Figure 4.

Mismatches between mRNA production and changes in PolII occupancy. (a) Scatterplot of mRNA change versus PolII occupancy change. PolII data are taken from mid-CDS probes, and change from 0 to 30 minutes of diamide treatment is shown on the x-axis. mRNA data from Gasch et al. [18] is shown on the y-axis. The red line shows the LOWESS fit of mRNA/PolII change. (b) Example genes with excess, typical, and a dearth of mRNA produced per change in PolII occupancy. Data for mRNA change and PolII change at mid-CDS are plotted at the same scale. (c) Definition of mRNA excess per PolII change. As in (b), but for 30 minutes of heat shock. Genes that fall more than 0.5 above (red) or below (green) the LOWESS fit (red line) of mRNA/PolII change are indicated. (d) Genes with excess mRNA production are subject to extensive overlapping noncoding transcription. Average extent of overlap with other transcripts defined in Xu et al. [22] are shown for the three gene classes defined in (c).