THE POU-DOMAIN FACTOR BRN-3.0 RECOGNIZES CHARACTERISTIC SITES IN THE HERPES-SIMPLEX VIRUS GENOME

The restriction of herpes virus latency to mammalian sensory ganglia h as led to a search for tissue-specific regulatory molecules in these n eurons which alter viral gene expression, We have recently shown that the POU-domain transcriptional regulator Brn-3.0 is abundantly express ed in the adult trigeminal ganglion, To begin to examine the hypothesi s that Brn-3.0 might participate in the regulation of the HSV life-cyc le, we used Brn-3.0 POU-domain protein as an affinity matrix, and bioc hemically screened the entire HSV genome for sites of Brn-3.0 binding. This screen identified several sites of the form T A/T A A T N A N T A/T, which significantly do not include the previously identified HSV octamer sequences. All of the selected sites occur in the <25% of the HSV genome which has not been assigned to open reading frames, suggest ing that these sites may be transcriptional regulatory elements recogn ized by Brn-3.0 or another homeobox factor with similar DNA binding pr operties. However, these sites do not interact with Brn-3.0 with suffi ciently high affinity to directly mediate transcriptional activation b y Brn-3.0 alone in transfection assays. The experiments described also provide an effective general method for exhaustive screening of large viral genomes or subgenomic fragments of eukaryotic DNA for sites of interaction with specific transcription factors.