Extended Data Fig. 10: Studying transcription activators and repressors.
From: Prediction of histone post-translational modification patterns based on nascent transcription data
a. Bar plots display absorbance quantified at 590 nm for AlmarBlue dye incubated with K562 cells during Triptolide, or Triptolide and Trichostatin A treatments. Two technical replicates were averaged for each time point. R1 and R2 define separate biological replication of the experiment. b. Scatterplots display the loss in H3K4me3 (left) and H3K27ac (right) as a function of Pol II transcription (top) or change in transcription (bottom). Changes in histone marks and transcription were calculated as log2 fold changes between 4 h of Triptolide treatment and untreated cells. Plots show Spearman’s Rho between conditions. (c-h) Scatterplots show experimental DNase-I hypersensitivity (x axis) as a function of predicted DNase-I hypersensitivity (y axis) in 100 bp windows intersected with transcriptional repressors (C-E) or transcriptional activators (F-H). (i-j) Meta (I) and Violin (J) plots display TBP (TATA-binding protein) CUT&RUN signal at gene promoters and enhancers in a short 30 min Triptolide time course.
