We found 948 genes bound by Stat3 and 1459 genes bound by c-Myc.
The genes bound by E2f4 show functional pathway enrichment in cell cycle, proliferation, and DNA repair, as expected (Figure 2D).
To our surprise, we found that most of the genes bound by E2F4 were highly species-specific.
We find that that most genes bound by E2F4 are common to numerous primary tissues within a species.
Additionally, genes bound by Yap6, Cin5, Phd1, and Skn7 were shown to be strongly de-repressed upon knockout of Tup1.
Genes bound by Stat3 include Sall4, Mycn, Rest, Stat3, Mbd3, Jmjd3, Tdgf1, and Fbxo15 (Figure 2B, Table S1).
Additionally, a cohort of genes bound by a transcription factor under a specific environmental condition [26] also served as a stress-responsive gene set.
Given that some PARP3 associates with PRC2, we sought to compare genes bound by PARP3 with those associated with SUZ12 or enriched for H3K27me3.
We tested whether the mouse genes bound by E2f4 in liver, kidney, and testes were dependent on the presence of E2f4 for proper transcription.
Genes bound by c-Myc include Oct4, Sox2, Mycn, Rest, Stat3, Mbd3, Jmjd3, Gdf3, Fbxo15, Klf5, Klf7, and Klf9 (Figure 2A, Table S2).
Since both alleles are transcribed, the hypothesis that transcription is allele-specific is not supported for these ZNF genes bound by both H3K9me3 and H3K36me3.
