Figure 1

Circadian gene expression rhythms in Neurospora. (A) Circadian time course of RNA-seq (left panel) and RNAPII-S2P ChIP-seq (right panel) reads of csp1 in constant dark. RNAPII-S2P signals were generally enriched at the end of the genes, indicating that the phospho-S2 antibody was specific for the elongating/terminating polymerase [37,38]. (B) Rose plot (upper panel) and histogram (lower panel) of the phase distribution of rhythmic RNA levels and RNAPII-S2P profiles by ARSER. (C) Venn diagram showing the overlap of genes with rhythmic RNA levels and RNAPII-S2P profiles. (D) Heat-maps showing the relative RNA levels (left panel) and RNAPII-S2P occupancy (right panel) of genes with robust rhythms identified by ARSER (P value <0.05 for both RNA and RNAPII-S2P). (E) Box-plots showing the RNA amplitude (left panel) and coverage (right panel) of the rhythmic genes identified only by RNA-seq (RNA only, grey), identified only by RNAPII-S2P ChIP-seq (S2P only, blue) and identified by both methods (RNA + S2P, light red). False discovery rates (FDR %) versus amplitude and coverage are shown in the panels above the corresponding box-plots. (F) Same as in E, shown for RNAPII-S2P amplitude (left panel) and coverage (right panel). CHIP-seq, chromatin immunopreciptation sequencing; RNAPII, RNA polymerase II.