CCGG Sites Research Articles

The onset of oncogene hypomethylation in the livers of rats fed methyl-deficient, amino acid-defined diets.

This study examines proto-oncogene hypomethylation in rat livers during the early stages of hepatocarcinogenesis by dietary methyl deprivation in the presence and absence of initiation by diethylnitrosamine (DEN). Male weanling F344 rats were fed a complete diet, or a diet deficient in methionine and choline (MDD). Half the animals in each dietary group were given a single initiating dose of DEN (20 mg/kg). Animals from each of the treatment groups were killed at 1, 3, 8, 16 and 32 weeks, and hepatic DNA was isolated. This DNA was digested with the restriction enzymes MspI and HpaII to determine the extent of methylation of the CCGG sequences in c-Ha-ras, c-Ki-ras and c-fos proto-oncogenes. The results indicate that the administration of the MDD produced hypomethylation of these proto-oncogenes at all times investigated, independent of DEN initiation. The methylation changes in the c-Ha-ras gene increased in intensity throughout the experiment until at 32 weeks they were similar to the patterns seen in both neoplastic and preneoplastic livers of rats fed the deficient diet for 18 months. These results demonstrate that early, selective hypomethylation of some, but not all, CCGG sites occurs in rats undergoing hepatocarcinogenesis by dietary methyl deprivation.

Differential methylation at the 5? and the 3? CCGG sites flanking the X chromosomal hypervariable DXS255 locus

The degree of methylation at the 5' and 3' CCGG sequences flanking the variable number of tandem repeat (VNTR) region of the DXS255 locus at Xp11.22 was analysed separately in several haematopoietic cell lineages. The 5' CCGG site on active chromosomes was found to be completely methylated in B and T lymphocytes and granulocytes. Methylation of the 5' site on inactive X chromosomes differed between females (0%-60%), but was consistent in different cell lineages obtained from individual females. In contrast, methylation at the 3' CCGG site on active chromosomes was found to vary in B lymphocytes (40%-100%), whereas complete methylation was found in T lymphocytes and granulocytes. The extent of methylation on inactive X chromosomes was found to differ significantly between B lymphocytes (17%), T lymphocytes (54%) and granulocytes (82%). Thus, methylation at the 5' CCGG site seems to be primarily related to the status of X chromosome inactivation, whereas methylation at the 3' CCGG site is mainly subject to cell-lineage-specific influences.

Lack of 5-methylcytosine in Dictyostelium discoideum DNA.

We find no evidence for the presence of 5-methylcytosine in the DNA of Dictyostelium discoideum. Methylation was absent from CCGG sites in repetitive DNA and in DNA from the actin multigene family. Nor was 5-methylcytosine detected in total DNA when base composition was determined by means of h.p.l.c.

5-Azacytidine-induced hypomethylation of tobacco HRS60 tandem DNA repeats in tissue culture

The methylation status and 5-azacytidine-induced hypomethylation of CCGG sites within a family of tandemly organized, highly repeated DNA sequences of the Nicotiana tabacum L. nuclear genome (HRS60 family) were studied. As shown by in-situ hybridization experiments, the HRS60 family is clustered in a few regions of some tobacco chromosomes. The DNAs of leaf-derived calli, leaf-derived calli cultured on media with 5-azacytidine, and leaves were cleaved with restriction endonucleases differing in the sensitivity to the methylation of cytosine. After electrophoresis and Southern blotting they were hybridized with the HRS60 probe. We show that (i) CpG dinucleotides, and partially also CpCpG trinucleotides, of the HRS60 family are methylated in DNAs of the non-treated calli and leaves, and (ii) that these DNA repeats are sensitive to the action of a hypomethylating drug, 5-azacytidine.

Acceleration of chronic myeloid leukemia correlates with calcitonin gene hypermethylation

Calcitonin gene methylation at CCGG sites were determined in 39 chronic myeloid leukemia patients by isoschizomeric restriction endonuclease analysis. A total of 27 patients were analyzed while still in the chronic phase: 20 patients had a normal gene, and seven had a hypermethylated gene. There were 12 patients initially studied in accelerated or blastic phases. All but one patient showed gene hypermethylation, suggesting a good correlation between gene methylation and disease stage. All five patients who, while still in the chronic phase, had a major 3.1-kb hypermethylated calcitonin gene fragment, accelerated within 2 to 27 months. In consecutively analyzed patients, the initially normal calcitonin gene changed to a hypermethylated state as the disease escalated. The hypermethylation predicted disease acceleration with a median lead time of 6 months before any morphologic or clinical signs of disease progression were seen. The disease progressed in 8 of 27 patients initially studied in the chronic phase: in only two patients this occurred without predictive methylation changes. The results suggest that the assessment of calcitonin gene methylation status may be a promising tool for monitoring chronic myeloid leukemia disease escalation.

Acceleration of Chronic Myeloid Leukemia Correlates With Calcitonin Gene Hypermethylation

Calcitonin gene methylation at CCGG sites were determined in 39 chronic myeloid leukemia patients by isoschizomeric restriction endonuclease analysis. A total of 27 patients were analyzed while still in the chronic phase: 20 patients had a normal gene, and seven had a hypermethylated gene. There were 12 patients initially studied in accelerated or blastic phases. All but one patient showed gene hypermethylation, suggesting a good correlation between gene methylation and disease stage. All five patients who, while still in the chronic phase, had a major 3.1-kb hypermethylated calcitonin gene fragment, accelerated within 2 to 27 months. In consecutively analyzed patients, the initially normal calcitonin gene changed to a hypermethylated state as the disease escalated. The hypermethylation predicted disease acceleration with a median lead time of 6 months before any morphologic or clinical signs of disease progression were seen. The disease progressed in 8 of 27 patients initially studied in the chronic phase: in only two patients this occurred without predictive methylation changes. The results suggest that the assessment of calcitonin gene methylation status may be a promising tool for monitoring chronic myeloid leukemia disease escalation.

Transgenic mice mimic the methylation pattern of the human HLA-DRα gene

The methylation pattern of the human HLA-DRα gene has been studied in different tissues of transgenic mice. Offspring from two transgenic lines was selected for this analysis, carrying the integrated HLA-DRα gene in either single or multiple (8–10) copies per diploid genome. In transgenic animals two distinct methylation patterns of the HLA-DRα gene are generated, due to a complete methylation of all the GCGC and CCGG sites the former, and to unmethylation restricted to one or both the GCGC sites located in the 5′ portion of the HLA-DRα gene, the latter. Unmethylation restricted to the 5′ portion of the HLA-DRα gene is a highly conserved feature in human tissues and in vitro cultured cell lines; therefore, it is concluded that the methylation pattern of the human HLA-DRα transgene may be faithfully reconstituted in transgenic animals. Northern blotting analysis of the RNA isolated from tissues of the transgenic mouse carrying single-copy HLA-DRα transgene demonstrates its tissue specific expression, suggesting that transgenic mice may represent an “in vivo” experimental system to study the relationship between methylation state and transcriptional activation.

Analysis of methylation in the c-MYC gene in five human myeloma cell lines

Genomic alterations of the human c-MYC gene were analysed in five human myeloma cell lines established in Kawasaki Medical School and compared with those of normal lymphocytes, Raji cells from Burkitt's lymphoma, and an Epstein-Barr virus positive lymphoblastoid cell line (LCL). Although no structural chromosome aberrations at 8q24, the c-MYC locus, were distinct, the mRNA level of c-MYC in these myeloma cell lines was 30-50-fold that in normal peripheral blood lymphocytes. Regarding the methylation of c-MYC, DNAs of the myeloma cell lines were digested with MspI plus EcoRI or HpaII plus EcoRI, and hybridized with three genomic 32P-labelled probes; the first, second and third exons of the human c-MYC gene, respectively. The extent of methylation in cytosine at a single CCGG site in the third exon substantially decreased in these myeloma cell lines as compared with that in normal tonsillar B, LCL and Raji cells. No significant differences in hypomethylation between these myeloma, normal B, LCL and Raji cells was detected in the first and second exon of c-MYC. These results suggest that the hypomethylation in the third exon of c-MYC might be related to the enhanced expression of c-MYC in these human myeloma cell lines.

Hydrocortisone-induced enhancement of expression and changes in methylation of pepsinogen genes in stomach mucosa of the developing rat

Administration of hydrocortisone to infant rats caused a precocious increase in levels of mucosal pepsinogen and its mRNA together with morphological maturation of pepsinogen-producing cells. The increase in levels of pepsinogen mRNA was induced rapidly and was associated with increase in levels of its precursors, suggesting transcriptional regulation of pepsinogen genes by hydrocortisone. Methylation analysis with the methylation-sensitive restriction enzymes, HpaII and HhaI, revealed that hydrocortisone also induced sequential demethylation changes of CCGG and GCGC sites in and around pepsinogen genes. Most of these changes occurred after increases in transcription of the genes and did not appear to play a causal role in gene activation. Superficially, the observed demethylations corresponded to the sequential processes of morphological maturation of pepsinogen-producing cells. Thus, these changes in methylation are probably linked to hydrocortisone-induced differentiation of pepsinogen-producing cells and may reflect the mechanism in vivo for the maturation of pepsinogen genes.

De novo methylation of the MyoD1 CpG island during the establishment of immortal cell lines.

CpG dinucleotides are unevenly distributed in the vertebrate genome. Bulk DNA is depleted of CpGs and most of the cytosines in the dinucleotide in this fraction are methylated. On the other hand, CpG islands, which are often associated with genes, are unmethylated at testable sites in all normal tissues with the exception of genes on the inactive X chromosome. We used Hpa II/Msp I analysis and ligation-mediated polymerase chain reaction to examine the methylation of the MyoD1 CpG island in adult mouse tissues, early cultures of mouse embryo cells, and immortal fibroblastic cell lines. The island was almost devoid of methylation at CCGG sites in adult mouse tissues and in low-passage mouse embryo fibroblasts. In marked contrast, the island was methylated in 10T 1/2 cells and in six other immortal cell lines showing that methylation of this CpG island had occurred during escape from senescence. The island became even more methylated in chemically transformed derivatives of 10T 1/2 cells. Thus, CpG islands not methylated in normal tissues may become modified to an abnormally high degree during immortalization and transformation.

CisModification of the Steroid 21-Hydroxylase Gene Prevents Its Expression in the Y1 Mouse Adrenocortical Tumor Cell Line

The Y1 mouse adrenocortical tumor cell line retains the ability to synthesize and secrete steroids, but does not express steroid 21-hydroxylase (C21) and, therefore, does not produce 21-hydroxylated steroids. In this investigation the mechanisms underlying the loss of C21 activity in the Y1 cell line were explored. A 9-kilobase BglII fragment containing the C21 gene was cloned from the Y1 genome. This genomic clone directed the synthesis of C21 transcripts and 21-hydroxylated steroid products when transfected back into the Y1 cell line. As determined by restriction endonuclease digestions with MspI and HpaII, enzymes that distinguish between unmethylated and methylated CCGG sites, the endogenous C21 gene was extensively methylated in Y1 adrenal cells and in cells from other mouse tissues that do not normally express this gene. In contrast, the C21 gene was hypomethylated in primary cultures of mouse adrenal cells which normally synthesize large amounts of C21. The cloned C21 gene transfected into Y1 cells initially was unmethylated, but became extensively methylated with prolonged culture of the cells; prolonged culture of these transfectants also resulted in a loss of C21 expression. Loss of C21 expression in Y1 transfectants, however, temporally preceded the extensive methylation of the transfected C21 gene. Furthermore, treatment of Y1 cells with 5-azacytidine caused a demethylation of the endogenous C21 gene, but did not result in the recovery of C21 expression. These results indicate that Y1 cells contain a functional C21 gene that has been silenced by a reversible cis-modification event.(ABSTRACT TRUNCATED AT 250 WORDS)

DNA cytosine methylation in brain of patients with Alzheimer's disease

We developed a novel quantitative assay to test the hypothesis that defects in DNA cytosine methylation might be responsible for the brain chromatin abnormalities and transcriptional alterations observed in patients with Alzheimer's disease (AD). We found no significant difference in percent methylation of CCGG sites from brain DNA of 44 patients with AD compared with 20 normal subjects. These results, however, would not exclude genomic redistribution of methylcytosine in AD, or disturbed methylation of a limited population of critical brain-specific genes.

Methylation of chick UbI and UbII polyubiquitin genes and their differential expression during spermatogenesis

Northern analysis demonstrated that levels of ubiquitin transcript increased during the chicken testis maturation process, in agreement with the previously published increase of ubiquitin during this differentiation process. Specific probes for four different ubiquitin genes (two polyubiquitins, UbI and UbII, and two ubiquitin-fusion genes, UbCep52 and UbCep80) allowed us to analyse the expression of each individual gene. UbI polyubiquitin gene was expressed in all the tissues tested, and its transcript was the most abundant ubiquitin RNA in all of them. Unspliced UbI transcript, already detected in stressed chicken-embryo fibroblast, was also present in immature testis and reticulocytes. UbII, a chicken polyubiquitin gene not previously found expressed and not heat-shock-inducible, was specifically stimulated during the testis maturation process. Two minor ubiquitin fusion transcripts of 0.6 and 0.7 kb, corresponding to UbCep52 and UbCep80 respectively, were also found in chicken testis. Although differentially expressed, it was found that UbI and UbII chicken polyubiquitin genes had an HTF ('HpaII tiny fragments') island (CpG-rich and constitutively unmethylated region) in their 5' proximal non-coding region. In addition, we demonstrated the coexistence of 3' and/or 5' relatively distal methylated sites together with these 5' proximal HTF islands in both chicken polyubiquitin genes. 3' and 5' distal UbI CCGG sites were specifically hypermethylated in mature testis, whereas a 3' distal UbII CCGG site was found to be about 50% methylated in all DNAs tested.

Analysis of methylation and distribution of CpG sequences on human active and inactive X chromosomes by in situ nick translation

In situ nick translation of fixed mitotic chromosomes after HpaII or MspI digestion allows us to detect different DNA methylation levels along chromosomes. We used this technique to analyse the methylation levels of CCGG sites in the active and inactive X chromosomes of female human cells. In addition, we analysed the distribution of these sites with respect to the banding pattern. Our data show that the inactive X, as a whole, is more methylated than the active one and that CCGG sequences are preferentially located on R-positive bands.

METHYLATION PATTERN OF THE HLA‐DRα GENE IN HUMAN TISSUES

The CCGG and GCGC sites of the human HLA-DR alpha gene are hypermethylated in human tissues (including B-lymphocytes, T-lymphocytes, muscle, brain, sperm, skin, kidney, suprarenal and mammary glands) and three B-lymphoid cell lines. Therefore, the HLA-DR alpha gene can be transcribed even though extensively methylated. The only exception to the hypermethylated state of the HLA-DR alpha gene is represented by one or both of the two HhaI sites (H1 and H2) localized in the 5' portion of the gene. Analysis of the computer-generated secondary structure of the HLA-DR alpha mRNA suggests that the H1 and H2 sites belong to a region (5'-GAGCGCCCA-3'/5'-UGAGCGCUC-3') exhibiting extensive base pairing. Therefore, unmethylation of these CG sites can contribute in preventing mCG----TG/CA changes in this region, which would lead to extensive alterations of the secondary structure of the 5' portion of the HLA-DR alpha MRNA. On the other hand, the selective pressure to maintain unaltered the methylated CG dinucleotides in the coding regions of the HLA-DR alpha gene could be due to codon restrictions, since the majority of the methylation-related CG----TG or CG----CA variations would generate aminoacid changes. Accordingly, the analysis of different HLA-DR alpha genomic sequences indicates that variations of the CpG dinucleotides occur only in the non-coding portions of the HLA-DR alpha gene.

Demethylation of the Gene Expressing a Yolk Protein Precursor in Quail

Japanese quail produce more egg-yolk protein per gram of body weight than chickens do. Because cytosine phosphoguanine (CpG) methylation has been reported to correlate inversely with gene activity, the demethylation of cytosine residues in the quail vitellogenin 2 (Vg2) gene was assessed as a possible contributing factor. Vitellogenin genes are normally transcribed in the liver of female Japanese quail that are sexually mature. Changes in the methylation pattern of CCGG sites1 of the quail Vg2 gene were studied using the methyl-sensitive restriction endonucleases Msp I and Hpa II. At least five CCGG sites were detected within the transcribed region of the Vg 2 gene; one or two of these sites were hypomethylated in all tissues examined in male and female quail, two sites underwent transcription-dependent demethylation in the liver of laying females and also in the liver of males following estradiol injection (64 μmol estradiol/mL of absolute ethanol at .25 mL/100 g of BW), and another site was demethylated in the liver of estradiol-injected males but not in laying females. Two further sites present within the 5′ flanking sequences or 5′ structural region2 underwent transcription-dependent demethylation in the liver of laying females and of estradiol-treated males; one or both of these sites appears to be demethylated in the oviduct. Another site, within the 3′ flanking sequences or the 3′ structural gene region, underwent estradiol-dependent demethylation in the liver and the oviduct. The expression-linked demethylation of the CCGG sites in the Vg2 gene of quail appears to be similar to that reported for the chicken VTGII gene. The results of this study did not explain the enhanced production of yolk protein in Japanese quail, but did suggest the presence of a fundamental, conserved mechanism that must play an important role in the expression of the avian Vg gene.

Nucleotide-sequence-specific de novo methylation in a somatic murine cell line.

DNA fragments encoding the mouse steroid 21-hydroxylase (C21 or Cyp21A1) gene are de novo methylated when introduced into the mouse adrenocortical tumor cell line Y1 by DNA-mediated gene transfer. Although CCGG sequences within the C21 gene are de novo methylated, CCGG sites within flanking vector sequences, other mammalian gene sequences driven by the C21 promoter, and the neomycin-resistance gene, which was cotransfected with the C21 gene, do not become methylated. At least two separate signals for de novo methylation are encoded within the gene since three fragments derived from the C21 gene were methylated de novo. Specific de novo methylation of C21-derived sequences does not occur in L cells or Y1 kin8 cells; this suggests that the cellular factors needed for de novo methylation of the C21 gene are not ubiquitous. Most DNA sequences are not de novo methylated when introduced into somatic cells and DNA sequences other than the C21 gene are not de novo methylated when introduced into Y1 cells. Several groups have suggested that de novo methylation occurs in early embryonic cells and that somatic cells strictly maintain their methylation pattern by a semiconservative methyltransferase. Our results suggest that de novo methylation of specific nucleotide sequences can occur in some mammalian somatic cells.

Methylation state of cellular genes and oncogenes as a marker of malignancy in human carcinomas.

The methylation pattern of the human HLA-DR alpha gene was analyzed in primary tumors and lymph node metastases isolated from patients with a variety of tumors, including thyroid, pancreas, breast and gastric carcinomas and melanomas. In normal tissues (including breast, muscle, brain, sperm, T-and B-lymphocytes) the HLA-DR alpha gene is hypermethylated at CCGG and GCGC sites. In all tissues studied, the only constantly unmethylated region was located in the 5' portion of the gene. Our results indicate that the HLA-DR alpha gene is hypomethylated in metastatic lymph nodes, as well as in the carcinomas and melanomas studied. These findings lend support to the hypothesis that DNA hypomethylation of the human HLA-DR alpha gene may represent a molecular marker of malignant tumors.

In situ methylation of insect chromosomes with methylase HpaII

A method of in situ DNA methylation with the prokaryotic methylase HpaII has been developed on fixed mitotic and meiotic chromosomes of the insect species Baetica ustulata. Incorporation of methyl groups into the chromosomal DNA is revealed by autoradiography using a labelled substrate and by its ability to prevent endonuclease digestion. The method allows direct visualization of clusters of methylatable CCGG sites. The distribution of these clusters in the chromosome complement of Baetica shows two separate domains of heterochromatic DNA which differ in their methylation patterns. Each is distributed at equivalent locations in both homologous and nonhomologous chromosomes. The existence of two compartments, one methylated and the other unmethylated, in the heterochromatic DNA could be interpreted as a remnant of the ancestral echinoderm-like pattern of methylation.

Differential Hypomethylation of the c-MYC Protooncogene in Bladder Cancers at Different Stages and Grades

The 5-methylcytosine content of c-myc proto-oncogene DNA obtained from samples of normal bladders and of bladders with transitional cell carcinoma of different stage and grade was analyzed. Five CCGG sites (from the third coding region to the 3’ flanking region of the gene) which showed different methylation in normal and neoplastic samples were identified. The overall c-myc methylation levels were significantly reduced in carcinomas. Furthermore, a significant correlation between disease invasiveness and methylation level was found. Nevertheless, in each group of patients with the same histological grade, heterogeneity has been observed. This might be suggestive of different prognosis of the disease.