Fig. 3

Ctr9 knockdown decreases genome-wide RNA polymerase II occupancy. a Representative genome browser views of RNA polymerase II (RNAPII) ChIP-seq profiles at TFF1 and GREB1 genes under the four indicated treatments. b A matrix describing the approach used to identify differential RNAPII binding peaks. c A matrix describing the approach used to identify genes with differential RNAPII binding peaks. RNAPII-bound gene is defined as gene that contains one or more RNAPII binding peaks within the gene body. d Metagene analysis showing total RNAPII occupancy measured by ChIP-seq in cells under the four indicated treatments. All RNAPII-bound genes were normalized to same length with 2 kb extended upstream from TSS and 2 kb downstream from TTS for analyzing the average density. TSS, transcription start site; TTS, transcription termination sites. e Metagene analyses showing total RNAPII occupancy measured by ChIP-seq for Ctr9 knockdown decreased genes (upper) and increased genes (bottom) selected from the microarray gene expression data set. f Venn diagram showing the overlap between genes with RNAPII binding increased by E2 treatment and genes with RNAPII binding decreased by Ctr9 KD in the presence of E2