Results

There is a burst of gene expression of DNA binding proteins at dawn

(Michael et al. 2008) noted that there was a spike in phytohormone gene expression in the early morning, and suggested that this gene expression burst might be gated by phytochrome B-linked inhibition at night.  In particular, their study focussed on 182 hand-curated phytohormone genes, of which 40 were identified as having spikes in expression an hour after dawn.  This set of curated phytohormone genes had a high proportion of genes that were involved in biosynthesis and catabolism, but we were curious whether there would be an enrichment for phytohormone associated transcription factors and other DNA-binding proteins in the morning, as these are likely to regulate these phytohormone biosynthesis and catabolism genes (Table S1 ).
Overall, 39% of DNA binding proteins have peak gene expression immediately before or an hour after dawn (Figure S1 ).  We find that there is a significant enrichment for ABA and ethylene-linked DNA binding proteins that have maximal expression in this time period compared to other DNA binding proteins (58% and 55%, p<0.005 in both cases using a Fisher Exact test with Bonferroni correction), which is consistent with the observations in Michael et al, 2008 (Figure 1Ai,ii ).  There is also an enrichment for DNA-binding proteins that are associated with GO terms related to light (53%, p<0.02) and stress (55%, p<0.002)– seeFigure 1Aiii,iv .  However, we found no significant enrichment for auxin-associated DNA binding proteins or circadian clock genes (Figure S1 ).
Consistent with the role of phytochromes in regulating the dawn peak (Michael et al. 2008), we observe that DNA binding factors that have peak expression in the hour before dawn have increased expression in  phyABCDE both before and after dawn (Figure 1B).  In contrast, genes that have peak expression in the hour after dawn do not have perturbed expression in phyABCDE .  This observe the same trends in elf3-1 , which is consistent with evidence that phytochromes interact with ELF3 (Ezer et al. 2017) (Figure S2 ).