Fig 2: ZC3H4 depletion stabilises unproductive transcripts.(a) Integrative Genomics Viewer (IGV) track of the transcription read-through defect at PTPN11 following CPSF30 or ZC3H4 depletion. Blue and red tracks indicate sense/antisense transcripts respectively, grey bar indicates a change in y-axis scale so that comparatively weaker read-through signals can be visualised next to the gene body (left scale for upstream of TES; right for downstream). Y-axis scale is RPKM. (b) Metagene comparison of transcription upstream, across, and downstream of, protein-coding genes in nuclear RNA from CPSF30-mAID cells treated or not with auxin and from HCT116 cells transfected with control or ZC3H4 siRNAs. CPSF30 traces are from the same samples presented in Figure 1C. Positive and negative signals represent sense and antisense reads, respectively. (c) IGV track view of transcription at the MYC PROMPT in RNA-seq samples obtained from control or ZC3H4 siRNA-treated HCT116 cells. We also show a track from HCT116 cells acutely depleted of DIS3-AID (DIS3 + IAA) (Davidson et al., 2019) to highlight the normal extent of this unstable transcript. Y-axis scale is RPKM. (d) Log2 fold change of siZC3H4 vs. siControl or DIS3+ vs. - auxin for RNA upstream of 6057 non-neighbouring, actively transcribed genes, plotted as heat maps. Line graphs are an XY depiction of heat map data. Log2 fold changes are smaller in siZC3H4 samples versus DIS3 depletion because this is an average of all genes in the heat map, a smaller fraction of which are affected by ZC3H4. (e) IGV plot of a known SE upstream of MYC (the location is shown by blue bar under trace). Samples are shown from HCT116 cells treated with control or ZC3H4 siRNAs as well as DIS3-AID cells treated with auxin (the latter from Davidson et al., 2019) to show the normal extent of unstable eRNAs over this region. Y-axis scale is RPKM. (f) Log2 fold change of RNA signal for siZC3H4 vs. siControl or DIS3+ vs. - auxin for 111 SEs. The bed file detailing super-enhancer coordinates in HCT116 cells was taken from dbSUPER.org.