Unknown,Transcriptomics,Genomics,Proteomics

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EBNA1 ChIP-seq and MNase-seq in EBV-positive MUTU cell lines


ABSTRACT: Epstein-Barr Virus (EBV), which is associated with multiple human tumors, persists as a minichromosome in the nucleus of B-lymphocytes and induces malignancies through incompletely understood mechanisms. Here, we present a large-scale functional genomic analysis of EBV. Our experimentally generated nucleosome positioning maps and viral protein binding data were integrated with over 700 publicly available high-throughput sequencing data sets for human lymphoblastoid cell lines mapped to the EBV genome. We found that viral lytic genes are coexpressed with cellular cancer-associated pathways, suggesting that the lytic cycle may play an unexpected role in virus-mediated oncogenesis. Host regulators of viral oncogene expression and chromosome structure were identified and validated, revealing a role for the B-cell-specific protein Pax5 in viral gene regulation and the cohesin complex in regulating higher order chromatin structure. Our findings provide a deeper understanding of latent viral persistence in oncogenesis and establish a valuable viral genomics resource for future exploration. Six sequencing experiments were performed. One EBNA1 ChIP-seq was controlled with IgG ChIP-seq. Two MNase-seq biological replicates were each conrolled by input seq using the same cells subjected to MNase digestion.

ORGANISM(S): Human Herpesvirus 5

SUBMITTER: Aaron Arvey 

PROVIDER: E-GEOD-39913 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

An atlas of the Epstein-Barr virus transcriptome and epigenome reveals host-virus regulatory interactions.

Arvey Aaron A   Tempera Italo I   Tsai Kevin K   Chen Horng-Shen HS   Tikhmyanova Nadezhda N   Klichinsky Michael M   Leslie Christina C   Lieberman Paul M PM  

Cell host & microbe 20120801 2


Epstein-Barr virus (EBV), which is associated with multiple human tumors, persists as a minichromosome in the nucleus of B lymphocytes and induces malignancies through incompletely understood mechanisms. Here, we present a large-scale functional genomic analysis of EBV. Our experimentally generated nucleosome positioning maps and viral protein binding data were integrated with over 700 publicly available high-throughput sequencing data sets for human lymphoblastoid cell lines mapped to the EBV g  ...[more]

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