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We are grateful to Laurie Boyer for providing lists of PcG bound genes.
See Supplementary Figure S2 for additional examples of Ubx bound genes.
Strikingly, a specific subset of Ring1b bound genes was not affected following Ring1b deletion.
We next analyzed the chromatin state of the Ring1b bound genes with HCPs.
A similar fraction of deregulated Ring1b bound genes with HCPs was bivalently marked (73%; 87/119; Figure 6E).
Of the 1219 Ring1b bound genes, identified by Boyer and colleagues, 1078 were represented on our microarray.
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66.6% of Pch-bound genes were not bound by Ler.
We tried to extend the core transcriptional regulatory network based on the combination of the core-bound genes and the TFs that bind to subsets of the core-bound genes.
To validate these bioinformatics analyses, all Msl1- and/or Nsl1-bound genes were divided into three categories: Msl1- and Nsl1-bound genes (category 1), genes bound only by Nsl1 (category 2) and genes bound only by Msl1 (category 3).
Many Atf1/Pcr1-bound genes were found to be unresponsive to H2O2 treatment (see Figure 5A).
We therefore concluded that Atf1/Pcr1-bound genes were generally the Atf1/Pcr1-dependent or Atf1-specific H2O2-induced genes.
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