The majority of the clock-controlled genes have similar RNA and RNAPII-S2P profiles. (A) Heat-maps showing the relative RNA levels (left panels) and RNAPII-S2P occupancy profiles (right panels) for rhythmically expressed genes. Group 1: genes with similar phases of RNA levels and RNAPII-S2P. One or both profiles were identified as rhythmic by ARSER (P <0.05). Group 2: genes with significantly rhythmic RNAPII-S2P profiles and non-significantly rhythmic, out of phase RNA abundance profile. Group 3: genes with significantly rhythmic RNA profiles and non-significantly rhythmic, out of phase RNAPII-S2P occupancy profile. (B) Amplitude of RNA-seq (upper panel) and RNAPII-S2P ChIP-seq profiles (lower panel) of the three groups in comparison to 362 genes with both significant RNA and RNAPII-S2P rhythms (RNA + S2P). (C) Same as in B, shown for RNA (upper panel) and RNAPII-S2P ChIP-seq coverage (lower panel). CHIP-seq, chromatin immunopreciptation sequencing; RNAPII, RNA polymerase II.