Nucleosomes on Immediate Early genes.

<p><b>A</b> and <b>B</b>. The nucleosome signal is shown for the region covering two immediate early genes, which are diploid in the HSV-1 genome. The two gene copies have been inverted and aligned with each other to show that the array signal is similar but not identical. Spaces in the graph lines are “poorly performing” oligos where no signal could be measured. Between the array signal information we have mapped the transcribed gene (green). The red balls indicate the predicted position of nucleosomes with 5 consecutive positive hybridizing oligos. The orange balls indicate where we have inferred a nucleosome from 4 positive oligos and assumed there is a fifth positive oligo that is not recorded because of a “poorly performing” oligo, or some other technical problem. Gene features from the NCIB database are also shown. <b>C</b> To confirm our nucleosome positioning we used ChIP and Q-PCR (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0117471#sec002" target="_blank">Methods</a>), selecting primers to amplify regions of ICP0 that we designated as having a probable nucleosome (green), or NFR (red). <b>D</b>. Nucleosome Saturation for each Immediate Early gene. The predicted number of nucleosomes for each IE gene were compared to the maximum number of nucleosomes possible (assuming a standard cell 200nt/nucleosome repeat pattern) to give the nucleosome saturation, which is expressed as a %.