The lytic gene expression of several members of the human herpesvirus family has been profiled by using gene-expression microarrays; however, the lytic cascade of roseoloviruses has not been studied in similar depth. Based on the complete DNA genome sequences of human herpesvirus 6 variant A (HHV-6A) and variant B (HHV-6B), we constructed a cDNA microarray containing DNA probes to their predicted open reading frames, plus 914 human genes. Gene-expression profiling of HHV-6B strain Z29 in SupT1 cells over a 60 h time-course post-infection, together with kinetic classification of the HHV-6B genes in the presence of either cycloheximide or phosphonoacetic acid, allowed the placement of HHV-6B genes into defined kinetic classes. Eighty-nine HHV-6B genes were divided into four different expression kinetic classes: eight immediate-early, 44 early, 33 late and four biphasic. Clustering of genes with similar expression profiles implied a shared function, thus revealing possible roles of previously uncharacterized HHV-6B genes.
INTRODUCTIONHuman herpesvirus 6 (HHV-6) is a betaherpesvirus, first isolated in 1986 from individuals with lymphoproliferative disorders (Salahuddin et al., 1986). Primary infection occurs in early childhood (Hall et al., 1994), when it can cause febrile illnesses including exanthem subitum (ES) (Yamanishi et al., 1988;Zerr et al., 2005). Following initial infection, HHV-6 establishes lifelong latency in the host, with monocytes (Kondo et al., 1991) and bone-marrow progenitor cells (Luppi et al., 1999) being suggested as the sites of latency. HHV-6 reactivation in immunocompromised hosts can be pathogenic, particularly in the transplant setting, and has been associated with encephalitis, bone-marrow suppression and graft rejection (Clark & Griffiths, 2003).Two variants of HHV-6 exist (-6A and -6B), each with distinct genetic, antigenic and biological properties (Pellett & Black, 1996; Schirmer et al., 1991). HHV-6A is not associated consistently with disease, but HHV-6B is the cause of ES in childhood (Dewhurst et al., 1993;Yamanishi et al., 1988;Zerr et al., 2005). Publication of the complete DNA genome sequences of HHV-6A and -6B (Dominguez et al., 1999;Gompels et al., 1995;Isegawa et al., 1999) confirmed the close relatedness of the two variants.However, significant sequence variations observed at the right end of the unique region, plus the existence of variant-specific open reading frames (ORFs), may explain the differential properties described for HHV-6A and -6B (Clark, 2000).As HHV-6 replicates predominantly in CD4 + T cells in vitro and in vivo (Lopez et al., 1988;Lusso et al., 1988), there is interest in the regulation of viral gene expression in its target cell type. We have previously described the use of DNA microarrays for expression profiling of two gammaherpesviruses, Kaposi's sarcoma-associated herpesvirus (Jenner et al., 2001) and murine gammaherpesvirus 68 (Ahn et al., 2002), and demonstrated the functional predictions of uncharacterized viral genes and transcription from inte...