The rDNA chromatin is extensively remodelled during UBF elimination.

<p>A) Psoralen crosslinking analysis of the rRNA genes in <i>Ubf^fl/fl/Er-cre^+/+</i> and <i>Ubf^wt/wt/Er-cre^+/+</i> cells at the indicated times pHT. The probe position is indicated in the upper diagram, and the lower panel shows a typical electrophoretic separation of actively transcribed “a” and inactive “i” genes. The right-hand panel displays a quantitation of the fraction of transcriptionally active and inactive genes at each time point. Elimination of UBF at 48 h pHT correlates with full inactivation of the rRNA genes. B) and C) Changes in histone modifications penta-acetyl H4 (H4ac) and H3K9me3, and relative Histone H1, H2AZ, H1.4, H1.4-S187p and chromosomal protein HP1α levels associated with the rDNA during UBF elimination (hours pHT). The grey band indicates the extent of the rRNA gene Enhancer sequences. Mapping of amplicons is as in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004505#pgen-1004505-g003" target="_blank">Figure 3A</a>. Again here <i>Ubf</i> gene recombination and UBF protein levels were assayed in parallel and closely followed those shown in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004505#pgen-1004505-g002" target="_blank">Figure 2A and B</a>. The data shown in B and C are given after subtraction of the parallel preimmune Control ChIP data. They are derived from single ChIP preparations analyzed in triplicate, but are representative of the data from biological replicates, see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004505#s4" target="_blank">Materials and Methods</a>.