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 has led to a search for tissue-specific regulatory molecules in these neurons which alter viral gene expression. We have recently shown that the POU-domain transcriptional regulator Brn-3.0 is abundantly expressed in the adult trigeminal ganglion. To begin to examine the hypothesis that Brn-3.0 might participate in the regulation of the HSV life-cycle, we used Brn-3.0 POU-domain protein as an affinity matrix, and biochemically screened the entire HSV genome for sites of Brn-3.0 binding. This screen identified several sites of the form TA/TA A T N A N TA/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, suggesting that these sites may be transcriptional regulatory elements recognized by Brn-3.0 or another homeobox factor with similar DNA binding properties. However, these sites do not interact with Brn-3.0 with sufficiently high affinity to directly mediate transcriptional activation by Brn-3.0 alone in transfection assays. The experiments described also provide an effective general method for exhaustive screening of large viral genomes or sub-genomic fragments of eukaryotic DNA for sites of interaction with specific transcription factors.