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 ).