Figure 3

Relationship between RNAPII occupancy and mRNA abundance. Correlation between the genome-wide detection of unmodified CTD (panel A), Ser5-P (panel B) and Ser2/5-P (panel C) forms of RNAPII and mRNA levels was calculated using Pearson’s correlation coefficient (PCC) between the mean-centered profile of all probes with p <0.05 and the corresponding gene transcripts. The data have been presented as bar graphs with bins of PCC ranging from −1 to +1 on the x-axis plotted against the number of probes falling into each bin on the y-axis. The phaseograms in the right-hand panels represent probes which are highly positively correlated with gene expression (r ≥0.4), and in the left-hand panels display probes showing negative correlation with gene expression (r ≤ -0.4). One-third of the probes do not show any correlation. The order of the probes represented in the phaseograms for RNAPII binding is the same as those used in the mRNA phaseogram. On the basis of this analysis, we identify four subsets of genes with respect to the correlation between RNAPII binding and mRNA abundance. These are early/positive (RNAPII binds early in the IDC and is positively correlated with mRNA levels), early/negative and late/positive and late/negative.