Limits...
Genome-wide analysis of DNA methylation associated with HIV infection based on a pair of monozygotic twins.

Zhang Y, Li SK, Tsui SK - Genom Data (2015)

Bottom Line: Therefore, using methylated DNA immunoprecipitation-microarray method (MeDIP-microarray), we found the increased DNA methylation level in peripheral blood mononuclear cells from HIV infected twin compared to her normal sibling.Moreover, several distinguished differential methylation regions (DMRs) in HIV infected twin worth further study.The raw data has been deposited in Gene Expression Omnibus (GEO) datasets with reference number GSE68028.

View Article: PubMed Central - PubMed

Affiliation: School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong.

ABSTRACT
Alteration of DNA methylation in mammalian cells could be elicited by many factors, including viral infections [1]. HIV has shown the ability to interact with host cellular factors to change the methylation status of some genes [2], [3], [4]. However, the change of the DNA methylation associated with HIV infection based on the whole genome has not been well illustrated. In this study, a unique pair of monozygotic twins was recruited: one of the twins was infected with HIV without further anti-retroviral therapy while the other one was healthy, which could be considered as a relatively ideal model for profiling the alterations of DNA methylation associated with HIV infection. Therefore, using methylated DNA immunoprecipitation-microarray method (MeDIP-microarray), we found the increased DNA methylation level in peripheral blood mononuclear cells from HIV infected twin compared to her normal sibling. Moreover, several distinguished differential methylation regions (DMRs) in HIV infected twin worth further study. The raw data has been deposited in Gene Expression Omnibus (GEO) datasets with reference number GSE68028.

No MeSH data available.


Related in: MedlinePlus

Potential interactions between hyper-methylated genes in HIV + twin and known genes required for HIV infection by STRING [6]. The green pentagram indicated that the genes were know genes required for HIV infection reported by others [5]; the orange rectangle indicated that the genes were hyper-methylated in HIV + twin with peak value > 5.0; the yellow pentagon indicated that the genes were known to be required in HIV infection, but could also be hyper-methylated in HIV + twin with peak value > 3.0.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4664672&req=5

f0005: Potential interactions between hyper-methylated genes in HIV + twin and known genes required for HIV infection by STRING [6]. The green pentagram indicated that the genes were know genes required for HIV infection reported by others [5]; the orange rectangle indicated that the genes were hyper-methylated in HIV + twin with peak value > 5.0; the yellow pentagon indicated that the genes were known to be required in HIV infection, but could also be hyper-methylated in HIV + twin with peak value > 3.0.

Mentions: The raw image files were obtained by MS 200 Microarray Scanner and MS 200 Data Collection Software. Then, the DEVA version 1.2.1 software (Data Extraction Visualization Analysis software, Roche, NimbleGen) was used for further analysis. Then, the result of microarray was analyzed by DEVA version 1.2.1 software (Roche, NimbleGen) using default parameters. In detail, 100929_HG19_Deluxe_Prom_Meth_HX1.ncd, 100929_HG19_Deluxe_Prom_Meth_HX1.ndf, 100929_HG19_Deluxe_Prom_Meth_HX1.pos and 100929_HG19_Deluxe_Prom_Meth_HX1.gff files were imported as the design files; the hg19 genome build was selected for organisms. The proper annotation files were selected for the identification of the features of the probes. After analyzing, the results of log2 ratios, P-score derived from Kolmogorov–Smirnov (KS) test were processed and obtained. The final results were presented as peak value based on P-score. The larger peak value from the designated region indicated that its differential methylation level was higher. The threshold for defining the differential methylation regions (DMRs) was set to 3.0. In Tables 1 and 2, the resulting list of the most differentially methylated regions (peak value > 5.0) from the HIV + twin and HIV − twin was shown. In addition, the hyper-methylated genes identified in HIV + twin were combined with the reported host genes required for HIV infection [5] to predict the potential protein–protein interactions by STRING [6]. The potential or known relationships among the genes were shown in Fig. 1.


Genome-wide analysis of DNA methylation associated with HIV infection based on a pair of monozygotic twins.

Zhang Y, Li SK, Tsui SK - Genom Data (2015)

Potential interactions between hyper-methylated genes in HIV + twin and known genes required for HIV infection by STRING [6]. The green pentagram indicated that the genes were know genes required for HIV infection reported by others [5]; the orange rectangle indicated that the genes were hyper-methylated in HIV + twin with peak value > 5.0; the yellow pentagon indicated that the genes were known to be required in HIV infection, but could also be hyper-methylated in HIV + twin with peak value > 3.0.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664672&req=5

f0005: Potential interactions between hyper-methylated genes in HIV + twin and known genes required for HIV infection by STRING [6]. The green pentagram indicated that the genes were know genes required for HIV infection reported by others [5]; the orange rectangle indicated that the genes were hyper-methylated in HIV + twin with peak value > 5.0; the yellow pentagon indicated that the genes were known to be required in HIV infection, but could also be hyper-methylated in HIV + twin with peak value > 3.0.
Mentions: The raw image files were obtained by MS 200 Microarray Scanner and MS 200 Data Collection Software. Then, the DEVA version 1.2.1 software (Data Extraction Visualization Analysis software, Roche, NimbleGen) was used for further analysis. Then, the result of microarray was analyzed by DEVA version 1.2.1 software (Roche, NimbleGen) using default parameters. In detail, 100929_HG19_Deluxe_Prom_Meth_HX1.ncd, 100929_HG19_Deluxe_Prom_Meth_HX1.ndf, 100929_HG19_Deluxe_Prom_Meth_HX1.pos and 100929_HG19_Deluxe_Prom_Meth_HX1.gff files were imported as the design files; the hg19 genome build was selected for organisms. The proper annotation files were selected for the identification of the features of the probes. After analyzing, the results of log2 ratios, P-score derived from Kolmogorov–Smirnov (KS) test were processed and obtained. The final results were presented as peak value based on P-score. The larger peak value from the designated region indicated that its differential methylation level was higher. The threshold for defining the differential methylation regions (DMRs) was set to 3.0. In Tables 1 and 2, the resulting list of the most differentially methylated regions (peak value > 5.0) from the HIV + twin and HIV − twin was shown. In addition, the hyper-methylated genes identified in HIV + twin were combined with the reported host genes required for HIV infection [5] to predict the potential protein–protein interactions by STRING [6]. The potential or known relationships among the genes were shown in Fig. 1.

Bottom Line: Therefore, using methylated DNA immunoprecipitation-microarray method (MeDIP-microarray), we found the increased DNA methylation level in peripheral blood mononuclear cells from HIV infected twin compared to her normal sibling.Moreover, several distinguished differential methylation regions (DMRs) in HIV infected twin worth further study.The raw data has been deposited in Gene Expression Omnibus (GEO) datasets with reference number GSE68028.

View Article: PubMed Central - PubMed

Affiliation: School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong.

ABSTRACT
Alteration of DNA methylation in mammalian cells could be elicited by many factors, including viral infections [1]. HIV has shown the ability to interact with host cellular factors to change the methylation status of some genes [2], [3], [4]. However, the change of the DNA methylation associated with HIV infection based on the whole genome has not been well illustrated. In this study, a unique pair of monozygotic twins was recruited: one of the twins was infected with HIV without further anti-retroviral therapy while the other one was healthy, which could be considered as a relatively ideal model for profiling the alterations of DNA methylation associated with HIV infection. Therefore, using methylated DNA immunoprecipitation-microarray method (MeDIP-microarray), we found the increased DNA methylation level in peripheral blood mononuclear cells from HIV infected twin compared to her normal sibling. Moreover, several distinguished differential methylation regions (DMRs) in HIV infected twin worth further study. The raw data has been deposited in Gene Expression Omnibus (GEO) datasets with reference number GSE68028.

No MeSH data available.


Related in: MedlinePlus