HSV is a large
double stranded DNA virus, capable of causing a variety of diseases from the
common cold sore to devastating
encephalitis. Although
DNA within the HSV virion does not contain any
histone protein, within 1 h of infecting a cell and entering its nucleus the viral genome acquires some
histone protein (
nucleosomes). During lytic
infection, partial
micrococcal nuclease (MNase) digestion does not give the classic ladder band pattern, seen on digestion of cell
DNA or latent
viral DNA. However, complete digestion does give a mono-
nucleosome band, strongly suggesting that there are some
nucleosomes present on the viral genome during the lytic
infection, but that they are not evenly positioned, with a 200 bp repeat pattern, like cell
DNA. Where then are the
nucleosomes positioned? Here we perform HSV-1 genome wide
nucleosome mapping, at a time when viral replication is in full swing (6 hr PI), using a microarray consisting of 50mer
oligonucleotides, covering the whole viral genome (152 kb). Arrays were probed with MNase-protected fragments of
DNA from infected cells. Cells were not treated with crosslinking agents, thus we are only mapping tightly bound
nucleosomes. The data show that
nucleosome deposition is not random. The distribution of signal on the arrays suggest that
nucleosomes are located at preferred positions on the genome, and that there are some positions that are not occupied (
nucleosome free regions -NFR or
Nucleosome depleted regions -NDR), or occupied at frequency below our limit of detection in the population of genomes. Occupancy of only a fraction of the possible sites may explain the lack of a typical MNase partial digestion band ladder pattern for HSV
DNA during lytic
infection. On average,
DNA encoding Immediate Early (IE), Early (E) and Late (L) genes appear to have a similar density of
nucleosomes.