Figure EV4. CDK12 directs expression of replication and DNA damage response genes downstream of the E2F/RB pathway.

1. CDK12 directs expression of DNA replication genes downstream of the E2F/RB pathway. Graphs present ChIP‐qPCR data for E2F1 and E2F3 in AS CDK12 HCT116 cells either treated or not with 3‐MB‐PP1 for 4 h. qPCR primers were designed at promoters of indicated genes. n = 3 replicates; error bars represent SEM. Ir is intergenic region; noAb corresponds to no antibody immunoprecipitation control.
2. CDK12 inhibition does not lead to differential recruitment of RNAPII to E2F target genes. The plots show log2 fold‐changes of RNAPII occupancy on promoters of E2F target genes (y‐axis) plotted against corresponding log2 fold‐changes in mRNA expression from nuclear RNA‐seq (x‐axis). Promoter occupancy was quantified as read counts in the ±3 kb regions around the transcription start site (TSS). For each gene, we selected the transcript with the most read counts in the RNAPII ChIP‐seq samples (normalized to library size) in the ±3 kb regions around the TSS and transcription termination site (TTS). Corresponding RNAPII ChIP‐seq and nuclear RNA‐seq experiments are presented in Fig 5A and B. E2F target genes were obtained from Bracken et al 40; rho = Spearman rank correlation coefficient.