Figure 2

ChIP-on-chip reveals two classes of genes distinguished by recruitment of RNAPII either early or late in the IDC. (A) Three phaseograms (blue-yellow scale) representing temporal occupancy patterns for the three forms of RNAPII detected in this study: unphosphorylated CTD, Ser5-P and Ser2/5-P. The data were filtered to include only those loci where RNAPII shows an oscillating profile with p <0.05 and a fold change ≥1.5 across the life cycle. The yellow-blue color scale represents the mean-centered log transformed ratios of ChIP/input values across the IDC (T1 to T6). Two prominent probe clusters binding the Ser2/5-P form of RNAPII early vs late in the IDC are marked with orange rectangles. The phaseogram on the far right (green-red scale) depicts the phase of peak gene expression for the P. falciparum transcriptome across the IDC. (B-C) ChIP-qPCR confirms the presence of two classes of genes distinguished by enrichment in RNAPII binding either early or late in the IDC. Using immunoprecipitated DNA, quantitative real time PCR was carried out on representative genes chosen from the early (B) and late (C) categories to validate the ChIP occupancy profiles of Ser2/5-P RNAPII across the IDC. Primers for real time PCR were designed to amplify 200–300 bp regions around the respective probe on the microarray. The x-axis gives time points T1 to T6 and the y-axis shows the fold change. Solid lines represent real time PCR profiles, whereas dashed lines give the microarray (ChIP-on-chip) profile at the same probe region. The fine dotted line represents the mRNA levels across the six time points determined by hybridization of cDNA to the microarrays. Error bars show standard deviation of triplicate determinations. See also Additional files 2, 3 and 4: Figures S1, S2 and S3.