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PubMed2006

High-resolution mapping of DNA methylation in human genome using oligonucleotide tiling array.

DNA methylation is an epigenetic mark crucial in regulation of gene expression. Aberrant DNA methylation causes silencing of tumor suppressor genes and promotes chromosomal instability in human cancers. Most of previous studies for DNA methylation have focused on limited genomic regions, such as selected genes or promoter CpG islands (CGIs) containing recognition sites of methylation-sensitive restriction enzymes. Here, we describe a method for high-resolution analysis of DNA methylation using oligonucleotide tiling arrays. The input material is methylated DNA immunoprecipitated with anti-methylcytosine antibodies. We examined the ENCODE region ( approximately 1% of human genome) in three human colorectal cancer cell lines and identified over 700 candidate methylated sites (CMS), where 24 of 25 CMS selected randomly were subsequently verified by bisulfite sequencing. CMS were enriched in the 5' regulatory regions and the 3' regions of genes. We also compared DNA methylation patterns with histone H3 and H4 acetylation patterns in the HOXA cluster region. Our analysis revealed no acetylated histones in the hypermethylated region, demonstrating reciprocal relationship between DNA methylation and histone H3 and H4 acetylation. Our method recognizes DNA methylation with little bias by genomic location and, therefore, is useful for comprehensive high-resolution analysis of DNA methylation providing new findings in the epigenomics.

Acetylation↗
PubMed2005

Study of tissue-specific CpG methylation of DNA in extended genomic loci.

Modern approaches for studies on genome functioning include investigation of its epigenetic regulation. Methylation of cytosines in CpG dinucleotides is an inherited epigenetic modification that is responsible for both functional activity of certain genomic loci and total chromosomal stability. This review describes the main approaches for studies on DNA methylation. Under consideration are site-specific approaches based on bisulfite sequencing and methyl-sensitive PCR, whole-genome approaches aimed at searching for new methylation hot spots, and also mapping of unmethylated CpG sites in extended genomic loci.

Animals↗
PubMed2025

Epigenetic maps of pearl millet reveal a prominent role for CHH methylation in regulating tissue-specific gene expression.

UNLABELLED: Pearl millet (Pennisetum glaucum) is a major staple food in arid and semi-arid regions of sub-Saharan Africa, India, and South Asia. However, how epigenetic mechanisms regulate tissue-specific gene expression in this crop remains poorly understood. In this study, we profiled multiple epigenetic features in the young panicles and roots of pearl millet using RNA-seq, ATAC-seq, whole-genome bisulfite sequencing, and ChIP-seq (H3K4me3 and H3K36me3). We identified thousands of genes that were differentially expressed between these two tissues. Root-specific genes were enriched for plant hormone signaling, oxidative phosphorylation, and stress responses. Analysis of chromatin accessibility revealed that root-specific accessible chromatin regions (ACRs) were enriched in binding motifs for stress-responsive transcription factors (e.g., NAC, WRKY), whereas ACRs in young panicles were enriched in motifs for developmental regulators (e.g., AP2/ERF). DNA methylation profiling revealed 25,141 tissue-specific differentially methylated regions, with CHH methylation-rather than CG or CHG methylation-showing the strongest tissue specificity. Promoters of root-specific genes had higher levels of CHH methylation compared to those of young panicle-specific genes, suggesting that the roles of CHH methylation in regulating transcription might be tissue dependent. Notably, promoter-associated H3K4me3 marked panicle-specific genes, whereas root-specific expression was primarily linked to chromatin accessibility, suggesting a transcription factor-mediated regulatory mechanism. Together, our findings highlight the distinct epigenetic frameworks governing tissue-specific gene expression in pearl millet and provide valuable insights for advancing the genetic improvement of this crop. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42994-025-00243-2.

CHH methylation↗
PubMed2005

Aberrant methylation at HOXA10 may be responsible for its aberrant expression in the endometrium of patients with endometriosis.

OBJECTIVE: HOXA10, expressed in endometrium, plays an important role in uterine receptivity at the time of implantation. In the endometrium of women with endometriosis, its expression is reduced. The aim of this study was to determine whether the observed aberrant expression of HOXA10 is caused by aberrant methylation of the gene. STUDY DESIGN: Endometrial tissues were collected from 6 women with laparoscopically confirmed endometriosis, and 4 women who underwent tubal ligation and were confirmed to have no endometriosis. In addition, menstrual blood from 5 women with no gynecologic complaints was collected and also used as controls. Methylation-specific polymerase chain reaction (PCR) and bisulfite sequencing were performed in 3 fragments in 2 regions of HOXA10 to detect difference in methylation patterns. Real-time reverse transcriptase (RT)-PCR was also performed to measure expression levels of HOXA10 in select cases and controls. RESULTS: In all 3 fragments, there were highly statistically significant differences in methylation patterns between women with endometriosis and those without endometriosis. The expression level of HOXA10 was lower in women with endometriosis than those without, as previously reported. CONCLUSION: There is aberrant methylation in the endometrium of women with endometriosis compared with those without endometriosis. The aberrant methylation at HOXA10 may be responsible for the aberrant gene expression in the endometrium of women with endometriosis. This finding suggests that endometriosis may also be an epigenetic disease.

Base Sequence↗
PubMed2026

Dual Mechanisms Underlie the Repression of Repressor Element 1-Silencing Transcription Factor Expression in Lung Neuroendocrine Carcinoma Cells.

Recent advances in genetic analysis have led to further subtyping of small-cell lung carcinoma (SCLC). The major subtypes of SCLC are the achaete-scute family bHLH transcription factor 1 (ASCL1)-predominant (SCLC-A), neuronal differentiation 1 (NEUROD1)-predominant (SCLC-N), and POU class 2 homeobox 3 (POU2F3) (SCLC-P) subtypes. SCLC-A and SCLC-N tumors express chromogranin A (CHGA) and synaptophysin (SYP), but SCLC-P tumors do not. Large-cell neuroendocrine carcinoma, another type of neuroendocrine carcinoma (NEC), also frequently expresses CHGA and SYP. Because CHGA and SYP expression is controlled by a transrepressor, repressor element 1-silencing transcription factor (REST), the mechanisms underlying REST suppression in NEC were investigated, with a focus on miRNAs and epigenetics, to determine the causes of the differences in the expression of CHGA and SYP between SCLC-A/N and SCLC-P cells. The results showed that miR-375-3p, which was induced by ASCL1 and NEUROD1, repressed REST expression by binding to the 3'-untranslated region of REST mRNA. Bisulfite sequencing and experiments using a DNA methyltransferase inhibitor, a histone deacetylase inhibitor, and chromatin immunoprecipitation-based quantitative PCR revealed that promoter/enhancer hypermethylation and histone deacetylation causes REST gene inactivation in SCLC-A/N. These phenomena were also observed in a large-cell neuroendocrine carcinoma cell line that expressed high levels of ASCL1 and NEUROD1. Taken together, these findings suggest that NEC has dual repressive effects on REST expression, resulting in strict regulation of the expression of CHGA, SYP, and other REST-controlled neuronal/neuroendocrine-specific genes.

Humans↗
PubMed2026

Chronic psychological stress potentiates IgE class switch recombination via glucocorticoid receptor-mediated epigenetic reprogramming of B cells.

BACKGROUND: Chronic psychological stress is a well-recognized factor in the exacerbation of allergic diseases, with IgE playing a central role in their pathophysiology. However, the exact molecular mechanisms by which stress hormones directly influence IgE production and contribute to allergic responses remain largely uncharacterized. OBJECTIVE: This study aimed to elucidate the direct mechanisms through which chronic psychological stress, via elevated cortisol, regulates IgE class switch recombination (CSR) in B cells and contributes to stress-aggravated allergic inflammation in vivo. METHODS: We employed a chronic restraint stress (CRS) mouse model to investigate the impact of psychological stress on humoral immunity. In vitro experiments utilized primary murine B cells treated with physiological cortisol concentrations (250 nM), incorporating molecular techniques such as CRISPR-Cas9-mediated gene knockdown, chromatin immunoprecipitation (ChIP), whole-genome bisulfite sequencing, and pharmacological inhibitors of epigenetic enzymes. Primary human B cells and the U266 human myeloma cell line were used for translational validation. In vivo validation was performed using an ovalbumin (OVA)-induced allergic airway inflammation model with B cell-specific glucocorticoid receptor (GR) knockout mice. RESULTS: Chronic psychological stress significantly elevated plasma corticosterone and serum IgE levels in mice, with no changes in IgG1 or IgM. In purified in vitro B-cell cultures, cortisol promotes epigenetic remodeling at the Iε promoter region and enhances Iε germline transcript expression in an isotype-specific manner, and this effect was recapitulated in human B cells. GR bound to the Iε promoter's Amp_1 region (-154 to -62 bp), and CRISPR-Cas9-mediated GR knockdown abolished cortisol-induced IgE production. Mechanistically, cortisol increases enrichment of activating histone marks (H3K27ac, H3K4me3) and reduces H3K27me3 at the Iε promoter region, and induces site-specific DNA hypomethylation; inhibition of histone acetyltransferases (HATs) or DNA demethylation attenuated this effect. In vivo, B cell-specific GR knockout completely abrogated stress-induced exacerbation of allergic airway inflammation, including elevated serum IgE, eosinophilic inflammation, and airway hyperresponsiveness (AHR). CONCLUSION: Our findings support a mechanistic model in which chronic psychological stress, through elevated glucocorticoids, acts via GR to promote epigenetic remodeling at the Iε promoter region in B cells to enhance IgE synthesis and exacerbate allergic responses. This study provides a critical molecular link between the neuroendocrine system and adaptive immunity, offering promising therapeutic targets for stress-aggravated IgE-mediated diseases.

Animals↗
PubMed2003

Aberrant methylation of the specific CpG island portion regulates cyclooxygenase-2 gene expression in human gastric carcinomas.

Although it has been well established that overexpression of cyclooxygenase-2 (Cox-2) favors tumorigenesis and metastasis, the molecular mechanism that regulates Cox-2 expression has not been well defined in gastric carcinoma. Aberrant methylation of the CpG island is known to be one of the powerful mechanisms for the suppression of gene expression, and usually, CpG islands are very rich in promoter region and exon-1 region. But, it is controversial whether Cox-2 gene expression is regulated by methylation of promoter region or exon-1 region. In this study, we examined whether the hyper-methylation mediated transcriptional silencing of Cox-2 also occurred in human gastric carcinoma tissues and which portion of CpG island methylation is important in Cox-2 gene expression. Genomic DNAs from human gastric carcinoma tissues were treated with three methylation-sensitive restriction enzymes and then Southern blot analysis was performed. Out of 30 primary gastric tumor samples, 26 cases (86.6%) showed overexpression of Cox-2. Four cases (13.3%) with relatively decreased Cox-2 gene expression were associated with the presence of aberrant methylation of Cox-2 CpG island. We also found that methylation of promoter region and not exon-1 region is related with the transcriptional silencing of Cox-2 in gastric carcinoma cancer by detailed methylation mapping using bisulfite sequencing analysis. Our results suggest that the DNA methylation-mediated transcriptional silencing of Cox-2 is a predominant mechanism for the down-regulation of Cox-2 expression in human gastric carcinoma. Furthermore, the results suggest that methylation of not exon-1 region but promoter region is important to regulation of Cox-2 gene expression.

Blotting, Southern↗
PubMed2005

Reduced expression of the E-cadherin gene and its aberrant DNA methylation in hamster pancreatic tumors.

The expression of the E-cadherin gene and its DNA methylation status in the 5' upstream region were investigated in pancreatic duct adenocarcinomas (PDAs) induced by N-nitrosobis(2-oxopropyl)amine (BOP) in hamsters. Female Syrian golden hamsters received 70mg/kg BOP, followed by repeated exposure to an augmentation pressure regimen consisting of a choline-deficient diet combined with dl-ethionine then l-methionine and a further administration of 20mg/kg BOP. A total of 15 PDAs were obtained, along with total RNA for assessment of expression by real-time quantitative reverse transcription-polymerase chain reaction. The expression of the E-cadherin was significantly reduced in PDAs (p<0.05) compared with normal pancreatic tissue. For the analysis of methylation status, bisulfite sequencing was performed with two normal pancreatic tissues and six tumors. The normal pancreatic tissue was all demethylated in this region of E-cadherin. In contrast, six PDAs were highly methylated, correlating with reduced expression of the E-cadherin. These results suggest that aberrant DNA methylation of the E-cadherin gene may play a role in the development of PDAs induced by BOP in hamsters.

Adenocarcinoma↗
PubMed2006

Reduced expression of the Tslc1 gene and its aberrant DNA methylation in rat lung tumors.

TSLC1 gene inactivation due to promoter methylation has been reported in several human cancers. Here, we investigated the expression of the Tslc1 gene and its methylation pattern in lung adenocarcinomas induced by N-nitrosobis(2-hydroxypropyl)amine (BHP). Six-week-old male Wistar rats were given 2000 ppm BHP in their drinking water for 12 weeks and maintained without further treatment until they were sacrificed at 25 weeks. Total RNA was extracted from a total of 11 lung adenocarcinomas and their Tslc1 gene expressions were analyzed by real-time quantitative reverse transcription-polymerase chain reaction. Tslc1 expression was significantly reduced in the lung adenocarcinomas compared with three normal lung tissues (p < 0.05). Bisulfite sequence analysis of four lung adenocarcinomas and two normal lung tissues revealed that the 5' upstream region of the Tslc1 gene was highly methylated in the four lung adenocarcinomas, but unmethylated in the two normal lung tissues. These results suggest that aberrant Tslc1 gene methylation may be involved in BHP-induced development of lung adenocarcinomas in rats.

Animals↗
PubMed2006

Involvement of aberrant DNA methylation on reduced expression of lysophosphatidic acid receptor-1 gene in rat tumor cell lines.

Lysophosphatidic acid (LPA) is a bioactive phospholipid that stimulates cell proliferation, migration, and protects cells from apoptosis. It interacts with specific G protein-coupled transmembrane receptors. Recently, it has been reported that alterations of LPA receptor expression might be important in the malignant transformation of tumor cells. Therefore, to assess an involvement of DNA methylation in reduced expression of the LPA receptor-1 (lpa1) gene, we investigated the expression of the lpa1 gene and its DNA methylation patterns in rat tumor cell lines. Both rat brain-derived neuroblastoma B103 and liver-derived hepatoma RH7777 cells used in this study indicated no expression of lpa1. For the analysis of methylation status, bisulfite sequencing was performed with B103 and RH7777 cells, comparing with other lpa1 expressed cells and normal tissues of brain and liver. The lpa1 expressed cells and tissues were all unmethylated in this region of lpa1. In contrast, both B103 and RH7777 cells were highly methylated, correlating with reduced expression of the lpa1. Treatment with 5-aza 2'-deoxycytidine induced expression of lpa1 gene in B103 and RH7777 cells after 24h. In RH7777 cells treated with 5-aza 2'-deoxycytidine, stress fiber formation was also observed in response to LPA in RH7777 cells, but not in untreated RH7777 cells. These results suggest that aberrant DNA methylation of the lpa1 gene may be involved in its reduced expression in rat tumor cells.

Animals↗
PubMed2006

Aberrant DNA methylation of the 5' upstream region of Tslc1 gene in hamster pancreatic tumors.

To determine if the Tslc1 gene is involved in pancreatic carcinogenesis, the expression level of Tslc1 and the DNA methylation status of its 5' upstream region were investigated in pancreatic duct adenocarcinomas (PDAs) induced in hamsters by N-nitrosobis(2-oxopropyl)amine (BOP). Female Syrian golden hamsters received 70 mg/kg of BOP followed by repeated exposure to an augmentation pressure regimen consisting of a choline-deficient diet combined with ethionine-methionione-BOP injection. Total RNA was extracted from 11 PDAs and the level of Tslc1 expression was measured in each by real-time quantitative reverse transcription (RT)-polymerase chain reaction (PCR). The expression level of Tslc1 was significantly reduced in PDAs (p < 0.05) compared with normal pancreatic tissues. In order to assess the DNA methylation status of the 5' upstream region of Tslc1, bisulfite sequencing was performed. Although this region was unmethylated in normal pancreatic tissue, it was highly methylated in four PDAs, correlating with reduced Tslc1 expression. These results suggest that a reduction in the expression of Tslc1 due to aberrant DNA methylation might be involved in the development of PDAs induced in hamsters by BOP.

5' Untranslated Regions↗
PubMed2006

Developmental changes in DNA methylation and covalent histone modifications of chromatin associated with the epsilon-, gamma-, and beta-globin gene promoters in Papio anubis.

The baboon is a suitable and relevant animal model to study the mechanism of human globin gene switching. This investigation addresses the role of DNA methylation and histone coding in globin gene switching in the baboon, Papio anubis. Bisulfite sequencing and chromatin immunoprecipitation studies were performed in erythroid cells purified from fetuses of varying gestational ages and from adult bone marrow to analyze the manner that changes in DNA methylation of the epsilon-, gamma-, and beta-globin promoters and association of ac-H3, ac-H4, H3-dimeK4, H3-dimeK36, and H3-dimeK79 with the epsilon-, gamma-, and beta-globin promoters occur during development. Changes in DNA methylation of the epsilon- and gamma-globin gene promoters during transitional stages of globin gene switching were consistent with the stochastic model of methylation and a role of DNA methylation in gene silencing. Enrichment of ac-H3, ac-H4, and pol II at the promoters of developmentally active genes was observed, while the pattern of distribution of H3-dimeK4 and H3-dimeK79 suggests that these modifications are found near both currently and formerly active promoters. Enrichment of H3-dimeK36 at the silenced epsilon-globin gene promoter was observed. These studies demonstrate that coordinated epigenetic modifications in the chromatin structure of the beta-like globin gene promoters accompany the highly regulated changes in expression patterns of these genes during development.

Animals↗
PubMed2005

Differential expression of MHC class II molecules in highly metastatic breast cancer cells is mediated by the regulation of the CIITA transcription Implication of CIITA in tumor and metastasis development.

We analyzed the differential gene expression between variants of MDA-MB-435 human breast cancer cell line that share an identical genetic background but have different metastatic ability. The major histocompatibility complex class II was found down-regulated in highly metastatic cells and correlated with MHC transactivator (CIITA) expression. Constitutive CIITA expression observed in poorly metastatic is driven by promoters III and IV of CIITA gene. Conversely, both promoters were ineffective in highly metastatic cells. The MHC class II and CIITA expression was restored in these cells upon stimulation with IFNgamma or by the treatment with a hypomethylating agent. Both treatments induced USF-1 and IRF binding complexes to promoter IV but only IFNgamma induced the binding of 435-Lung2 nuclear proteins to an ARE-1 site at the promoter III. Neither Southern blot nor bisulfite sequencing of promoter IV demonstrated strong hypermethylation of this promoter at the IFNgamma-responsive elements such as GAS, E-box or IRF-1. We suggest that partial or hemimethylation of promoter IV is sufficient to silence the CIITA expression in highly metastatic cells and that this epigenetic mechanism is responsible for the lack of MHC-II expression. Forced CIITA expression restored the MHC-II antigen expression in 435-Lung2 cells and abrogates spontaneous lung metastasis in both SCID and nude mice but also affected the tumorigenicity in nude mice. The increase in NK cell infiltration in nude mice bearing CIITA-tumors correlated with sign of tumor cell apoptosis and the increase in the number of NK cells in the spleens, suggesting that NK cells might be responsible for the observed antitumor activity.

Animals↗
PubMed2005

5-Aza-2'-deoxycytidine induces retinoic acid receptor-beta(2) demethylation and growth inhibition in esophageal squamous carcinoma cells.

Esophageal squamous cell carcinoma (ESCC) is one of the most common tumors in human. Previous studies showed that multiple genetic and epigenetic alterations involved in carcinogenesis of esophagus, whereas the molecular mechanisms are poorly understood. So far, more and more ESCC-related genes have been found and retinoic acid receptor beta(2) (RARbeta(2)) is such a gene which was recognized as a putative tumor suppressor gene since reduced RARbeta(2) mRNA expression has been observed in several solid tumors, including ESCC. A growing evidence indicated that RARbeta(2) was required for the growth inhibitory effect of retinoic acid (RA). However, the molecular mechanism of its inactivation remained obscure in ESCC. The RARbeta2 methylation status was assessed by methylation-specific PCR (MSP) in 12 ESCC cell lines and compared with their mRNA and protein expression level. Bisulfite sequencing of RARbeta(2) promoter region was performed to confirm the MSP results. After 5-aza-2'-deoxycytidine (5-aza-dc) treatment the expression of RARbeta(2) was reversed in two RARbeta(2)-downregulated cell lines. Therefore, hypermethylation of the promoter regions of RARbeta2 gene is a major mechanism of transcriptional inactivation and might be involved in tumor development of esophagus in some ESCC cell lines suggesting that multiple mechanisms contribute to the loss of RARbeta(2) expression in ESCC cell lines. Furthermore, the methylation status of RARbeta(2) promoter region and its expression was analyzed in 51 ESCC tissue samples with their adjacent normal epithelia and two normal esophageal epithelia. The results showed that there was a statistically significant correlation between methylation status of RARbeta(2) and tumor grade; Moreover, a relationship between methylation status and decreased RARbeta(2) expression was found only in G(2) stage tumors. After 5-aza-dc treatment, RARbeta(2) restoration was accompanied by growth inhibition and this might be one of the mechanisms but not the only mechanism for the tumor cell growth inhibition by 5-aza-dc. This study may have clinical applications for ESCC therapy and prevention.

Adult↗
PubMed2006

Methylation status of the Ep-CAM promoter region in human breast cancer cell lines and breast cancer tissue.

We examined the methylation status of the Ep-CAM promoter region of human breast cancer cell lines and breast cancer tissue using MethyLight technology and bisulfite sequencing. We found the promoter of Ep-CAM-negative breast cancer cell lines Hs 578T to be methylated to a higher degree as compared to positive cell lines MCF-7. Demethylation of cell lines was performed using 5-aza-2'-deoxycytidine. Ep-CAM RNA and protein expression could be partially restored by treating cells with 5-Aza-2'-deoxycytidine. In most primary breast cancer tissue, methylation of the Ep-CAM gene could be detected at a low level and no correlation was found with Ep-CAM protein expression in tumour tissue. Taken together, these data suggest that methylation of the Ep-CAM promoter is not a crucial mechanism for regulation of Ep-CAM expression in breast cancer. Thus, most important regulatory mechanisms have to be supposed in vivo.

Antigens, Neoplasm↗
PubMed2005

Analysis of CpG methylation in the killifish CYP1A promoter.

Fundulus heteroclitus (Atlantic killifish or mummichog) inhabiting a creosote-contaminated Superfund site on the Elizabeth River (VA, USA), exhibit a lack of induction of cytochrome P4501A (CYP1A) mRNA, immunodetectable protein, and catalytic activity after exposure to typical inducers. This "refractory CYP1A phenotype" is not explained by alterations in mRNA expression of known CYP1A transcription factors. Furthermore, the refractory phenotype is lost progressively during development in laboratory-reared F1 generation fish. Thus, while heritable, the refractory CYP1A phenotype does not appear to be genetically based. To test the hypothesis that cytosine methylation at CpG sites in the promoter region of CYP1A underlies the refractory CYP1A phenotype, we employed bisulfite sequencing to compare the methylation status of CpG sites in the CYP1A promoter region of DNA from killifish from the Elizabeth River and a reference site. We examined genomic DNA both from livers of wild-caught adult killifish and from pools of F1 generation embryos raised in the laboratory. In fish from both the contaminated and the reference site, cytosine methylation was not detectable at any of the 34 CpG sites examined, including 3 that are part of putative xenobiotic response elements.

Animals↗
PubMed2006

5' CpG island methylation analysis identifies the MAGE-A1 and MAGE-A3 genes as potential markers of HCC.

OBJECTIVES: The change in DNA methylation patterns can be used to distinguish between normal and cancer cells. The aim of the present study was to examine the 5' CpG island methylation patterns of the cancer-testis antigen (CT antigen) gene family, MAGE-As, in hepatocellular carcinoma (HCC), and to develop the DNA demethylation pattern as a novel tumor biomarker. METHODS: We used bisulfite-sequencing PCR (BSP) to map the methylation status of the CpG site among the promoter of the MAGE-A gene family in several HCC cell lines including Hep G2, BEL7402, BEL7404, and BEL7407, and normal peripheral blood white blood cells (WBCs). According to differences of the methylation pattern between HCC cell lines and the control, methylation-special PCRs (MSP) have been developed. The developed MSPs were used to detect the paraffin-embedded slices that were pathologically diagnosed as HCC, hepatocirrhosis, hepatitis, and healthy. RESULTS: We found that several CpG sites among the MAGE-A1 and MAGE-A3 promoters have different methylation patterns in the HCC cell lines as compared to those in normal WBCs. Two sets of MSP primers were designed to distinguish the HCC genomic DNA and normal control cell genomic DNA as novel tumor biomarkers, and the biomarkers were validated on the archived paraffin sections of liver primary tissue. In the detection of 34 HCCs and 17 tumor-free liver tissues, the clinical sensitivity and specificity were 91.2% and 100%, respectively. CONCLUSION: Detection of aberrant methylation patterns of MAGEs CpG islands using MSP may be useful for diagnosis of HCC.

Adult↗
PubMed2007

The DNA glycosylase/lyase ROS1 functions in pruning DNA methylation patterns in Arabidopsis.

The Arabidopsis DNA glycosylase/lyase ROS1 participates in active DNA demethylation by a base-excision pathway. ROS1 has been shown to be required for demethylating a transgene promoter. To determine the function of ROS1 in demethylating endogenous loci, we carried out bisulfite-sequencing analysis of several transposons and other genes in the ros1 mutant. In the wild-type, although CpG sites at the majority of these loci are heavily methylated, many of the CpXpG and CpXpX sites have low levels of methylation or are not at all methylated. However, these CpXpG and CpXpX sites become heavily methylated in the ros1 mutant. Associated with this increased DNA methylation, these loci show decreased expression in the ros1 mutant. Our results suggest that active DNA demethylation is important in pruning the methylation patterns of the genome, and even the normally "silent" transposons are under dynamic control by both methylation and demethylation. This dynamic control may be important in keeping the plant epigenome plastic so that it can efficiently respond to developmental and environmental cues.

Arabidopsis↗