Published in Proc Natl Acad Sci U S A on August 27, 2008
Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet (2012) 15.21
Linking DNA methylation and histone modification: patterns and paradigms. Nat Rev Genet (2009) 12.08
A decade of exploring the cancer epigenome - biological and translational implications. Nat Rev Cancer (2011) 11.33
Principles and challenges of genomewide DNA methylation analysis. Nat Rev Genet (2010) 10.71
Epigenetics in cancer. Carcinogenesis (2009) 7.49
Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains. Nat Genet (2011) 5.70
Genome-scale analysis of aberrant DNA methylation in colorectal cancer. Genome Res (2011) 4.84
Dnmt3a-dependent nonpromoter DNA methylation facilitates transcription of neurogenic genes. Science (2010) 4.60
Developmental programming of CpG island methylation profiles in the human genome. Nat Struct Mol Biol (2009) 3.96
Functional enhancers at the gene-poor 8q24 cancer-linked locus. PLoS Genet (2009) 3.59
DZNep is a global histone methylation inhibitor that reactivates developmental genes not silenced by DNA methylation. Mol Cancer Ther (2009) 3.56
Mutation of A677 in histone methyltransferase EZH2 in human B-cell lymphoma promotes hypertrimethylation of histone H3 on lysine 27 (H3K27). Proc Natl Acad Sci U S A (2012) 3.22
Epigenetic modifications as therapeutic targets. Nat Biotechnol (2010) 3.16
Interplay between the cancer genome and epigenome. Cell (2013) 3.05
DNA methylation dynamics in health and disease. Nat Struct Mol Biol (2013) 2.58
Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk. Genome Res (2012) 2.49
DNA methylation screening identifies driver epigenetic events of cancer cell survival. Cancer Cell (2012) 2.45
Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity. Nat Cell Biol (2010) 2.38
EMT and stem cell-like properties associated with miR-205 and miR-200 epigenetic silencing are early manifestations during carcinogen-induced transformation of human lung epithelial cells. Cancer Res (2011) 2.32
Cancer DNA methylation: molecular mechanisms and clinical implications. Clin Cancer Res (2009) 2.31
Gene body methylation can alter gene expression and is a therapeutic target in cancer. Cancer Cell (2014) 2.28
Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues. Nat Genet (2012) 2.20
Polycomb-repressed genes have permissive enhancers that initiate reprogramming. Cell (2011) 2.14
EZH2-mediated epigenetic silencing in germinal center B cells contributes to proliferation and lymphomagenesis. Blood (2010) 2.11
A DNA hypermethylation module for the stem/progenitor cell signature of cancer. Genome Res (2012) 1.92
DNA methylation directly silences genes with non-CpG island promoters and establishes a nucleosome occupied promoter. Hum Mol Genet (2011) 1.83
Curcumin analogue CDF inhibits pancreatic tumor growth by switching on suppressor microRNAs and attenuating EZH2 expression. Cancer Res (2011) 1.80
Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA. Genome Res (2012) 1.78
Characterization of the cartilage DNA methylome in knee and hip osteoarthritis. Arthritis Rheumatol (2014) 1.77
Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation. Genome Res (2010) 1.77
DNA methylation and cellular reprogramming. Trends Cell Biol (2010) 1.77
DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes. Genome Biol (2013) 1.71
PDGFR blockade is a rational and effective therapy for NPM-ALK-driven lymphomas. Nat Med (2012) 1.67
A heterozygous IDH1R132H/WT mutation induces genome-wide alterations in DNA methylation. Genome Res (2012) 1.63
Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer. Genome Res (2014) 1.63
Targeting DNA methylation for epigenetic therapy. Trends Pharmacol Sci (2010) 1.61
Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia. Genome Biol (2013) 1.57
CpG island hypermethylation in human astrocytomas. Cancer Res (2010) 1.57
Genome-wide profiling of histone h3 lysine 4 and lysine 27 trimethylation reveals an epigenetic signature in prostate carcinogenesis. PLoS One (2009) 1.54
CDKN1C (p57) is a direct target of EZH2 and suppressed by multiple epigenetic mechanisms in breast cancer cells. PLoS One (2009) 1.52
Tet1 and 5-hydroxymethylation: a genome-wide view in mouse embryonic stem cells. Cell Cycle (2011) 1.51
A blueprint for engineering cell fate: current technologies to reprogram cell identity. Cell Res (2013) 1.50
Relationship between gene body DNA methylation and intragenic H3K9me3 and H3K36me3 chromatin marks. PLoS One (2011) 1.50
Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb target genes. Genome Biol (2013) 1.47
Unique DNA methylation patterns distinguish noninvasive and invasive urothelial cancers and establish an epigenetic field defect in premalignant tissue. Cancer Res (2010) 1.47
DNA methylation reprogramming in cancer: does it act by re-configuring the binding landscape of Polycomb repressive complexes? Bioessays (2013) 1.45
DNA methylation: superior or subordinate in the epigenetic hierarchy? Genes Cancer (2011) 1.45
Intragenic DNA methylation: implications of this epigenetic mechanism for cancer research. Br J Cancer (2011) 1.44
Dynamic and static maintenance of epigenetic memory in pluripotent and somatic cells. Nature (2014) 1.34
Differences in DNA methylation signatures reveal multiple pathways of progression from adenoma to colorectal cancer. Gastroenterology (2014) 1.32
DNMT1 and DNMT3B modulate distinct polycomb-mediated histone modifications in colon cancer. Cancer Res (2009) 1.26
Coordinate regulation of DNA methylation and H3K27me3 in mouse embryonic stem cells. PLoS One (2013) 1.24
Gestational choline supply regulates methylation of histone H3, expression of histone methyltransferases G9a (Kmt1c) and Suv39h1 (Kmt1a), and DNA methylation of their genes in rat fetal liver and brain. J Biol Chem (2008) 1.21
Offspring of mothers fed a high fat diet display hepatic cell cycle inhibition and associated changes in gene expression and DNA methylation. PLoS One (2011) 1.19
miRNA gene promoters are frequent targets of aberrant DNA methylation in human breast cancer. PLoS One (2013) 1.17
DNA hypermethylation accompanied by transcriptional repression in follicular lymphoma. Genes Chromosomes Cancer (2009) 1.16
Epigenetic cross-talk between DNA methylation and histone modifications in human cancers. Yonsei Med J (2009) 1.15
Aging and DNA methylation. BMC Biol (2015) 1.15
Epigenetic silencing mediated through activated PI3K/AKT signaling in breast cancer. Cancer Res (2011) 1.13
Genomic insights into cancer-associated aberrant CpG island hypermethylation. Brief Funct Genomics (2013) 1.11
Global profiling of histone and DNA methylation reveals epigenetic-based regulation of gene expression during epithelial to mesenchymal transition in prostate cells. BMC Genomics (2010) 1.10
Functional DNA demethylation is accompanied by chromatin accessibility. Nucleic Acids Res (2013) 1.09
Genome-wide age-related DNA methylation changes in blood and other tissues relate to histone modification, expression and cancer. Carcinogenesis (2013) 1.08
Epigenetic mediated transcriptional activation of WNT5A participates in arsenical-associated malignant transformation. Toxicol Appl Pharmacol (2008) 1.08
Genome-wide DNA methylation maps in follicular lymphoma cells determined by methylation-enriched bisulfite sequencing. PLoS One (2010) 1.06
Epigenetic and transcriptional changes which follow Epstein-Barr virus infection of germinal center B cells and their relevance to the pathogenesis of Hodgkin's lymphoma. J Virol (2011) 1.04
Epigenetic regulation of EMT: the Snail story. Curr Pharm Des (2014) 1.02
SINE retrotransposons cause epigenetic reprogramming of adjacent gene promoters. Mol Cancer Res (2012) 1.01
DNA methylation programming and reprogramming in primate embryonic stem cells. Genome Res (2009) 0.99
Methods for genome-wide analysis of DNA methylation in intestinal tumors. Mutat Res (2009) 0.99
Chromatin remodeling in mammary gland differentiation and breast tumorigenesis. Cold Spring Harb Perspect Biol (2010) 0.98
Combinatorial pharmacologic approaches target EZH2-mediated gene repression in breast cancer cells. Mol Cancer Ther (2009) 0.98
Epigenetic activation of SOX11 in lymphoid neoplasms by histone modifications. PLoS One (2011) 0.98
Boosting Wnt activity during colorectal cancer progression through selective hypermethylation of Wnt signaling antagonists. BMC Cancer (2014) 0.98
Dissecting DNA hypermethylation in cancer. FEBS Lett (2010) 0.98
Epigenomic alterations in localized and advanced prostate cancer. Neoplasia (2013) 0.96
De novo DNA methylation in the male germ line occurs by default but is excluded at sites of H3K4 methylation. Cell Rep (2013) 0.95
Absence of Runx3 expression in normal gastrointestinal epithelium calls into question its tumour suppressor function. EMBO Mol Med (2011) 0.95
Diametrically opposite methylome-transcriptome relationships in high- and low-CpG promoter genes in postmitotic neural rat tissue. Epigenetics (2012) 0.95
The role of DNA methylation in directing the functional organization of the cancer epigenome. Genome Res (2015) 0.94
The tumor suppressor microRNA-101 becomes an epigenetic player by targeting the polycomb group protein EZH2 in cancer. Cell Cycle (2009) 0.94
Heterogeneous epigenetic regulation of TIMP3 in prostate cancer. Epigenetics (2012) 0.94
Epigenomics of cancer - emerging new concepts. Biochimie (2012) 0.90
H3K4me3 inversely correlates with DNA methylation at a large class of non-CpG-island-containing start sites. Genome Med (2012) 0.90
Extracellular RNA mediates and marks cancer progression. Semin Cancer Biol (2014) 0.90
DNA methylation in the malignant transformation of meningiomas. PLoS One (2013) 0.90
Molecular marks for epigenetic identification of developmental and cancer stem cells. Clin Epigenetics (2010) 0.89
Identification of DNA methylation changes associated with human gastric cancer. BMC Med Genomics (2011) 0.89
Assessing the efficiency and significance of Methylated DNA Immunoprecipitation (MeDIP) assays in using in vitro methylated genomic DNA. BMC Res Notes (2010) 0.88
Parental epigenetic asymmetry of PRC2-mediated histone modifications in the Arabidopsis endosperm. EMBO J (2016) 0.87
Diffuse large B-cell lymphoma with combined TP53 mutation and MIR34A methylation: Another "double hit" lymphoma with very poor outcome? Oncotarget (2014) 0.87
Synergistic chromatin repression of the tumor suppressor gene RARB in human prostate cancers. Epigenetics (2014) 0.87
Epigenetics in Friedreich's Ataxia: Challenges and Opportunities for Therapy. Genet Res Int (2013) 0.87
Mutant WT1 is associated with DNA hypermethylation of PRC2 targets in AML and responds to EZH2 inhibition. Blood (2014) 0.87
Cancer associated epigenetic transitions identified by genome-wide histone methylation binding profiles in human colorectal cancer samples and paired normal mucosa. BMC Cancer (2011) 0.87
The 3D tissue microenvironment modulates DNA methylation and E-cadherin expression in squamous cell carcinoma. Epigenetics (2012) 0.86
Interrogating genomic and epigenomic data to understand prostate cancer. Biochim Biophys Acta (2012) 0.85
EZH2 in Bladder Cancer, a Promising Therapeutic Target. Int J Mol Sci (2015) 0.85
Epigenetic dysregulation in glioma. Cancer Sci (2014) 0.85
Treatment of breast cancer cells with DNA demethylating agents leads to a release of Pol II stalling at genes with DNA-hypermethylated regions upstream of TSS. Nucleic Acids Res (2011) 0.84
High-resolution profiling of histone methylations in the human genome. Cell (2007) 85.74
The epigenomics of cancer. Cell (2007) 30.91
Control of developmental regulators by Polycomb in human embryonic stem cells. Cell (2006) 28.21
A chromatin landmark and transcription initiation at most promoters in human cells. Cell (2007) 23.41
Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet (2007) 20.22
The mammalian epigenome. Cell (2007) 18.13
Dissecting direct reprogramming through integrative genomic analysis. Nature (2008) 16.47
Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet (2005) 15.37
Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions. Genes Dev (2006) 14.36
The Polycomb group protein EZH2 directly controls DNA methylation. Nature (2005) 13.67
Polycomb silencers control cell fate, development and cancer. Nat Rev Cancer (2006) 11.48
Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nat Genet (2006) 10.47
Epigenetic stem cell signature in cancer. Nat Genet (2006) 9.62
A stem cell-like chromatin pattern may predispose tumor suppressor genes to DNA hypermethylation and heritable silencing. Nat Genet (2007) 9.47
Gene expression alterations in prostate cancer predicting tumor aggression and preceding development of malignancy. J Clin Oncol (2004) 6.99
Suz12 binds to silenced regions of the genome in a cell-type-specific manner. Genome Res (2006) 6.75
Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation. Cell Stem Cell (2008) 5.40
Gene silencing in cancer by histone H3 lysine 27 trimethylation independent of promoter DNA methylation. Nat Genet (2008) 5.08
Evidence for an instructive mechanism of de novo methylation in cancer cells. Nat Genet (2006) 4.97
Hyperconserved CpG domains underlie Polycomb-binding sites. Proc Natl Acad Sci U S A (2007) 2.41
DNA methylation and complete transcriptional silencing of cancer genes persist after depletion of EZH2. Cancer Res (2007) 1.96
Global and gene-specific epigenetic patterns in human bladder cancer genomes are relatively stable in vivo and in vitro over time. Cancer Res (2001) 1.19
Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature (2009) 24.41
Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc Natl Acad Sci U S A (2002) 12.33
Epigenetics in human disease and prospects for epigenetic therapy. Nature (2004) 11.46
A decade of exploring the cancer epigenome - biological and translational implications. Nat Rev Cancer (2011) 11.33
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78
Three-dimensional folding and functional organization principles of the Drosophila genome. Cell (2012) 9.19
Specific activation of microRNA-127 with downregulation of the proto-oncogene BCL6 by chromatin-modifying drugs in human cancer cells. Cancer Cell (2006) 8.46
Epigenetics in cancer. Carcinogenesis (2009) 7.49
Model-based analysis of two-color arrays (MA2C). Genome Biol (2007) 7.28
The CREB coactivator TORC2 is a key regulator of fasting glucose metabolism. Nature (2005) 7.14
Epigenetic therapy of cancer: past, present and future. Nat Rev Drug Discov (2006) 6.39
Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nat Genet (2011) 5.97
Quantification of protein half-lives in the budding yeast proteome. Proc Natl Acad Sci U S A (2006) 5.62
Chromatin structure analyses identify miRNA promoters. Genes Dev (2008) 5.40
Deterministic direct reprogramming of somatic cells to pluripotency. Nature (2013) 5.18
Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science (2014) 4.91
Cancer epigenetics: modifications, screening, and therapy. Annu Rev Med (2008) 4.41
Distinct localization of histone H3 acetylation and H3-K4 methylation to the transcription start sites in the human genome. Proc Natl Acad Sci U S A (2004) 4.39
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res (2008) 4.08
Rethinking how DNA methylation patterns are maintained. Nat Rev Genet (2009) 4.03
Candidate exome capture identifies mutation of SDCCAG8 as the cause of a retinal-renal ciliopathy. Nat Genet (2010) 3.99
Demethylation of a hypermethylated P15/INK4B gene in patients with myelodysplastic syndrome by 5-Aza-2'-deoxycytidine (decitabine) treatment. Blood (2002) 3.89
A global view of pleiotropy and phenotypically derived gene function in yeast. Mol Syst Biol (2005) 3.70
Cancer genetics and epigenetics: two sides of the same coin? Cancer Cell (2012) 3.65
Cooperativity between DNA methyltransferases in the maintenance methylation of repetitive elements. Mol Cell Biol (2002) 3.61
Functional enhancers at the gene-poor 8q24 cancer-linked locus. PLoS Genet (2009) 3.59
DZNep is a global histone methylation inhibitor that reactivates developmental genes not silenced by DNA methylation. Mol Cancer Ther (2009) 3.56
EXPANDER--an integrative program suite for microarray data analysis. BMC Bioinformatics (2005) 3.43
The CpG island searcher: a new WWW resource. In Silico Biol (2003) 3.42
Functional anatomy of polycomb and trithorax chromatin landscapes in Drosophila embryos. PLoS Biol (2009) 3.24
BLUEPRINT to decode the epigenetic signature written in blood. Nat Biotechnol (2012) 3.24
Association of breast cancer DNA methylation profiles with hormone receptor status and response to tamoxifen. Cancer Res (2004) 3.23
Epigenetic modifications as therapeutic targets. Nat Biotechnol (2010) 3.16
Role of nucleosomal occupancy in the epigenetic silencing of the MLH1 CpG island. Cancer Cell (2007) 3.15
X chromosome repression by localization of the C. elegans dosage compensation machinery to sites of transcription initiation. Nat Genet (2007) 3.14
DNA methylation and breast carcinogenesis. Oncogene (2002) 3.03
Histone H3-lysine 9 methylation is associated with aberrant gene silencing in cancer cells and is rapidly reversed by 5-aza-2'-deoxycytidine. Cancer Res (2002) 3.02
DNA methylation: the nuts and bolts of repression. J Cell Physiol (2007) 3.00
Homeobox gene methylation in lung cancer studied by genome-wide analysis with a microarray-based methylated CpG island recovery assay. Proc Natl Acad Sci U S A (2007) 2.91
The putative tumor suppressor microRNA-101 modulates the cancer epigenome by repressing the polycomb group protein EZH2. Cancer Res (2009) 2.83
The IRE1alpha-XBP1 pathway of the unfolded protein response is required for adipogenesis. Cell Metab (2009) 2.52
Epigenetics and microRNAs. Pediatr Res (2007) 2.52
Cohesin-mediated interactions organize chromosomal domain architecture. EMBO J (2013) 2.48
Exome sequencing of a multigenerational human pedigree. PLoS One (2009) 2.48
DNA methylation screening identifies driver epigenetic events of cancer cell survival. Cancer Cell (2012) 2.45
Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nat Methods (2012) 2.42
Preferential response of cancer cells to zebularine. Cancer Cell (2004) 2.39
A micro-RNA signature associated with race, tumor size, and target gene activity in human uterine leiomyomas. Genes Chromosomes Cancer (2007) 2.35
Selective anchoring of DNA methyltransferases 3A and 3B to nucleosomes containing methylated DNA. Mol Cell Biol (2009) 2.34
Impairment of hepatic growth hormone and glucocorticoid receptor signaling causes steatosis and hepatocellular carcinoma in mice. Hepatology (2011) 2.33
Negative and positive regulation of gene expression by mouse histone deacetylase 1. Mol Cell Biol (2006) 2.28
Genome-scale ChIP-chip analysis using 10,000 human cells. Biotechniques (2007) 2.28
Hypomethylation of a LINE-1 promoter activates an alternate transcript of the MET oncogene in bladders with cancer. PLoS Genet (2010) 2.27
Identification of DNMT1 (DNA methyltransferase 1) hypomorphs in somatic knockouts suggests an essential role for DNMT1 in cell survival. Proc Natl Acad Sci U S A (2006) 2.25
Inhibition of DNA methylation and reactivation of silenced genes by zebularine. J Natl Cancer Inst (2003) 2.22
Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues. Nat Genet (2012) 2.20
Polycomb-repressed genes have permissive enhancers that initiate reprogramming. Cell (2011) 2.14
The genomic distribution and function of histone variant HTZ-1 during C. elegans embryogenesis. PLoS Genet (2008) 2.14
p53 gene and protein status: the role of p53 alterations in predicting outcome in patients with bladder cancer. J Clin Oncol (2007) 2.14
Statistical reliability of bone biopsy for the diagnosis of diabetic foot osteomyelitis. J Foot Ankle Surg (2011) 2.12
Expander: from expression microarrays to networks and functions. Nat Protoc (2010) 2.12
High STAT5 levels mediate imatinib resistance and indicate disease progression in chronic myeloid leukemia. Blood (2011) 2.08
Cooperative interactions between CBP and TORC2 confer selectivity to CREB target gene expression. EMBO J (2007) 2.07
Long-term epigenetic therapy with oral zebularine has minimal side effects and prevents intestinal tumors in mice. Cancer Prev Res (Phila) (2008) 2.04
Epigenetic activation of tumor suppressor microRNAs in human cancer cells. Cell Cycle (2006) 1.98
Epigenetic changes in cancer. APMIS (2007) 1.96
Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules. Genome Res (2012) 1.95
Footprinting of mammalian promoters: use of a CpG DNA methyltransferase revealing nucleosome positions at a single molecule level. Nucleic Acids Res (2005) 1.94
H2A.Z maintenance during mitosis reveals nucleosome shifting on mitotically silenced genes. Mol Cell (2010) 1.85
Comparison of biological effects of non-nucleoside DNA methylation inhibitors versus 5-aza-2'-deoxycytidine. Mol Cancer Ther (2005) 1.85
Primate CpG islands are maintained by heterogeneous evolutionary regimes involving minimal selection. Cell (2011) 1.84
DNA methylation directly silences genes with non-CpG island promoters and establishes a nucleosome occupied promoter. Hum Mol Genet (2011) 1.83
High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers. Nucleic Acids Res (2009) 1.80