Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Use of the B cell transcription program results in hypomethylation and overexpression of key genes in EBV-mediated conversion of resting to proliferative B cells

ABSTRACT: We investigated the effects of experimental EBV infection of B cells on DNA methylation profiles by using high-throughput analysis. Remarkably, we observed hypomethylation of around 250 genes, but no hypermethylation. Hypomethylation did not occur at repetitive sequences, consistent with the absence of genomic instability in lymphoproliferative cells. Changes in methylation only occurred after cell divisions started, without the participation of the active demethylation machinery, and were concomitant with acquisition of B cells of the ability to proliferate. Gene ontology analysis, expression profiling, high-throughput analysis of the presence of transcription factor-binding motifs and occupancy revealed that most genes undergoing hypomethylation are active and display the presence of NFkB p65 and other B cell-specific transcription factors. Promoter hypomethylation associated with upregulation of genes relevant for the phenotype of proliferating lymphoblasts. Interestingly, pharmacologically-induced demethylation increased the efficiency of transformation of resting B cells to lymphoblastoid cells, suggesting the establishment of a productive cooperation between hypomethylation and lymphocyte proliferation. Bisulfite-converted DNA from 12 samples (6 Bcell, 6 Bcell immortalized) were hybridized to the Illumina Infinium 27k Human Methylation Beadchip v1.2.

ORGANISM(S): Homo sapiens

SUBMITTER: Fatima Al-Shahrour

PROVIDER: E-GEOD-41957 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Human aging implies many phenotypic modifications and an increased susceptibility to many common diseases, phenomena that cannot be fully explained by the constrained genetic setting. An alternative pathway that could explain the age-associated alterations is epigenetic drifts. To address this issue, we performed Whole Genome Bisulfite Sequencing (WGBS) of a newborn and of a centenarian. The centenarian DNA exhibited a significant loss in DNA methylation and a poor correlation in the methylation status of neighboring CpGs throughout the genome. From a gene-regulatory region standpoint, we observed that the DNA hypomethylation events occurred mainly at CpG-poor promoters and in tissue-specific genes, whereas a greater level of DNA methylation was observed in CpG island promoters. Most importantly, we extended the study to a larger cohort of newborn and nonagenarian samples using a 450,000 CpG-site DNA methylation microarray. The 450K DNA methylation approach enabled validation of the WGBS data and revealed additional age-related DNA methylation events. Interestingly, we also observed the DNA methylation fingerprint characteristic of a healthy aged cell in samples from patients with premature-aging disorders such as Hutchinson-Gilford progeria and Werner syndrome. Overall, we suggest that defects in the physiological DNA methylation profile contribute to the process of human aging. As the disease associated cells were immortalized B cells, the effect of EBV immortalization was determined in advance to the study using immortalized and naive B cells. DNA was quantified by Quant-iT PicoGreen dsDNA Reagent (Invitrogen) and the integrity was analyzed in a 1.3% agarose gel. Bisulfite conversion of 600 ng of each sample was perform according to the manufacturer's recommendation for Illumina Infinium Assay. Effective bisulphite conversion was checked for three controls that were converted simultaneously with the samples. 4 ul of bisulfite converted DNA were used to hybridize on Infinium HumanMethylation 450 BeadChip, following Illumina Infinium HD Methylation protocol. Chip analysis was performed using Illumina HiScan SQ fluorescent scanner. The intensities of the images are extracted using GenomeStudio (2010.3) Methylation module (1.8.5) software. Methylation score of each CpG is represented as beta value.

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Use of the B cell transcription program results in hypomethylation and overexpression of key genes in EBV-mediated conversion of resting to proliferative B cells

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