Mapping the Human Herpesvirus 6B Transcriptome

Abstract

ABSTRACT The “omics” revolution of recent years has simplified the study of RNA transcripts produced during viral infection and under specific defined conditions. In the quest to find new and differentially expressed transcripts during the course of human herpesvirus 6B (HHV-6B) infection, we made use of large-scale RNA sequencing to analyze the HHV-6B transcriptome during productive infection of human Molt-3 T cells. Analyses were performed at different time points following infection, and specific inhibitors were used to classify the kinetic class of each open reading frame (ORF) reported in the annotated genome of the HHV-6B Z29 strain. The initial search focused on HHV-6B-specific reads matching new HHV-6B transcripts. Differential expression of new HHV-6B transcripts was observed in all samples analyzed. The presence of many of these new HHV-6B transcripts was confirmed by reverse transcriptase PCR and Sanger sequencing. Many of these transcripts represented new splice variants of previously reported open reading frames (ORFs), including some transcripts that have yet to be defined. Overall, our work demonstrates the diversity and the complexity of the HHV-6B transcriptome. IMPORTANCE RNA sequencing (RNA-seq) is an important tool for studying RNA transcripts, particularly during active viral infection. We made use of RNA-seq to study human herpesvirus 6B (HHV-6B) infection. Using six different time points, we were able to identify the presence of differentially spliced genes at 6, 9, 12, 24, 48, and 72 h postinfection. Determination of the RNA profiles in the presence of cycloheximide (CHX) or phosphonoacetic acid (PAA) also permitted identification of the kinetic class of each ORF described in the annotated GenBank file. We also identified new spliced transcripts for certain genes and evaluated their relative expression over time. These data and next-generation sequencing (NGS) of the viral DNA have led us to propose a new version of the HHV-6B Z29 GenBank annotated file, without changing ORF names, to facilitate trace-back and correlate our work with previous studies on HHV-6B.