RNA sequencing analyses of gene expression during Epstein-Barr virus infection of primary B lymphocytes

Chong Wang, Difei Li, Luyao Zhang, Sizun Jiang, Jun Liang, Yohei Narita, Isabella Hou, Qian Zhong, Zeguang Zheng, Haipeng Xiao, Benjamin E. Gewurz, Mingxiang Teng, Bo Zhao

Research output: Contribution to journalArticlepeer-review

61 Scopus citations

Abstract

Epstein-Barr virus (EBV) infection of human primary resting B lymphocytes (RBLs) leads to the establishment of lymphoblastoid cell lines (LCLs) that can grow indefinitely in vitro. EBV transforms RBLs through the expression of viral latency genes, and these genes alter host transcription programs. To globally measure the transcriptome changes during EBV transformation, primary human resting B lymphocytes (RBLs) were infected with B95.8 EBV for 0, 2, 4, 7, 14, 21, and 28 days, and poly(A) plus RNAs were analyzed by transcriptome sequencing (RNA-seq). Analyses of variance (ANOVAs) found 3,669 protein-coding genes that were differentially expressed (false-discovery rate [FDR] 0.01). Ninety-four percent of LCL genes that are essential for LCL growth and survival were differentially expressed. Pathway analyses identified a significant enrichment of pathways involved in cell proliferation, DNA repair, metabolism, and antiviral responses. RNA-seq also identified long noncoding RNAs (lncRNAs) differentially expressed during EBV infection. Clustered regularly interspaced short palindromic repeat (CRISPR) interference (CRISPRi) and CRISPR activation (CRISPRa) found that CYTOR and NORAD lncRNAs were important for LCL growth. During EBV infection, type III EBV latency genes were expressed rapidly after infection. Immediately after LCL establishment, EBV lytic genes were also expressed in LCLs, and 4% of the LCLs express gp350. Chromatin immune precipitation followed by deep sequencing (ChIP-seq) and POLR2A chromatin interaction analysis followed by paired-end tag sequencing (ChIA-PET) data linked EBV enhancers to 90% of EBV-regulated genes. Many genes were linked to enhancers occupied by multiple EBNAs or NF-B subunits. Incorporating these assays, we generated a comprehensive EBV regulome in LCLs.

Original languageEnglish (US)
Article numbere00226-19
JournalJournal of virology
Volume93
Issue number13
DOIs
StatePublished - 2019
Externally publishedYes

Bibliographical note

Funding Information:
This work was funded by NIAID AI123420, NCI CA047006 (B.Z.), NCI P30CA076292 (M.T.), and NIAID AI137337 (B.E.G.). B.E.G. is a Burroughs Wellcome Career Award for Medical Scientists recipient.

Publisher Copyright:
© 2019 American Society for Microbiology. All Rights Reserved.

Keywords

  • ChIA-PET
  • ChIP-seq
  • EBNA
  • EBV
  • LncRNA
  • RNA-seq

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