Bellacosa; Fiscal Year: 2010..b>DNA methylation is an important epigenetic modification of the mammalian genome consisting in the formation of 5-..
- Genome Wide Analysis of DNA MethylationJoseph Ecker; Fiscal Year: 2006This proposal aims to identify functional, non-coding elements in eukaryotic genomes by surveying genome-wide DNA methylation. Cytosine DNA methylation controls developmental gene expression in mammals during genomic imprinting and X-..
- DNA Methylation Profiles in a Polygenic Mouse Model of Diet-Induced ObesityJan Bressler; Fiscal Year: 2007..It is the long-term goal of this proposal to evaluate whether modifications in DNA methylation patterns that may result in either activation or silencing of genes can be detected when comparing obese and ..
- Epigenetic regulation of HIV latencyERIC M VERDIN; Fiscal Year: 2010..We have recently reported that DNA methylation of the HIV promoter plays an important role in the establishment and maintenance of HIV latency...
- Genome-wide DNA Methylation Profiles Associated with Abnormal Intrauterine GrowthFrancine Einstein; Fiscal Year: 2009..We offer a novel hypothesis that conditions during fetal development alter epigenetic patterns of DNA methylation in non-embryonic stem cells, which may be a marker for, or contribute to, susceptibility to T2DM and other ..
- Genome-wide DNA Methylation Profiles Associated with Abnormal Intrauterine GrowthCristina Montagna; Fiscal Year: 2010..We offer a novel hypothesis that conditions during fetal development alter epigenetic patterns of DNA methylation in non-embryonic stem cells, which may be a marker for, or contribute to, susceptibility to T2DM and other ..
- GENETIC ASPECTS OF DNA METHYLATIONERIC SELKER; Fiscal Year: 1993..a link has been demonstrated between methylation and inactivity of DNA, the function and mechanism of DNA methylation remains unclear...
- The Role of DNMT3B in the DNA Methylation of Cancer CellsLUCY ANN GODLEY; Fiscal Year: 2010Epigenetic changes, such as DNA methylation and histone modifications, alter chromatin structure and regulate gene transcription...
- Epigenetic Regulation of MMP-13MARY GOLDRING; Fiscal Year: 2007..is not only controlled by transcriptional activators and repressors, but also depends on the epigenetic DNA methylation of the promoter, which is the mechanism whereby genes that are never expressed by a somatic cell are ..
- GENETIC ASPECTS OF DNA METHYLATIONERIC SELKER; Fiscal Year: 2007b>DNA methylation is required for normal development of higher eukaryotes. Methylation is required for X-inactivation and genomic imprinting in mammals, and abnormal methylation is associated with cancer...
- Epigenetic Mechanisms of Memory StorageEDWIN TED G ABEL; Fiscal Year: 2010Epigenetic modifications such as histone acetylation and DNA methylation are critical for the long-lasting regulation of gene expression during development and may be a major mechanism of information storage in the brain...
- De Novo Methyltransferase Function in Chromatin and CancerKeith D Robertson; Fiscal Year: 2010b>DNA methylation is an essential regulator of transcription, chromatin structure, development, and genomic stability in mammalian cells that is mediated by a family of DNA methyltransferases (DNMTs): DNMT1, DNMT3A, and DNMT3B...
- ROLE OF DNA METHYLTRANSFERASE 3B IN LUNG TUMORIGENESISLi Mao; Fiscal Year: 2009..Epigenetic alterations, particularly aberrant DNA methylation, play as important a role as genetic alterations in lung tumorigenesis...
- DNA Methylation and Ovarian CancerKenneth P Nephew; Fiscal Year: 2010..During the initial funding period, we demonstrated that increased DNA methylation and alterations in histone methylation are strongly associated with ovarian cancer chemoresistance...
- DNA Methylation and Ovarian CancerKenneth Nephew; Fiscal Year: 2009..During the initial funding period, we demonstrated that increased DNA methylation and alterations in histone methylation are strongly associated with ovarian cancer chemoresistance...
- DNA METHYLOME STUDY IN TYPE 1 DIABETESART PETRONIS; Fiscal Year: 2009..More specifically, we will investigate DNA methylation, which is one of the key epigenetic mechanisms...
- RNAi and DNA Methylation Control Genomic Stability and Transcriptional SilencingJohn Frazer; Fiscal Year: 2007..RNA Interference (RNAi) and DNA methylation are two chromatin-modifying activities that regulate eukaryotic genomes...
- Epigenetics Landscape of Chronic Kidney DiseaseKatalin Susztak; Fiscal Year: 2009..We propose to use the HELP assay to determine DNA methylation patterns of microdissected glomerular and tubulointerstitial samples. 2...