DNA methylation

Expression profiles of DNA repair-related genes in rat target organs under subchronic cadmium exposure

Y. X. Lei, Lu, Q., Shao, C., He, C. C., Lei, Z. N., and Lian, Y. Y., “Expression profiles of DNA repair-related genes in rat target organs under subchronic cadmium exposure”, vol. 14, pp. 515-524, 2015.

We aimed to evaluate the toxicity of long-term exposure to different cadmium (Cd) doses in rats and expression profiles of DNA repair-related genes. The model rats were exposed to different concentrations of CdCl2 for 3 months, and 5 DNA repair-related genes - hMSH2, MLH1, XRCC1, hOGG1, ERCC1 - were cloned in different tissues, including the liver, kidney, heart, and lung. Accumulated amounts of Cd were detected in the tissues.

Cumulative methylation alternations of gene promoters and protein markers for diagnosis of epithelial ovarian cancer

B. L. Xing, Li, T., Tang, Z. H., Jiao, L., Ge, S. M., Qiang, X., and OuYang, J., “Cumulative methylation alternations of gene promoters and protein markers for diagnosis of epithelial ovarian cancer”, vol. 14, pp. 4532-4540, 2015.

DNA methylation plays an important role in carcinogenesis and cancer development. In this study, we examined gene methylation in epithelial ovarian cancer (EOC) using cationic conjugated polymer (CCP)-based fluorescence resonance energy transfer (FRET) to evaluate the application of cumulative methylation alternations of genes associated with cancer antigen 125 for early cancer diagnosis.

Transcriptional regulation of CD4 gene expression in porcine kidney epithelial cells by virus-like double-stranded RNA and DNA methyltransferase inhibitor

X. S. Wang, Ao, H., Zhai, L. W., Bai, L. J., He, W. Y., Wang, C. D., and Yu, Y., “Transcriptional regulation of CD4 gene expression in porcine kidney epithelial cells by virus-like double-stranded RNA and DNA methyltransferase inhibitor”, vol. 13, pp. 3346-3355, 2014.

The effects of virus-like double-stranded RNA (dsRNA, PolyI:C) and DNA methyltransferase inhibitor (Aza-CdR) on CD4 gene expression were investigated in a porcine kidney cell line (PK15). We found that expression levels of TLR3 and IFNαwere significantly upregulated by PolyI:C, compared to the untreated PK15 cells, which shows that PolyI:C successfully mimics viral infection in PK15 cells.

Comprehensive gene expression analysis of the DNA (cytosine-5) methyltransferase family in rice (Oryza sativa L.)

F. Ahmad, Huang, X., Lan, H. X., Huma, T., Bao, Y. M., Huang, J., and Zhang, H. S., “Comprehensive gene expression analysis of the DNA (cytosine-5) methyltransferase family in rice (Oryza sativa L.)”, vol. 13, pp. 5159-5172, 2014.

Cytosine DNA methylation is a conserved epigenetic regulatory mechanism in both plants and animals. DNA methyltransferases (DNA MTases) not only initiate (de novo) but also maintain the process of DNA methylation. Here, we characterized the genome-wide expression profiles of 10 cytosine DNA MTase genes belonging to 4 subfamilies, MET1, CMT, DNMT2, and DRM, in rice.

Analysis of DNA methylation patterns and levels in maize hybrids and their parents

T. J. Liu, Sun, L. F., Shan, X. H., Wu, Y., Su, S. Z., Li, S. P., Liu, H. K., Han, J. Y., and Yuan, Y. P., “Analysis of DNA methylation patterns and levels in maize hybrids and their parents”, vol. 13, pp. 8458-8468, 2014.

Heterosis is the superior performance of heterozygous individuals and has been widely exploited in plant breeding, although the underlying regulatory mechanisms still remain largely elusive. To understand the molecular basis of heterosis in maize, in this study, roots and leaves at the seedling stage and embryos and endosperm tissues 15 days after fertilization of 2 elite hybrids and their parental lines were used to estimate the levels and patterns of cytosine methylation by the methylation-sensitive amplification polymorphism method.

De novo DNA methylation of the paternal genome in 2-cell mouse embryos

X. S. Ma, Wang, X. G., Qin, L., Song, C. L., Lin, F., Song, J. M., Zhu, C. C., and Liu, H. L., “De novo DNA methylation of the paternal genome in 2-cell mouse embryos”, vol. 13, pp. 8632-8639, 2014.

The developmental dynamics of DNA methylation events have been well studied. Active demethylation of the paternal genome occurs in the zygote, passive demethylation occurs during cleavage stages, and de novo methylation occurs by the blastocyst stage. It is believed that the paternal genome has lower levels of methylation during early development than the maternal genome. However, in this study, we provide direct and indirect evidence of genome-wide de novo DNA methylation of the paternal genome after the first cell cycle in mouse embryos.

Position effect variegation and epigenetic modification of a transgene in a pig model

Z. Yin, Kong, Q. R., Zhao, Z. P., Wu, M. L., Mu, Y. S., Hu, K., and Liu, Z. H., “Position effect variegation and epigenetic modification of a transgene in a pig model”, vol. 11, pp. 355-369, 2012.

Sequences proximal to transgene integration sites are able to regulate transgene expression, resulting in complex position effect variegation. Position effect variegation can cause differences in epigenetic modifications, such as DNA methylation and histone acetylation. However, it is not known which factor, position effect or epigenetic modification, plays a more important role in the regulation of transgene expression.

Genetic instability and CpG methylation in the 5'-flanking region of the PAI-1 gene in Chinese patients with gastric cancer

J. Liu, Li, X., Yu, N., Yang, Y. - Q., Li, X., Ye, Z. - Y., and Li, J. - C., “Genetic instability and CpG methylation in the 5'-flanking region of the PAI-1 gene in Chinese patients with gastric cancer”, vol. 11, pp. 2899-2908, 2012.

We explored a possible correlation of genetic instability and CpG methylation in the 5'-flanking region of the PAI-1 gene with clinicopathologic features of gastric cancer in Chinese patients and looked for molecular markers for diagnosing gastric tumor development. Microsatellite instability and loss of heterozygosity of the PAI-1 gene locus D7S515, D7S471 and pai-1 in 50 specimens of gastric cancer and relevant pericancerous tissues were detected by PCR-single strand conformation polymorphism (PCR-SSCP) with sliver staining.

Methylation-sensitive amplification polymorphism analysis of fat and muscle tissues in pigs

J. D. Ma, Li, M. Z., Zhou, S. L., Zhou, C. W., and Li, X. W., “Methylation-sensitive amplification polymorphism analysis of fat and muscle tissues in pigs”, vol. 11, pp. 3505-3510, 2012.

DNA methylation may be involved in regulating the expression of protein-coding genes, resulting in different fat and muscle phenotypes. Using a methylation-sensitive amplified polymorphism approach, we obtained 7423 bands by selective amplification of genomic DNA from six different fat depots and two heterogeneous muscle types from Duroc/Landrace/Yorkshire cross-bred pigs.

5-Aza-2’-deoxycytidine may influence the proliferation and apoptosis of cervical cancer cells via demethylation in a dose- and time-dependent manner

T. T. Yao, Mo, S. M., Liu, L. Y., Lu, H. W., Huang, M. L., and Lin, Z. Q., “5-Aza-2’-deoxycytidine may influence the proliferation and apoptosis of cervical cancer cells via demethylation in a dose- and time-dependent manner”, vol. 12, pp. 312-318, 2013.

The methylation of tumor suppressor genes has been shown to be involved in many human cancers. 5-Aza-2’-deoxycytidine (5-Aza-CdR) can reactivate the expression of methylated tumor suppressor genes. In our study, 2 human cervical cancer cell lines, HeLa and SiHa, were treated with different concentrations (20, 10, 5, and 2.5 μM) of 5-Aza-CdR for 24, 48, and 72 h. After incubation, cells were analyzed by 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide assay and flow cytometry. The expression of RASSF1A and APAF-1 was detected by RT-PCR.

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