DNA Zip Codes in Herpesvirus Genomes

The genomes of 39 herpesviruses were examined for the presence of DNA zip codes, sequence elements found in yeast to be involved in gene localization to the nuclear periphery and transcriptional memory. Tests were carried out with three different zip codes and with viruses in all three subfamilies of the Herpesviridae. All genomes were found to have have at least three zip codes with 30 the most observed. Zip codes in many alphaherpesviruses and in human cytomegalovirus were found to be symmetrically arranged within the S genome segment, a region that inverts actively during virus replication. This suggests zip codes may be involved in the segment inversion process. Zip codes located in 16 alphaherpesvirus promoters were examined separately from those in other locations. The genes most likely to have a zip code containing promoter were found to be those encoding glycoprotein B and transcription factor ICP4. Of the two, zip codes associated with ICP4 are of particular interest as their ability to mediate transcriptional memory is well-suited for a role in reactivation of alphaherpesviruses from the latent state.