Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound   Target Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound

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Query: EC:2.1.1.37 (DNA methyltransferase)
4,983 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The DNMT3-like protein, DNMT3L, is required for germ line DNA methylation, although it is inactive as a DNA methyltransferase per se. Previous studies have shown that DNMT3L physically associates with the active de novo DNA methyltransferases, DNMT3A and DNMT3B, and stimulates their catalytic activities in a cell culture system. However, the mechanism by which DNMT3L stimulates de novo methylation remains unclear. Here, we have purified the full-length human DNMT3A2 and DNMT3L proteins and determined unique conditions that allow for the proper reconstitution of the stimulation of DNMT3A2 de novo methyltransferase activity by DNMT3L. These conditions include the use of buffers resembling physiological conditions and the preincubation of the two proteins. Under these conditions, maximal stimulation is reached at equimolar amounts of DNMT3L and DNMT3A2 proteins, and the catalytic efficiency of DNMT3A2 is increased up to 20-fold. Biochemical analysis revealed that whereas DNMT3L on its own does not significantly bind to the methyl group donor, S-adenosyl-L-methionine (SAM), it strongly increases the binding of SAM to DNMT3A2. DNA binding, on the contrary, was not appreciably improved. Analysis of DNA methyltransferase complexes in solution using size exclusion chromatography revealed that DNMT3A2 forms large structures of heterogeneous sizes, whereas DNMT3L appears as a monomer. Binding of DNMT3L to DNMT3A2 promotes a dramatic reorganization of DNMT3A2 subunits and leads to the formation of specific complexes with enhanced DNA methyltransferase activity and increased SAM binding.
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PMID:Reconstitution and mechanism of the stimulation of de novo methylation by human DNMT3L. 1682 25

The study was purposed to investigate the effect of arsenic trioxide (As(2)O(3))- induced p16 gene demethylation by a sensitive and specific PCR-based method (nested-methylation specific PCR, n-MSP) and DNA sequencing for rapid analysis of the promoter demethylation status, and to explore the possible mechanism of the p16 gene demethylation in human multiple myeloma U266 cells induced by As(2)O(3). The methylation status of the p16 gene in U266 cell line before and after treatment with As(2)O(3) was detected by the nested-methylation specific PCR and DNA sequencing, the mRNA of p16, DNA methyltransferase (DNMT 1, DNMT3A and 3B) gene were determined by RT-PCR, and the induced growth inhibition of U266 cell was assayed by growth curve, MTT and CFU; the DNA content of U266 cells was analyzed by flow cytometry after being exposed to As(2)O(3). The results showed that (1) all cytosines in CpG dinucleotides in untreated U266 cell not were changed, while all cytosines in treated U266 cells with As(2)O(3) had been converted to thymidine. (2) p16 gene was not expressed in U266 cell line after methylation. As compared with the beta-actin, the expression of U266 cell p16 gene mRNA was increased to (0.22 +/- 0.10), (0.59 +/- 0.11), (0.68 +/- 0.09) after exposed to 0.5 micromol/L, 1.0 micromol/L and 2.0 micromol/L As(2)O(3) for 72 hours respectively. (3) As(2)O(3) could significantly down-regulate DNA methyltransferase 1 (DNMT 1), DNMT3A and DNMT3B gene at mRNA level in a dose-dependent manner. (4) U266 cells line grew slowly and arrested at G(0) - G(1) phase after treatment with three different concentrations of As(2)O(3). It is concluded that As(2)O(3) can activate and up-regulate the expression of p16 gene which inhibits the proliferation of U266 cell through inducing the G(0) - G(1) arrest by demethylation or/and by inhibiting DNMT 1, DNMT3A and 3B gene.
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PMID:[n-MSP detection of p16 gene demethylation and transcription in human multiple myeloma U266 cell line induced by arsenic trioxide]. 1749 May 27

It has been recently demonstrated that in colonic carcinoma, CXCL12 expression undergoes epigenetic regulation by methylation of cytosine in cytosine-guanosine (CpG) dinucleotides of the promoter sequence. Using lentiviral vectors, we generated stable RNA interference-mediated knockdown of DNMT1 and DNMT3B in MCF-7 breast cancer and AsPC1 pancreatic carcinoma cell lines. Employing reverse transcription real-time quantitative PCR and immunofluorescence analysis, we determined re-expression levels of CXCL12 transcript and protein in these cells. Bisulfite sequencing revealed that the level of promoter demethylation appeared more effective in cells expressing DNMT1 siRNA than in those expressing DNMT3B siRNA, and this correlated with higher expression of CXCL12. Moreover, the combined expression of DNMT1 and DNMT3B siRNAs enhanced promoter demethylation that was associated only with a slight increase of CXCL12 expression. However, the demethylating agent 5-Aza-2'-deoxycytidine exhibited the strongest effect on promoter demethylation, which correlated with the highest expression level of CXCL12 transcript and protein in MCF-7 and AsPC1 cells. Our findings suggest that DNMT1 plays a key role in maintenance of methylation, and DNMT3B may act as an accessory DNA methyltransferase to epigenetically silence CXCL12 expression in MCF-7 and AsPC1 cells.
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PMID:RNA interference-mediated knockdown of DNMT1 and DNMT3B induces CXCL12 expression in MCF-7 breast cancer and AsPC1 pancreatic carcinoma cell lines. 1753 57

Immunodeficiency-centromeric instability-facial dysmorphism syndrome, characterized by variable immunodeficiency, centromeric instability, and facial anomalies caused by epigenetic dysregulation resulting in hypomethylation, is caused in many patients by mutations in DNMT3B, a DNA methyltransferase gene; associated infections are a major cause of serious sequelae and death. Hematopoietic stem cell transplantation may improve the clinical course in immunodeficiency-centromeric instability-facial dysmorphism syndrome. We report 3 unrelated patients with persistent infections and intestinal complications who successfully underwent hematopoietic stem cell transplantation after nonmyeloablative or myeloablative conditioning regimens using HLA-matched donors. In all cases, donor chimerism led to resolution of intestinal complications and infections, growth improvement, and correction of the immunodeficiency.
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PMID:Hematopoietic stem cell transplantation corrects the immunologic abnormalities associated with immunodeficiency-centromeric instability-facial dysmorphism syndrome. 1790 20

Epigenetic events play a prominent role during cancer development. This is evident from the fact that almost all cancer types show aberrant DNA methylation. These abnormal DNA methylation levels are not restricted to just a few genes but affect the whole genome. Previous studies have shown genome-wide DNA hypomethylation and gene-specific hypermethylation to be a hallmark of most cancers. Molecules like DNA methyltransferase act as effectors of epigenetic reprogramming. In the present study we have examined the possibility that the reprogramming genes themselves undergo epigenetic modifications reflecting their changed transcriptional status during cancer development. Comparison of DNA methylation status between the normal and cervical cancer samples was carried out at the promoters of a few reprogramming molecules. Our study revealed statistically significant DNA methylation differences within the promoter of DNMT3L. A regulator of de novo DNA methyltransferases DNMT3A and DNMT3B, DNMT3L promoter was found to have lost DNA methylation to varying levels in 14 out of 15 cancer cervix samples analysed. The present study highlights the importance of DNA methylation profile at DNMT3L promoter not only as a promising biomarker for cervical cancer, which is the second most common cancer among women worldwide, but also provides insight into the possible role of DNMT3L in cancer development.
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PMID:DNA methylation profile at the DNMT3L promoter: a potential biomarker for cervical cancer. 1796 99

LSH, a protein related to the SNF2 family of chromatin-remodeling ATPases, is required for efficient DNA methylation in mammals. How LSH functions to support DNA methylation and whether it associates with a large protein complex containing DNA methyltransferase (DNMT) enzymes is currently unclear. Here we show that, unlike many other chromatin-remodeling ATPases, native LSH is present mostly as a monomeric protein in nuclear extracts of mammalian cells and cannot be detected in a large multisubunit complex. However, when targeted to a promoter of a reporter gene, LSH acts as an efficient transcriptional repressor. Using this as an assay to identify proteins that are required for LSH-mediated repression we found that LSH cooperates with the DNMTs DNMT1 and DNMT3B and with the histone deacetylases (HDACs) HDAC1 and HDAC2 to silence transcription. We show that transcriptional repression by LSH and interactions with HDACs are lost in DNMT1 and DNMT3B knockout cells but that the enzymatic activities of DNMTs are not required for LSH-mediated silencing. Our data suggest that LSH serves as a recruiting factor for DNMTs and HDACs to establish transcriptionally repressive chromatin which is perhaps further stabilized by DNA methylation at targeted loci.
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PMID:LSH cooperates with DNA methyltransferases to repress transcription. 1796 91

It has previously been shown that the ribosomal RNA (rRNA) promoter is regulated through epigenetic mechanisms. It is unclear however whether epigenetic marks are stable in somatic cells or whether and how they vary with cell cycle dynamics. Here we present an analysis of epigenetic marks in cells positioned at different phases of the cell cycle following synchronization using a double thymidine block. We show that the levels of acetylated histone 4 are highest in early S phase, coinciding with the peak of binding of the transcriptional activators UBF and MBD3 to the rRNA promoter. Additionally, binding of the DNA methyltransferase DNMT1 is highest during mid-S phase, while DNMT3B binding peaks later in G2. Bisulfite mapping of the rRNA promoter reveals that the DNA methylation state varies during the cell cycle being lowest during early and late S phase. Interestingly, although the interaction of RNA polymerase I with the promoter and its progress along the gene coincides with epigenetic activation, the burst in levels of rRNA transcript did not occur until after DNA synthesis was complete. This suggests that although the rRNA promoter is poised for transcription early in the cell cycle, the accumulation of rRNA transcripts requires additional signals later in the cell cycle. This data is consistent with the idea that epigenetic states are dynamic in somatic cells and might participate in physiological cellular responses.
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PMID:Dynamic epigenetic states of ribosomal RNA promoters during the cell cycle. 1823 21

Stable silencing of the INK4b-ARF-INK4a tumor suppressor locus occurs in a variety of human cancers, including malignant rhabdoid tumors (MRTs). MRTs are extremely aggressive cancers caused by the loss of the hSNF5 subunit of the SWI/SNF chromatin-remodeling complex. We found previously that, in MRT cells, hSNF5 is required for p16(INK4a) induction, mitotic checkpoint activation, and cellular senescence. Here, we investigated how the balance between Polycomb group (PcG) silencing and SWI/SNF activation affects epigenetic control of the INK4b-ARF-INK4a locus in MRT cells. hSNF5 reexpression in MRT cells caused SWI/SNF recruitment and activation of p15(INK4b) and p16(INK4a), but not of p14(ARF). Gene activation by hSNF5 is strictly dependent on the SWI/SNF motor subunit BRG1. SWI/SNF mediates eviction of the PRC1 and PRC2 PcG silencers and extensive chromatin reprogramming. Concomitant with PcG complex removal, the mixed lineage leukemia 1 (MLL1) protein is recruited and active histone marks supplant repressive ones. Strikingly, loss of PcG complexes is accompanied by DNA methyltransferase DNMT3B dissociation and reduced DNA methylation. Thus, various chromatin states can be modulated by SWI/SNF action. Collectively, these findings emphasize the close interconnectivity and dynamics of diverse chromatin modifications in cancer and gene control.
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PMID:SWI/SNF mediates polycomb eviction and epigenetic reprogramming of the INK4b-ARF-INK4a locus. 1833 16

The immunodeficiency, centromeric region instability, and facial anomalies syndrome (ICF) is the only disease known to result from a mutated DNA methyltransferase gene, namely, DNMT3B. Characteristic of this recessive disease are decreases in serum immunoglobulins despite the presence of B cells and, in the juxtacentromeric heterochromatin of chromosomes 1 and 16, chromatin decondensation, distinctive rearrangements, and satellite DNA hypomethylation. Although DNMT3B is involved in specific associations with histone deacetylases, HP1, other DNMTs, chromatin remodelling proteins, condensin, and other nuclear proteins, it is probably the partial loss of catalytic activity that is responsible for the disease. In microarray experiments and real-time RT-PCR assays, we observed significant differences in RNA levels from ICF vs. control lymphoblasts for pro- and anti-apoptotic genes (BCL2L10, CASP1, and PTPN13); nitrous oxide, carbon monoxide, NF-kappaB, and TNFalpha signalling pathway genes (PRKCH, GUCY1A3, GUCY1B3, MAPK13; HMOX1, and MAP4K4); and transcription control genes (NR2F2 and SMARCA2). This gene dysregulation could contribute to the immunodeficiency and other symptoms of ICF and might result from the limited losses of DNA methylation although ICF-related promoter hypomethylation was not observed for six of the above examined genes. We propose that hypomethylation of satellite 2 at 1qh and 16qh might provoke this dysregulation gene expression by trans effects from altered sequestration of transcription factors, changes in nuclear architecture, or expression of noncoding RNAs.
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PMID:ICF, an immunodeficiency syndrome: DNA methyltransferase 3B involvement, chromosome anomalies, and gene dysregulation. 1843 6

Telomeres and adjacent subtelomeric regions are packaged as heterochromatin in many organisms. The heterochromatic features include DNA methylation, histones H3-Lys9 (Lysine 9) and H4-Lys20 (Lysine 20) methylation and heterochromatin protein1 alpha binding. Subtelomeric DNA is hypomethylated in human sperm and ova, and these regions are subjected to de novo methylation during development. In mice this activity is carried out by DNA methyltransferase 3b (Dnmt3b). Mutations in DNMT3B in humans lead to the autosomal-recessive ICF (immunodeficiency, centromeric region instability, facial anomalies) syndrome. Here we show that, in addition to several satellite and non-satellite repeats, the subtelomeric regions in lymphoblastoid and fibroblast cells of ICF patients are also hypomethylated to similar levels as in sperm. Furthermore, the telomeres are abnormally short in both the telomerase-positive and -negative cells, and many chromosome ends lack detectable telomere fluorescence in situ hybridization signals from either one or both sister-chromatids. In contrast to Dnmt3a/b(-/-) mouse embryonic stem cells, increased telomere sister-chromatid exchange was not observed in ICF cells. Hypomethylation of subtelomeric regions was associated in the ICF cells with advanced telomere replication timing and elevated levels of transcripts emanating from telomeric regions, known as TERRA (telomeric-repeat-containing RNA) or TelRNA. The current findings provide a mechanistic explanation for the abnormal telomeric phenotype observed in ICF syndrome and highlights the link between TERRA/TelRNA and structural telomeric integrity.
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PMID:Hypomethylation of subtelomeric regions in ICF syndrome is associated with abnormally short telomeres and enhanced transcription from telomeric regions. 1855 31


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