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

The correlation between DNA methylation and transcriptional expression of human dopamine transporter in cell lines

This study aims to investigate the relationship between DNA methylation and expression of human dopamine transporter (hDAT). We examined methylation status of hDAT in cells with various hDAT expression levels, including two dopaminergic neural cell lines (SK-N-AS and SH-SY-5Y) and one non-dopaminergic cell line (HEK293) by bisulfite sequencing PCR(BSP). The effects of DNA methyltransferase inhibitor 5-aza-dC or/and histone deacetylase inhibitor (HDACi, sodium butyrate, NaB) on the DNA methylation status and mRNA expression levels of hDAT were examined. The results revealed marked hypomethylation of the two promoter regions (-1214 to -856bp and -48 to 439bp, the first base of exon 1 was taken as +1 bp)of hDAT in SK-N-AS (4.7%±2.0^mC and 3.5%±1.0^mC, respectively) compared with SH-SY-5Y (88.0%±4.4%^mC and 81.1%±8.8%^mC) and HEK293 (90.7%±2.4^mC and 84.4%±8.6% ^mC) cell lines, indicating a cell-specific methylation regulation of hDAT. 5-aza-dC and NaB decreased hypermethylation,while increase hDAT expression in SH-SY-5Y cells and recovered hDAT mRNA expression in HEK293 cells. DNA methylation enabled the cell-specific differential expression of the hDAT gene. hDAT silencing was reversed by the introduction of DNA hypomethylation via 5-aza-dC or/and NaB.

NRF1 coordinates with DNA methylation to regulate spermatogenesis

Spermatogenesis is a highly coordinated process that requires tightly regulated gene expression programmed by transcription factors and epigenetic modifiers. In this study, we found that nuclear respiratory factor (NRF)-1, a key transcription factor for mitochondrial biogenesis, cooperated with DNA methylation to directly regulate the expression of multiple germ cell-specific genes, including Asz1 In addition, conditional ablation of NRF1 in gonocytes dramatically down-regulated these germline genes, blocked germ cell proliferation, and subsequently led to male infertility in mice. Our data highlight a precise crosstalk between transcriptional regulation by NRF1 and epigenetic modulation during germ cell development and unequivocally demonstrate a novel role of NRF1 in spermatogenesis.-Wang, J., Tang, C., Wang, Q., Su, J., Ni, T., Yang, W., Wang, Y., Chen, W., Liu, X., Wang, S., Zhang, J., Song, H., Zhu, J., Wang, Y. NRF1 coordinates with DNA methylation to regulate spermatogenesis.

MeDIP-seq reveals the features of mitochondrial genomic methylation in immature testis of Chinese mitten crab Eriocheir sinensis

In this study, the methylation of mitochondrial genome in the immature testis of Chinese mitten crab Eriocheir sinensis of the Yangtze River system was determined for the first time using MeDIP-seq. Our methylated DNA fragments covered more than 99% of the mitochondrial genome in E. sinensis loaded from GenBank. There were 8 mutated bases and 42 SNPs in the crab mitochondrial genome. The methylation presented in all genes as well as in an A + T region, but less in intergenic regions in the mitochondrial genome. However, the level of methylation of most genes coding proteins and the A + T region were high. But, the majority of genes encoding tRNAs were hypomethylated, and both the rRNA genes also showed methylation of low or median frequency. Especially, the level of methylation of the intergenic regions is the lowest. Those features indicated that the methylation of DNA may play an important role in gene expressing regulation in the mitochondrial genome of immature testis in E. sinensis.

Identification of specific DNA methylation sites on the Y-chromosome as biomarker in prostate cancer

As a diagnostic biomarker, prostate special antigen (PSA) tests always generate false positive results and lead to unnecessary and/or repeat biopsies. Therefore, there is an urgent need for developing more sensitive, specific diagnostic biomarkers. We epigenotyped methylated sites in cancer tissues and adjacent normal tissues from 66 patients. In comparison with normal adjacent tissues, we observed that there were 6 aberrant methylation sites in prostate cancer tissues on the Y-chromosome. We further performed pyrosequencing using urine of PCa patients and we identified one methylated site (cg05163709) as a potential biomarker. We evaluated the predictive capacity of the aberrant methylated sites using the area under receiver operating characteristic (ROC) curve (AUC). The ROC analysis showed a higher AUC for cg05163709 (0.915) than prostate-specific antigen (PSA, 0.769). These results indicated that aberrant DNA methylation of cg05163709 on the Y-chromosome could serve as a potential diagnostic biomarker with high sensitivity and specificity.

Methylation status of WWOX gene promoter CpG islands in epithelial ovarian cancer and its clinical significance

WW domain-containing oxidoreductase (WWOX) is a newly identified tumor suppressor gene that is associated with abnormal DNA methylation. The aim of this study was to evaluate the methylation status of CpG islands in the WWOX gene promoter region in cases of epithelial ovarian cancer and explore the correlation between the methylation status of the WWOX gene CpG islands and clinicopathological indices in patients with epithelial ovarian cancer. The methylation status of the WWOX gene CpG island was evaluated by methylation-specific polymerase chain reaction (MSP) in 48 patients with epithelial ovarian cancer, 18 patients with borderline epithelial ovarian tumors, 26 patients with epithelial benign tumors and 33 patients with normal ovarian tissues. Results showed that the rates of CpG island methylation in the WWOX gene promoter region in epithelial ovarian cancer tissues, borderline ovarian tumor tissues and benign ovarian tumor tissues were 43.75, 26.32 and 3.84%, respectively. The WWOX gene CpG islands were not methylated in normal ovarian tissues. The rate of CpG island methylation in epithelial ovarian cancer tissues was higher than that of other ovarian tissues and these differences were found to be statistically significant (P<0.01). The rate of CpG island methylation in the WWOX gene promoter region in late-stage (stage III and IV) epithelial ovarian cancer tissues was higher than that of early-stage (stage I and II) epithelial ovarian cancer tissues, and these differences were found to be statistically significant (P<0.05). In conclusion, epithelial ovarian cancer tissues showed CpG island hypermethylation in the WWOX gene promoter region, which may be an important mechanism leading to WWOX gene inactivation. Atypical methylation of WWOX gene is associated with the formation and progression of epithelial ovarian cancer, rendering it a potentially important indicator in the early diagnosis and prognosis of epithelial ovarian cancer.

Quantitative aberrations of hypermethylated RASSF1A gene sequences in maternal plasma in pre-eclampsia

OBJECTIVE

To study if quantitative aberrations in circulating placental-derived hypermethylated RASSF1A DNA in maternal plasma are associated with pre-eclamptic pregnancies.

METHOD

Maternal plasma and placental tissues from third-trimester pre-eclamptic women and gestational-age matched normotensive controls were studied. Real-time PCR was performed to quantify RASSF1A concentrations before and after methylation-sensitive restriction digestion in a duplex assay, where ss-actin concentrations were quantified as an internal control to confirm complete enzyme digestion.

RESULTS

The median concentrations of hypermethylated RASSF1A were 4.3-fold higher in maternal plasma of pre-eclamptic subjects than in controls. There was no significant difference between the extent of RASSF1A hypermethylation in placental tissues obtained from pre-eclamptic and control pregnancies.

CONCLUSION

This study demonstrated the potential utility of hypermethylated RASSF1A sequences in maternal plasma as a gender- and polymorphism-independent marker for pre-eclampsia.

Fetal DNA in maternal plasma: progress through epigenetics

The discovery of cell-free fetal DNA in maternal plasma has opened up new possibilities for noninvasive prenatal diagnosis. Most of the work in this field has focused on the detection of fetal genetic markers that are distinguishable from the background maternal DNA. The feasibility of detecting fetal epigenetic markers in maternal plasma using an imprinted locus was demonstrated in 2002. This work has recently led to the development of the first universal fetal epigenetic marker, hypomethylated maspin, which can be used for fetal DNA detection in maternal plasma, irrespective of fetal gender and genetic polymorphisms. It is expected that many more fetal epigenetic markers that can be used in this manner will be developed over the next few years. These markers may catalyze the eventual clinical use of circulating fetal DNA for noninvasive prenatal diagnosis, such as for the detection of fetal chromosomal aneuploidies.