DNA methylation and the regulation of gene transcription

Cellular and Molecular Life Sciences

Volumn 59, Issue 2, 2002, Pages 241-257

  Attwood, J T ^a   Yung, R L ^a   Richardson, B C ^b  

^a UNIVERSITY OF MICHIGAN   (United States)

^b VETERANS AFFAIRS MEDICAL CENTER   (United States)

Author keywords

Chromatine; DNA methylation; Gene regulation; Genomic imprinting; Histone deacetylase; Methylcytosine; Methylcytosine binding protein; Methyltransferase

Indexed keywords

BINDING PROTEIN; DNA; DNA METHYLTRANSFERASE; HISTONE DEACETYLASE; TRANSCRIPTION FACTOR;

CARCINOGENESIS; CONGENITAL DISORDER; DEACETYLATION; DNA BINDING; DNA METHYLATION; GENE CONTROL; GENE DELETION; GENETIC TRANSCRIPTION; GENOME IMPRINTING; HUMAN; PROTEIN FUNCTION; REVIEW;

5-METHYLCYTOSINE; ANIMALS; CPG ISLANDS; CYTOSINE; DNA METHYLATION; DNA-BINDING PROTEINS; GENE SILENCING; GENETIC DISEASES, INBORN; HUMANS; IMMUNITY; MICE; MODELS, GENETIC; SITE-SPECIFIC DNA METHYLTRANSFERASE (CYTOSINE-SPECIFIC); TRANSCRIPTION, GENETIC;

EID: 0036178007     PISSN: 1420682X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00018-002-8420-z     Document Type: Review

References (211)

1. The quantitative separation of purines, pyrimidines, and nucleosides by paper chromatography
2. DNA methylation and gene function
3. 5-Methylcytosine in eukaryotic DNA
4. Distribution of 5-methylcytosine in chromatin
5. Asymmetrical distribution of CpG in an 'average' mammalian gene
6. Unmethylated CpG islands associated with genes in higher plant DNA
7. CG dinucleotide clusters in MHC genes and in 5′ demethylated genes
8. Unmethylated domains in vertebrate DNA
9. CpG islands
10. DNA repair enzymes
11. Use of restriction enzymes to detect potential gene sequences in mammalian DNA
12. Alternative chromatin structure at CpG islands
13. Choice of enzymes for mapping based on CpG islands in the human genome
14. The DNA methylation paradox
15. Cytosine methylation and the ecology of intragenomic parasites
16. The host defence function of genomic methylation patterns
17. Host defenses to parasitic sequences and the evolution of epigenetic control mechanisms
18. Cloning and sequencing of a cDNA encoding DNA methyltransferase of mouse cells. The carboxyl-terminal domain of the mammalian enzymes is related to bacterial restriction methyltransferases
19. A targeting sequence directs DNA methyltransferase to sites of DNA replication in mammalian nuclei
20. The activity of the murine DNA methyltransferase Dnmt1 is controlled by interaction of the catalytic domain with the N-terminal part of the enzyme leading to an allosteric activation of the enzyme after binding to methylated DNA
21. The Dnmt1 target recognition domain resides in the n terminus
22. HhaI methyltransferase flips its target base out of the DNA helix
23. Predictive motifs derived from cytosine methyltransferases
24. DNA (cytosine-5)-methyltransferases in mouse cells and tissues. Studies with a mechanism-based probe
25. Overexpression of DNA methyltransferase in myoblast cells accelerates myotube formation
26. De novo methylation of CpG island sequences in human fibroblasts overexpressing DNA (cytosine-5-)-methyltransferase
27. Infection with human immunodeficiency virus type 1 upregulates DNA methyltransferase, resulting in de novo methylation of the gamma interferon (IFN-gamma) promoter and subsequent downregulation of IFN-gamma production
28. Sex-specific exons control DNA methyltransferase in mammalian germ cells
29. Genomic imprinting disrupted by a maternal effect mutation in the Dnmt1 gene
30. Expression of an alternative Dumtl isoform during muscle differentiation
31. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality
32. Role for DNA methylation in genomic imprinting
33. X inactivation in the mouse embryo deficient for Dnmt1: Distinct effect of hypomethylation on imprinted and random X inactivation
34. Loss of genomic methylation causes p53-dependent apoptosis and epigenetic deregulation
35. Loss of DNA methylation has profound effects on T lymphocyte proliferation, survival and function
36. DNA hypomethylation perturbs the function and survival of CNS neurons in postnatal animals
37. Human DNA-(cytosine-5) methyltransferase-PCNA complex as a target for p21WAF1
38. DNMT1 forms a complex with Rb, E2F1 and HDAC1 and represses transcription from E2F-responsive promoters
39. DNMT1 binds HDAC2 and a new co-repressor, DMAP1, to form a complex at replication foci
40. De novo DNA cytosine methyltransferase activities in mouse embryonic stem cells
41. A candidate mammalian DNA methyltransferase related to pmtlp of fission yeast
42. Dnmt2 is not required for de novo and maintenance methylation of viral DNA in embryonic stem cells
43. Cloning and characterization of a family of novel mammalian DNA (cytosine-5) methyltransferases
44. Cloning, expression and chromosome locations of the human DNMT3 gene family
45. Dnmt3a binds deacetylases and is recruited by a sequence-specific repressor to silence transcription
46. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development
47. Inactivation of misselected CD8 T cells by CD8 gene methylation and cell death
48. The human DNA methyltransferases (DNMTs) 1, 3a and 3b: Coordinate mRNA expression in normal tissues and overexpression in tumors
49. Temporal and regional changes in DNA methylation in the embryonic, extraembryonic and germ cell lineages during mouse embryo development
50. Developmental pattern of gene-specific DNA methylation in the mouse embryo and germ line
51. Dynamics of demethylation and activation of the alpha-actin gene in myoblasts
52. DNA demethylation
53. Nuclear extracts of chicken embryos promote an active demethylation of DNA by excision repair of 5-methyldeoxycytidine
54. Mechanisms of DNA demethylation in chicken embryos. Purification and properties of a 5-methylcytosine-DNA glycosylase
55. Demethylation of DNA by purified chick embryo 5-methylcytosine-DNA glycosylase requires both protein and RNA
56. A chicken embryo protein related to the mammalian DEAD box protein p68 is tightly associated with the highly purified protein-RNA complex of 5- MeC-DNA glycosylase
57. Overexpression of 5-methylcytosine DNA glycosylase in human embryonic kidney cells EcR293 demethylates the promoter of a hormone-regulated reporter gene
58. The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites
59. A mammalian protein with specific demethylase activity for mCpG DNA
60. MBD2 is a transcriptional repressor belonging to the MeCP1 histone deacetylase complex
61. Mi-2 complex couples DNA methylation to chromatin remodelling and histone deacetylation
62. DNA modification mechanisms and gene activity during development
63. X inactivation, differentiation, and DNA methylation
64. DNA methylation at a CCGG sequence in the large intron of the rabbit beta-globin gene: Tissue-specific variations
65. Specific DNA methylation sites in the vicinity of the chicken beta-globin genes
66. DNA methylation: Organ specific variations in the methylation pattern within and around ovalbumin and other chicken genes
67. DNA methylation in the human gamma delta beta-globin locus in erythroid and nonerythroid tissues
68. Multiple new phenotypes induced in 10T1/2 and 3T3 cells treated with 5-azacytidine
69. Cellular differentiation, cytidine analogs and DNA methylation
70. Covalent bond formation between a DNA-cytosine methyltransferase and DNA containing 5-azacytosine
71. Toxicity of 5-aza-2′-deoxycytidine to mammalian cells is mediated primarily by covalent trapping of DNA methyltransferase rather than DNA demethylation
72. Effects of 5-azacytidine and its 2′-deoxyderivative on cell differentiation and DNA methylation
73. Effect of 5-azacytidine on the differentiation of human leukemia K-562 cells
74. Heritable high frequency modulation of antigen expression in neoplastic cells exposed to 5-aza-2′-deoxycytidine or hydroxyurea: Analysis and implications
75. Reactivation of an inactive human X chromosome: Evidence for X inactivation by DNA methylation
76. Genomic imprinting in mammals
77. Mechanisms of genomic imprinting
78. Genomic imprinting in mammals: An interplay between chromatin and DNA methylation?
79. Mechanisms of genomic imprinting
80. Genomic imprinting: Parental influence on the genome
81. Sequence conservation and variability of imprinting in the Beckwith-Wiedemann syndrome gene cluster in human and mouse
82. DNA demethylation reactivates a subset of imprinted genes in uniparental mouse embryonic fibroblasts
83. Transcriptional control: Imprinting insulation
84. Pausing for thought on the boundaries of imprinting
85. Imprinting: Focusing on the center
86. Insulators and boundaries: Versatile regulatory elements in the eukaryotic genome
87. Parent-specific gene expression and the triploid endosperm
88. Genomic imprinting in mammalian development: A parental tug-of-war
89. Do we understand the evolution of genomic imprinting?
90. Genomic imprinting, uniparental disomy and foetal growth
91. X-chromosome inactivation in mammals
92. The (epi)genetic control of mammalian X-chromosome inactivation
93. X-chromosome inactivation: Lessons from transgenic mice
94. X-chromosome inactivation: Counting, choice and initiation
95. In vitro methylation of the hamster adenine phosphoribosyltransferase gene inhibits its expression in mouse L cells
96. DNA methylation and the regulation of globin gene expression
97. DNA methylation represses transcription in vivo
98. CpG methylation inhibits proenkephalin gene expression and binding of the transcription factor AP-2
99. CpG methylation of the cAMP-responsive enhancer/promoter sequence TGACGTCA abolishes specific factor binding as well as transcriptional activation
100. Methylation-sensitive sequence-specific DNA binding by the c-Myc basic region
101. Sp1 binding is inhibited by (m)Cp(m)CpG methylation
102. Cytosine methylation does not affect binding of transcription factor Sp1
103. Histone deacetylase-independent transcriptional repression by methyl-CpG-binding protein 2
104. Purification, sequence and cellular localization of a novel chromosomal protein that binds to methylated DNA
105. Dissection of the methyl-CpG binding domain from the chromosomal protein MeCP2
106. MeCP2 is a transcriptional repressor with abundant binding sites in genomic chromatin
107. DNA methylation specifies chromosomal localization of MeCP2
108. Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex
109. Histone deacetylases: Silencers for hire
110. Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription
111. Identification of a mammalian protein that binds specifically to DNA containing methylated CpGs
112. Analysis of the NuRD subunits reveals a histone deacetylase core complex and a connection with DNA methylation
113. The minimal repression domain of MBD2b overlaps with the methyl-CpG-binding domain and binds directly to Sin3A
114. MBD2-MBD3 complex binds to hemi-methylated DNA and forms a complex containing DNMT1 at the replication foci in late S phase
115. Closely related proteins MBD2 and MBD3 play distinctive but interacting roles in mouse development
116. Identification and characterization of a family of mammalian methyl-CpG binding proteins
117. Genomic structure and chromosomal mapping of the murine and human Mbd1, Mbd2, Mbd3, and Mbd4 genes
118. Active repression of methylated genes by the chromosomal protein MBD1
119. 5-Methylcytosine DNA glycosylase activity is also present in the human MBD4 (G/T mismatch glycosylase) and in a related avian sequence
120. Regulation of interferon-gamma gene expression
121. Undermethylation of interferon-gamma gene in human T cell lines and normal T lymphocytes
122. Differentiation of the T helper phenotypes by analysis of the methylation state of the IFN-gamma gene
123. Hypomethylation of the interferon-gamma gene correlates with its expression by primary T-lineage cells
124. The proximal regulatory element of the interferon-gamma promoter mediates selective expression in T cells
125. IL-4 and prostaglandin E2 inhibit hypomethylation of the 5′ regulatory region of IFN-gamma gene during differentiation of naive CD4+ T cells
126. CD4+, but not CD8+, T cells from mammary tumor-bearing mice have a down- regulated production of IFN-gamma: Role of phosphatidyl serine
127. Modulation of chromatin structure regulates cytokine gene expression during T cell differentiation
128. Helper T cell differentiation is controlled by the cell cycle
129. Cutting edge: Chromatin remodeling at the IL-4/IL- 13 intergenic regulatory region for Th2-specific cytokine gene cluster
130. Distinct methylation of the interferon gamma (IFN-gamma) and interleukin 3 (IL-3) genes in newly activated primary CD8+ T lymphocytes: Regional IFN-gamma promoter demethylation and mRNA expression are heritable in CD44(high)CD8+ T cells
131. Effect of an inhibitor of DNA methylation on T cells. I. 5-Azacytidine induces T4 expression on T8+ T cells
132. Demethylated CD8 gene in CD4+ T cells suggests that CD4+ cells develop from CD8+ precursors
133. Specific demethylation of the CD4 gene during CD4 T lymphocyte differentiation
134. Coordinate change in phenotype in a mouse cell line selected for CD8 expression
135. Distinct methylation states of the CD8 beta gene in peripheral T cells and intraepithelial lymphocytes
136. Remethylation at sites 5′ of the murine Lyt-2 gene in association with shutdown of Lyt-2 expression
137. Methylation of class II trans-activator promoter IV: A novel mechanism of MHC class II gene control
138. Lack of CIITA expression is central to the absence of antigen presentation functions of trophoblast cells and is caused by methylation of the IFN-gamma inducible promoter (PIV) of CIITA
139. Methylation pattern of the HLA-DR alpha gene in human tissues
140. Differential expression of the HLA-DR genes in various melanoma cell lines treated with interferon-gamma: Methylation of the HLA-DR alpha gene in these lines is not correlated with its expression
141. Methylation patterns of HLA-DR alpha genes in six mononuclear cell lines
142. Methylation of the HLA-DR alpha gene is positively correlated with expression
143. Lack of correlation between hypomethylation and expression of the HLA-DR alpha gene
144. CpG islands and HTF islands in the HLA class I region: Investigation of the methylation status of class I genes leads to precise physical mapping of the HLA-B and -C genes
145. Developmental activation of the H-2K gene is correlated with an increase in DNA methylation
146. Developmental and tissue-specific regulation of the Q10 class I gene by DNA methylation
147. Methylation status and transcriptional expression of the MHC class I loci in human trophoblast cells from term placenta
148. V(D)J recombination becomes accessible
149. Expression of the J chain gene during B cell differentiation is inversely correlated with DNA methylation
150. Methylation patterns of immunoglobulin genes in lymphoid cells: Correlation of expression and differentiation with undermethylation
151. Methylation patterns of the T cell receptor beta-chain gene in T cells, large granular lymphocytes, B cells and monocytes
152. The methylation state of the T cell antigen receptor beta chain gene in subpopulations of mouse thymocytes
153. Biochemical and functional analyses of chromatin changes at the TCR- beta gene locus during CD4-CD8- to CD4+CD8+ thymocyte differentiation
154. Control of organ-specific demethylation by an element of the T-cell receptor-alpha locus control region
155. Chromatin remodeling by the T cell receptor (TCR)-beta gene enhancer during early T cell development: Implications for the control of TCR-beta locus recombination
156. Deletion of germline promoter PD beta 1 from the TCR beta locus causes hypermethylation that impairs D beta 1 recombination by multiple mechanisms
157. Immunodeficiency, centromeric heterochromatin instability of chromosomes 1, 9 and 16, and facial anomalies: The ICF syndrome
158. Segmentation of human chromosomes induced by 5-ACR (5-azacytidine)
159. An embryonic-like methylation pattern of classical satellite DNA is observed in ICF syndrome
160. The DNMT3B DNA methyltransferase gene is mutated in the ICF immunodeficiency syndrome
161. A progressive syndrome of autism, dementia, ataxia and loss of purposeful hand use in girls: Rett's syndrome: Report of 35 cases
162. Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl- CpG-binding protein 2
163. A mouse Mecp2-null mutation causes neurological symptoms that mimic Rett syndrome
164. Deficiency of methyl-CpG binding protein-2 in CNS neurons results in a Rett-like phenotype in mice
165. Mutations in a putative global transcriptional regulator cause X-linked mental retardation with alpha-thalassemia (ATR-X syndrome)
166. Mutations in ATRX, encoding a SWI/SNF-like protein, cause diverse changes in the pattern of DNA methylation
167. Genomic imprinting: Implications for human disease
168. Prader-Willi and Angelman syndromes. Disorders of genomic imprinting
169. Angelman and Prader-Willi syndromes share a common chromosome 15 deletion but differ in parental origin of the deletion
170. Overgrowth syndromes and genomic imprinting: From mouse to man
171. Beckwith-Wiedemann syndrome: Imprinting in clusters revisited
172. Identification of a gene (FMR-1) containing a CGG repeat coincident with a breakpoint cluster region exhibiting length variation in fragile X syndrome
173. Acetylated histones are associated with FMR1 in normal but not fragile X-syndrome cells
174. Effect of an inhibitor of DNA methylation on T cells. II. 5-Azacytidine induces self-reactivity in antigen-specific T4+ cells
175. CD4+ cells treated with DNA methylation inhibitors induce autologous B cell differentiation
176. Mechanisms of drug-induced lupus. II. T cells overexpressing lymphocyte function-associated antigen 1 become autoreactive and cause a lupuslike disease in syngeneic mice
177. Hydralazine and procainamide inhibit T cell DNA methylation and induce autoreactivity
178. Evidence for impaired T cell DNA methylation in systemic lupus erythematosus and rheumatoid arthritis
179. 5-Methylcytosine content of DNA in blood, synovial mononuclear cells and synovial tissue from patients affected by autoimmune rheumatic diseases
180. Mechanism of drug-induced lupus. I. Cloned Th2 cells modified with DNA methylation inhibitors in vitro cause autoimmunity in vivo
181. Alterations in DNA methylation: A fundamental aspect of neoplasia
182. Methylation matters
183. Cancer epigenetics comes of age
184. DNA hypermethylation in tumorigenesis: Epigenetics joins genetics
185. Allele-specific hypermethylation of the retinoblastoma tumor-suppressor gene
186. Hypermethylation in the retinoblastoma gene is associated with unilateral, sporadic retinoblastoma
187. Somatic inactivation of the VHL gene in Von Hippel-Lindau disease tumors
188. DAP-kinase loss of expression in various carcinoma and B-cell lymphoma cell lines: Possible implications for role as tumor suppressor gene
189. Incidence and functional consequences of hMLH1 promoter hypermethylation in colorectal carcinoma
190. Biallelic inactivation of hMLH1 by epigenetic gene silencing, a novel mechanism causing human MSI cancers
191. Promoter hypermethylation and BRCA1 inactivation in sporadic breast and ovarian tumors
192. Methylation of the oestrogen receptor CpG island links ageing and neoplasia in human colon
193. CpG island methylator phenotype in colorectal cancer
194. Aberrant methylation of gene promoters in cancer - Concepts, misconcepts and promise
195. The inheritance of epigenetic defects
196. Intragenomic specificity of DNA methylation in animals. Qualitative differences in tissues and changes in methylation of repeating sequences during aging, carcinogenesis and hormonal induction
197. Decreased methylation of the major mouse long interspersed repeated DNA during aging and in myeloma cells
198. Genomic 5-methyldeoxycytidine decreases with age
199. DNA methylation in aging of mice
200. The 5-methylcytosine in DNA of rats. Tissue and age specificity and the changes induced by hydrocortisone and other agents
201. Methylation of reiterated sequences in mammalian DNAs. Effects of the tissue type, age, malignancy and hormonal induction
202. Methylation of repetitive DNA sequences in the brain during aging of the rat
203. Endogenous virus genomes become hypomethylated tissue - Specifically during aging process of C57BL mice
204. Quantitative changes in T cell DNA methylation occur during differentiation and ageing
205. Biological significance of DNA methylation in the ageing process
206. Methylation of the c-myc gene changes during aging process of mice
207. Age-associated changes in DNA methylation and mRNA level of the c-myc gene in spleen and liver of mice
208. Aging DNA methylation and cancer
209. CpG-island methylation in aging and cancer
210. Changes in DNA methylation in neoplasia: Pathophysiology and therapeutic implications
211. Unexpected effects of a heterozygous Dnmt1 null mutation on age-dependent DNA hypomethylation and autoimmunity