Effects of DNA methylation on DNA-binding proteins and gene expression

Targeted mutation of the DNA methyltransferase gene results in embryonic lethality

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A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands

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Purification, sequence, and cellular localization of a novel chromosomal protein that binds to Methylated DNA

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Temporal and regional changes in DNA methylation in the embryonic, extraembryonic and germ cell lineages during mouse embryo development

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The essentials of DNA methylation

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CpG islands as gene markers in the human genome

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DNA methylation and gene activity

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Developmental pattern of gene-specific DNA methylation in the mouse embryo and germ line.Preprint

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DNA methylation inhibits transcription indirectly via a methyl-CpG binding protein

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Identification of a mammalian protein that binds specifically to DNA containing methylated CpGs

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Epigenetic regulation in hematopoiesis and its implications in the targeted therapy of hematologic malignancies

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Roles of Cell Division and Gene Transcription in the Methylation of CpG Islands

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DNA methylation and the expanding epigenetics of T cell lineage commitment

Wilson, C. B., Makar, K. W., Shnyreva, M., & Fitzpatrick, D. R. (2005) · Seminars in Immunology · doi:10.1016/j.smim.2005.01.005 · Cited by 142

Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation

Nam, A. S., Dusaj, N., Izzo, F., Murali, R., Myers, R. M., Mouhieddine, T. H., Sotelo, J., Benbarche, S., Waarts, M., Gaiti, F., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01179-9 · Cited by 140

Correlation between insulin-like growth factor-binding protein-3 promoter methylation and prognosis of patients with stage I non-small cell lung cancer.

Chang, Y. S., Wang, L., Liu, D., Mao, L., Hong, W. K., Khuri, F. R., & Lee, H. (2002) · PubMed · Cited by 136

Rett syndrome: a surprising result of mutation in MECP2

Dragich, J. M. (2000) · Human Molecular Genetics · doi:10.1093/hmg/9.16.2365 · Cited by 136

RFX1, a Transactivator of Hepatitis B Virus Enhancer I, Belongs to a Novel Family of Homodimeric and Heterodimeric DNA-Binding Proteins

Reith, W., Ucla, C., Barras, E., Gaud, A., Durand, B., Sanchez, C. H., Kobr, M., & Mach, B. (1994) · Molecular and Cellular Biology · doi:10.1128/mcb.14.2.1230 · Cited by 139

Site-specific DNA methylation in the neurofibromatosis (NF1) promoter interferes with binding of CREB and SP1 transcription factors

Mancini, D. N., Singh, S. M., Archer, T., & Rodenhiser, D. I. (1999) · Oncogene · doi:10.1038/sj.onc.1202764 · Cited by 133

Placental FKBP5 Genetic and Epigenetic Variation Is Associated with Infant Neurobehavioral Outcomes in the RICHS Cohort

Paquette, A. G., Lester, B. M., Koestler, D. C., Lesseur, C., Armstrong, D. A., & Marsit, C. J. (2014) · PLoS ONE · doi:10.1371/journal.pone.0104913 · Cited by 135

Promoter hypomethylation of a novel cancer/testis antigen gene CAGE is correlated with its aberrant expression and is seen in premalignant stage of gastric carcinoma

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5-Methylcytosine DNA Demethylation: More Than Losing a Methyl Group

Franchini, D., Schmitz, K.-M., & Petersen‐Mahrt, S. K. (2012) · Annual Review of Genetics · doi:10.1146/annurev-genet-110711-155451 · Cited by 133

Oxidative stress induces DNA demethylation and histone acetylation in SH-SY5Y cells: potential epigenetic mechanisms in gene transcription in Aβ production

Gu, X., Sun, J., Li, S., Wu, X., & Li, L. (2012) · Neurobiology of Aging · doi:10.1016/j.neurobiolaging.2012.10.013 · Cited by 132

Epigenetic regulation of the expression of genes involved in steroid hormone biosynthesis and action

Martinez-Arguelles, D. B., & Papadopoulos, V. (2010) · Steroids · doi:10.1016/j.steroids.2010.02.004 · Cited by 130

Lymphocyte activation by CpG dinucleotide motifs in prokaryotic DNA

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Effects of DNA Methylation on the Structure of Nucleosomes

Lee, J. Y., & Lee, T.-H. (2011) · Journal of the American Chemical Society · doi:10.1021/ja210273w · Cited by 134

Curcumin Chemosensitizes 5-Fluorouracil Resistant MMR-Deficient Human Colon Cancer Cells in High Density Cultures

Shakibaei, M., Buhrmann, C., Kraehe, P., Shayan, P., Lueders, C., & Goel, A. (2014) · PLoS ONE · doi:10.1371/journal.pone.0085397 · Cited by 125

Transcriptional Activation of the Epstein-Barr Virus Latency C Promoter after 5-Azacytidine Treatment: Evidence that Demethylation at a Single CpG Site Is Crucial

Robertson, K. D., Hayward, S. D., Ling, P. D., Samid, D., & Ambinder, R. F. (1995) · Molecular and Cellular Biology · doi:10.1128/mcb.15.11.6150 · Cited by 125

Characterization of cytosine methylated regions and 5-cytosine DNA methyltransferase (Ehmeth) in the protozoan parasite Entamoeba histolytica

Fisher, O. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh161 · Cited by 124

Epigenetic silencing mediated by CpG island methylation: potential as a therapeutic target and as a biomarker

Teodoridis, J. M., Strathdee, G. R., & Brown, R. E. (2004) · Drug Resistance Updates · doi:10.1016/j.drup.2004.06.005 · Cited by 124

Homocysteine and Hypomethylation A Novel Link to Vascular Disease

Lee, M.-E. (1999) · Trends in Cardiovascular Medicine · doi:10.1016/s1050-1738(99)00002-x · Cited by 123

Gene Silencing by Methyl‐CPG‐Binding Proteins

Nan, X., Cross, S. H., & Bird, A. P. (2007) · Novartis Foundation symposium · doi:10.1002/9780470515501.ch2 · Cited by 127

DNA Methylation Readers and Cancer: Mechanistic and Therapeutic Applications

Mahmood, N., & Rabbani, S. A. (2019) · Frontiers in Oncology · doi:10.3389/fonc.2019.00489 · Cited by 129

The Arabidopsis active demethylase ROS1 cis-regulates defence genes by erasing DNA methylation at promoter-regulatory regions

Halter, T., Wang, J., Amesefe, D., Lastrucci, E., Charvin, M., Singla‐Rastogi, M., & Navarro, L. (2021) · eLife · doi:10.7554/elife.62994 · Cited by 115

Epigenetic effects of glucocorticoids

Weaver, I. C. G. (2009) · Seminars in Fetal and Neonatal Medicine · doi:10.1016/j.siny.2008.12.002 · Cited by 123

DNA methylation patterns in lung carcinomas

Pfeifer, G. P., & Rauch, T. A. (2009) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2009.02.008 · Cited by 124

Shaping adult phenotypes through early life environments

Weaver, I. C. G. (2009) · Birth Defects Research Part C Embryo Today Reviews · doi:10.1002/bdrc.20164 · Cited by 121

CpG Island of Rat Sphingosine Kinase-1 Gene: Tissue-Dependent DNA Methylation Status and Multiple Alternative First Exons

Imamura, T., Ohgane, J., Ito, S., Ogawa, T., Hattori, N., Tanaka, S., & Shiota, K. (2001) · Genomics · doi:10.1006/geno.2001.6607 · Cited by 117

Mammalian hibernation: differential gene expression and novel application of epigenetic controls

Morin, P., & Storey, K. B. (2009) · The International Journal of Developmental Biology · doi:10.1387/ijdb.082643pm · Cited by 116

cAMP response element‐binding (CREB) recruitment following a specific CpG demethylation leads to the elevated expression of the matrix metalloproteinase 13 in human articular chondrocytes and osteoarthritis

Bui, C., Barter, M. J., Scott, J. L., Xu, Y., Galler, M., Reynard, L. N., Rowan, A. D., & Young, D. A. (2012) · The FASEB Journal · doi:10.1096/fj.12-206367 · Cited by 114

Transcriptional Regulation of the Genes Encoding the Cytochrome P-450 Steroid Hydroxylases

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Hypomethylation of the interferon‐γ gene correlates with its expression by primary T‐lineage cells

Melvin, A. J., McGurn, M. E., Bort, S. J., Gibson, C., & Lewis, D. B. (1995) · European Journal of Immunology · doi:10.1002/eji.1830250218 · Cited by 110

Regulation ofKEAP1expression by promoter methylation in malignant gliomas and association with patient’s outcome

Muscarella, L. A., Barbano, R., D’Angelo, V., Copetti, M., Coco, M., Balsamo, T., la Torre, A., Notarangelo, A., Troiano, M., Parisi, S., et al. (2011) · Epigenetics · doi:10.4161/epi.6.3.14408 · Cited by 108

Genomic structure and chromosomal mapping of the murine and human Mbd1, Mbd2, Mbd3, and Mbd4 genes

Hendrich, B., Abbott, C. M., McQueen, H. A., Chambers, D. M., Cross, S. H., & Bird, A. P. (1999) · Mammalian Genome · doi:10.1007/s003359901112 · Cited by 110

Review

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Detection of multiple gene hypermethylation in the development of esophageal squamous cell carcinoma

Nie, Y. (2002) · Carcinogenesis · doi:10.1093/carcin/23.10.1713 · Cited by 106

Epigenetic regulation of miR‐196b expression in gastric cancer

Tsai, K., Hu, L., Wu, C., Li, S., Lai, C., Kao, H., Fang, W., & Lin, W. (2010) · Genes, Chromosomes and Cancer · doi:10.1002/gcc.20804 · Cited by 88

Overview of Cancer Epigenetics

Jones, P. A. (2005) · Seminars in Hematology · doi:10.1053/j.seminhematol.2005.05.001 · Cited by 105

Increased expression of unmethylated CDKN2D by 5-aza-2′-deoxycytidine in human lung cancer cells

Zhu, W., Zunyan Dai, Y., Ding, H., Srinivasan, K., Hall, J., Duan, W., Villalona-Calero, M. A., Plass, C., & Otterson, G. A. (2001) · Oncogene · doi:10.1038/sj.onc.1204970 · Cited by 104

The CpG Island Promoter of the Human Proopiomelanocortin Gene Is Methylated in Nonexpressing Normal Tissue and Tumors and Represses Expression

Newell-Price, J. D. C., King, P., & Clark, A. (2001) · Molecular Endocrinology · doi:10.1210/mend.15.2.0599 · Cited by 102

Aberrant DNA methylation in cancer: potential clinical interventions

Strathdee, G. R., & Brown, R. E. (2002) · Expert Reviews in Molecular Medicine · doi:10.1017/s1462399402004222 · Cited by 104

Clinical significance of insulin-like growth factor-binding protein-3 expression in stage I non-small cell lung cancer.

Chang, Y. S., Kong, G., Sun, S., Liu, D., El‐Naggar, A. K., Khuri, F. R., Hong, W. K., Lee, H., & Gong, K. (2002) · PubMed · Cited by 99

Inhibition of the interferon-gamma/signal transducers and activators of transcription (STAT) pathway by hypermethylation at a STAT-binding site in the p21WAF1 promoter region.

Chen, B., He, L., Savell, V. H., Jenkins, J. J., & Parham, D. M. (2000) · PubMed · Cited by 99

Mammalian Methyltransferases and Methyl-CpG-Binding Domains: Proteins Involved in DNA Methylation

Hendrich, B., & Bird, A. P. (2000) · Current topics in microbiology and immunology · doi:10.1007/978-3-642-59696-4_4 · Cited by 100

Epigenetic regulation of fetal globin gene expression in adult erythroid cells

Ginder, G. D. (2014) · Translational research · doi:10.1016/j.trsl.2014.05.002 · Cited by 97

CpG methylation remodels chromatin structure in vitro

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siRNA-mediated transcriptional gene silencing: the potential mechanism and a possible role in the histone code

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Cell-Specific Transcriptional Regulation of Human Leukotriene B4 Receptor Gene

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Impact of CpG methylation on structure, dynamics and solvation of cAMP DNA responsive element

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Activity‐dependent regulation of alternative splicing patterns in the rat brain

Daoud, R., Berzaghi, M. D. P., Siedler, F., Hübener, M., & Stamm, S. (1999) · European Journal of Neuroscience · doi:10.1046/j.1460-9568.1999.00486.x · Cited by 96

Imprinting: a gamete's point of view

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Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein–DNA binding

Rao, S., Chiu, T.-P., Kribelbauer, J. F., Mann, R. S., Bussemaker, H. J., & Rohs, R. (2018) · Epigenetics & Chromatin · doi:10.1186/s13072-018-0174-4 · Cited by 97

DNA Methylation in Epigenetic Control of Gene Expression

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Human cytochrome P450 epoxygenases: Variability in expression and role in inflammation-related disorders

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Methylation of the nucleobases in RNA oligonucleotides mediates duplex–hairpin conversion

Micura, R., Pils, W., Höbartner, C., Grubmayr, K., Ebert, M., & Jaun, B. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.19.3997 · Cited by 94

Differential Incubation Temperatures Result in Dimorphic DNA Methylation Patterning of the SOX9 and Aromatase Promoters in Gonads of Alligator (Alligator mississippiensis) Embryos1

Parrott, B. B., Kohno, S., McCoy, J. A., & Guillette, L. J. (2013) · Biology of Reproduction · doi:10.1095/biolreprod.113.111468 · Cited by 94

C m C(A/T)GG DNA methylation in mature B cell lymphoma gene silencing

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Global DNA hypermethylation-associated cancer chemotherapy resistance and its reversion with the demethylating agent hydralazine

Segura-Pacheco, B. A., Pérez‐Cárdenas, E., Taja‐Chayeb, L., Chávez-Blanco, A. D., Vázquez, A. L. R., Benı́tez-Bribiesca, L., & Dueñas‐González, A. (2006) · Journal of Translational Medicine · doi:10.1186/1479-5876-4-32 · Cited by 93

Stage-by-Stage Change in DNA Methylation Status of Dnmt1 Locus during Mouse Early Development

Ko, Y., Nishino, K., Hattori, N., Arai, Y., Tanaka, S., & Shiota, K. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m413822200 · Cited by 93

The Expression of the Follicle-stimulating Hormone Receptor in Spermatogenesis

Heckert, L. L. (2002) · Recent Progress in Hormone Research · doi:10.1210/rp.57.1.129 · Cited by 92

Epigenetics Studies of Fetal Alcohol Spectrum Disorder: Where are We Now?

Lussier, A. A., Weinberg, J., & Kobor, M. S. (2017) · Epigenomics · doi:10.2217/epi-2016-0163 · Cited by 105

5-Methyl-2'-deoxycytidine in single-stranded DNA can act in cis to signal de novo DNA methylation.

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Chromatin-remodelling mechanisms in cancer

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Methylation in hMLH1 promoter interferes with its binding to transcription factor CBF and inhibits gene expression

Deng, G., Chen, A., Pong, E., & Kim, Y. S. (2001) · Oncogene · doi:10.1038/sj.onc.1204891 · Cited by 89

Frequent reduction of gap junctional intercellular communication and connexin43 expression in human and mouse lung carcinoma cells

Cesen-Cummings, K. (1998) · Carcinogenesis · doi:10.1093/carcin/19.1.61 · Cited by 91

Early Life Lead Exposure Causes Gender-Specific Changes in the DNA Methylation Profile of DNA Extracted from Dried Blood Spots

Sen, A., Heredia, N., Senut, M., Hess, M., Land, S. J., Qu, W., Hollacher, K., Dereski, M. O., & Ruden, D. M. (2015) · Epigenomics · doi:10.2217/epi.15.2 · Cited by 91

DNA methylation biomarkers for head and neck squamous cell carcinoma

Zhou, C., Ye, M., Ni, S., Li, Q., Ye, D., Li, J., Shen, Z., & Deng, H. (2018) · Epigenetics · doi:10.1080/15592294.2018.1465790 · Cited by 92

Ethnic diversity of DNA methylation in the OPRM1 promoter region in lymphocytes of heroin addicts

Nielsen, D. A., Hamon, S., Yuferov, V. P., Jackson, C., Ho, A., Ott, J., & Kreek, M. J. (2010) · Human Genetics · doi:10.1007/s00439-010-0807-6 · Cited by 89

The expression of DNA methyltransferases and methyl-CpG-binding proteins is not associated with the methylation status of p14ARF, p16INK4a and RASSF1A in human lung cancer cell lines

Sato, M., Horio, Y., Sekido, Y., Minna, J. D., Shimokata, K., & Hasegawa, Y. (2002) · Oncogene · doi:10.1038/sj.onc.1205581 · Cited by 89

A DNA Methylation Site in the Male-Specific P450 ( Cyp 2d-9) Promoter and Binding of the Heteromeric Transcription Factor GABP

Yokomori, N., Kobayashi, R., Moore, R., Sueyoshi, T., & Negishi, M. (1995) · Molecular and Cellular Biology · doi:10.1128/mcb.15.10.5355 · Cited by 88

Therapeutic Strategies to Enhance the Anticancer Efficacy of Histone Deacetylase Inhibitors

Miller, C. P., Singh, M. M., Valle, N. R.-D., Manton, C. A., & Chandra, J. (2011) · BioMed Research International · doi:10.1155/2011/514261 · Cited by 88

Evolution of dioecy and sex chromosomes via methylation driving Muller's ratchet

Gorelick, R. (2003) · Biological Journal of the Linnean Society · doi:10.1046/j.1095-8312.2003.00244.x · Cited by 89

Epigenetic silencing of the MGMT gene in cancer

Soejima, H., Wei, Z., & Mukai, T. (2005) · Biochemistry and Cell Biology · doi:10.1139/o05-140 · Cited by 90

CG Methylation

Vinson, C., & Chatterjee, R. (2012) · Epigenomics · doi:10.2217/epi.12.55 · Cited by 89

Oxygen, Epigenetics and Stem Cell Fate

Okazaki, K. M., & Maltepe, E. (2005) · Regenerative Medicine · doi:10.2217/17460751.1.1.71 · Cited by 90

Topics on Drug Metabolism

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Aberrant methylation of TMS1 in small cell, non small cell lung cancer and breast cancer

Virmani, A. K., Rathi, A., Sugio, K., Sathyanarayana, U. G., Toyooka, S., Kischel, F. C., Tonk, V. S., Padar, A., Takahashi, T., Roth, J. A., et al. (2003) · International Journal of Cancer · doi:10.1002/ijc.11206 · Cited by 86

Structural Effects of Cytosine Methylation on DNA Sugar Pucker Studied by FTIR

Bányay, M., & Gräslund, A. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)01104-x · Cited by 84

Nuclear matrix attachment regions antagonize methylation-dependent repression of long-range enhancer-promoter interactionsPreprint

Forrester, W. C., Fernández, L. Á., & Grosschedl, R. (1999) · Genes & Development · doi:10.1101/gad.13.22.3003 · Cited by 84

Multifaceted Roles of DNA Methylation in Neoplastic Transformation, from Tumor Suppressors to EMT and Metastasis

Casalino, L., & Verde, P. (2020) · Genes · doi:10.3390/genes11080922 · Cited by 83

Regional methylation of the 5' end CpG island of BRCA1 is associated with reduced gene expression in human somatic cells

Magdinier, F., Billard, L.-M., Wittmann, G., Frappart, L., Benchaïb, M., Lenoir, G., Guérin, J.-F., & Dante, R. (2000) · The FASEB Journal · doi:10.1096/fj.99-0817com · Cited by 90

Methylation of the minimal promoter of an embryonic globin gene silences transcription in primary erythroid cells

Singal, R., Ferris, R. C., Little, J. A., Wang, S. Z., & Ginder, G. D. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.25.13724 · Cited by 82

Control mechanisms in the regulation of telomerase reverse transcriptase expression in differentiating human teratocarcinoma cells

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ANRIL Promoter DNA Methylation: A Perinatal Marker for Later Adiposity

Lillycrop, K. A., Murray, R. J. S., Cheong, C. Y., Teh, A. L., Clarke-Harris, R., Barton, S. J., Costello, P. M., Garratt, E. S., Cook, E., Titcombe, P., et al. (2017) · EBioMedicine · doi:10.1016/j.ebiom.2017.03.037 · Cited by 85

Cloning and Characterization of EphA3 (Hek) Gene Promoter: DNA Methylation Regulates Expression in Hematopoietic Tumor Cells

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Mismatch repair genes in Lynch syndrome: a review

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α-Satellite DNA methylation in normal individuals and in ICF patients: heterogeneous methylation of constitutive heterochromatin in adult and fetal tissues

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Silence of the genes — mechanisms of long-term repression

Lande‐Diner, L., & Cedar, H. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1639 · Cited by 82

The role of epigenetic mechanisms in the regulation of gene expression in the cyclical endometrium

Retis-Resendiz, A. M., González-García, I. N., León‐Juárez, M., Camacho‐Arroyo, I., Cerbón, M. A., & Vázquez-Martínez, E. R. (2021) · Clinical Epigenetics · doi:10.1186/s13148-021-01103-8 · Cited by 87

The Epstein-Barr Virus Major Latent Promoter Qp Is Constitutively Active, Hypomethylated, and Methylation Sensitive

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DNA Methylation as a Target for Drug Design

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