Unknown,Transcriptomics,Genomics,Proteomics

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CAGE transcriptomes on EBV transformed lymphoblastoid cell lines from central European individuals

ABSTRACT: We hypothesized that mapping genetic variants associated with promoter and enhancer functions can provide novel insights into the mechanism through which eQTLs (expression quantitative trait loci) exert their effects on gene expression. To this end, we quantified genome-wide promoter usage and enhancer activity and tested the resulting molecular phenotypes for association with nearby genetic variants to discover cis-QTLs. To perform such analyzes, we have produced deep transcriptome profiling of 154 unrelated central European individuals, applying deepCAGE (Cap Analysis of Gene Expression) to nuclear enriched total RNA extracted from EBV transformed lymphoblastoid cell lines (LCLs). The LCLs were either purchased from Coriell Cell Repository (CEU, n=86) or from the GenCord collection (n=68, Gutierrez-Arcelus M et al. Elife 2013).

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Homo sapiens

SUBMITTER: Alexandre Fort

PROVIDER: E-MTAB-5835 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Epstein Barr virus (EBV) nuclear antigen 3C (EBNA3C) is an essential transcription factor for initiating and maintaining human B lymphocyte transformation to lymphoblastoid cell lines (LCLs). To comprehensively identify EBNA3C regulated cell genes in LCLs, oligonucleotide arrays were used to compare RNA abundances in 3 different LCLs transformed by an EBV that conditionally expresses EBNA3C. Cell RNA levels were assessed in actively growing LCLs, under non-permissive or permissive conditions or under non-permissive conditions after transcomplementation with wild type EBNA3C. A two-way ANOVA model with covariates including the 3 different clone effects and the 3 EBNA3C expression levels, identified 550 EBNA3C regulated genes, with False Discovery Rate <0.01 and >1.5 fold change. A seeded Bayesian network analysis of the 80 most significantly EBNA3C regulated genes that changed >1.5 fold, positioned RAC1, LYN and TNF upstream of other EBNA3C regulated genes. Further, Gene Set Enrichment Assay (GSEA) identified EBNA3C regulated genes to be enriched for MAP kinase signaling, cytokine-cytokine receptor interactions, JAK-STAT signaling, and cell adhesion molecule effects, implicating these pathways in LCL growth or survival. Moreover, 106 EBNA3C regulated genes could be placed in protein interaction networks. Since CXCL12 and CXCR4 signaling are implicated in LCL growth and were EBNA3C up-regulated, up-regulation of CXCL12 was validated by qRT-PCR and effects on induced LCL migration were confirmed. EBNA3C regulated genes significantly overlapped with EBNA2 and EBNA3A regulated genes, consistent with a central role for RBP/CSL in these effects. RNAs from three different Lymphoblastoid Cell Lines(LCLs) expressing conditional EBNA3C grown under permissive or non-permissive conditions for 7 days; the same LCLs transcompletemented with EBNA3C expressed in trans at full wild-type level were used to identify EBNA3C regualted cellular genes. Total cell RNAs were hybrdized to Affymetrix U-133 Plus 2.0 microarrays. A two way ANOVA model was developed with covariates including the 3 different clone effects and the 3 EBNA3C expression levels and identified 550 EBNA3C regulated genes.

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CAGE transcriptomes on EBV transformed lymphoblastoid cell lines from central European individuals

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