EBER2 RNA-induced transcriptome changes identify cellular processes likely targeted during Epstein Barr Virus infection

Abstract

BackgroundLittle is known about the physiological role of the EBER1 and 2 nuclear RNAs during Epstein Barr viral infection. The EBERs are transcribed by cellular RNA Polymerase III and their strong expression results in 106 to 107 copies per EBV infected cell, making them reliable diagnostic markers for the presence of EBV. Although the functions of most of the proteins targeted by EBER RNAs have been studied, the role of EBERs themselves still remains elusive.FindingsThe cellular transcription response to EBER2 expression using the wild-type and an internal deletion mutant was determined. Significant changes in gene expression patterns were observed. A functional meta-analysis of the regulated genes points to inhibition of stress and immune responses, as well as activation of cellular growth and cytoskeletal reorganization as potential targets for EBER2 RNA. Different functions can be assigned to different parts of the RNA.ConclusionThese results provide new avenues to the understanding of EBER2 and EBV biology, and set the grounds for a more in depth functional analysis of EBER2 using transcriptome activity measurements.

HMGA1 directly interacts with TAR to modulate basal and Tat-dependent HIV transcription

“…27 The previously described EBER2-Lb construct, comprising only the EBER2 RNA backbone, was used as a control in these experiments. 44 Both RNA chimeras were expressed at similar levels as assessed by quantitative RT-PCR (Fig. 4C).…”

“…For the overexpression of the 7SK L2 substructure under control of the strong viral EBER2 promoter of Epstein-Barr virus we utilized the vector EBER2 7SK L2. 27,44 Total RNA preparation and quantitative RT-PCR analyses. Total RNA from transfected or non-transfected cells was prepared using the RNeasy Midi Kit (Qiagen) as recommended by the manufacturer.…”

7SK small nuclear RNA directly affects HMGA1 function in transcription regulation

“…The data obtained were analyzed as described previously (31,41–44). Transcriptome data, annotated to MIAME I+II standards, were deposited in the public database MACE using Accession Nos.…”

TLR5 Signaling Stimulates the Innate Production of IL-17 and IL-22 by CD3negCD127+ Immune Cells in Spleen and Mucosa

“…Total RNA (2 mg) was processed on the Mouse Whole Genome Arrays version 2.0 (Applied Biosystems) (27). Data were analyzed using the NeONORM method, and heat maps were created as described previously (27,28).…”

“…Data were analyzed using the NeONORM method, and heat maps were created as described previously (27,28). Gene Ontology was analyzed using the Panther Protein Classification System (www.pantherdb.org).…”