Fig. 4: PHF6 is required for promoter-proximal pause release of RNA polymerase II.

a PHF6 co-immunoprecipitation of Pol II and its phosphorylated forms in G401 RT cells (n = 2 independent biological replicates) b Western blot analysis of the levels of Pol II Ser5P (promoter proximal) and Pol II Ser2P (elongating) forms in shCTRL and shPHF6 G401 cells (n = 3 independent biological replicates). Metagene plots of (c) Pol II Ser5P (promoter proximal) and d Pol II Ser2P (elongating) in shCTRL (black) and shPHF6 (red) conditions (n = 2 independent biological replicates) at PHF6-bound genes (n = 8728). e Metagene nascent transcriptional profiles (Bru-seq read density) of PHF6 bound genes stratified based on gene-length (10–60 kb) at the 5’ (TSS) of protein-coding genes in shCTRL and shPHF6 conditions in G401 cells (n = 3 independent biological replicates). f Example locus depicting Pol II Ser5P, Pol II Ser2P, and nascent transcription upon loss of PHF6 at PHF6-bound SMAD9. g Gene length distributions (log10 transformed) for all hg19 genes (blue) and 345 significantly downregulated PHF6 target genes defined in RT cell lines (TTC709, TTC549, G401) in magenta. h Scatter plot displaying correlation between differentially expressed genes from Bru-seq and mRNA-seq upon PHF6 knockdown in G401 cells. i Representative locus depicting Pol II Ser5P, Pol II Ser2P, nascent transcript, and mRNA upon loss of PHF6 at PHF6-bound Jun locus. j Gene ontology analysis by Metascape of significantly downregulated and upregulated genes upon PHF6 knockdown (adjusted p < 0.05 and log₂FC < 0 or log₂FC > 0) in G401 cells. Source data are provided as a Source Data file.