Flavin‐binding‐Kelch‐F‐box (FKF) and LOV‐Kelch protein 2 (LKP2) \cite{Zoltowski2014,Somers2004,Kim_2005}.  While phyB has also been implicated as a temperature sensor at night \cite{Legris_2016,Jung2016} and interacts with the Evening Complex (EC) that is part of the evening loop of the circadian clock \cite{Ezer2017,Huang2016}, it is unclear whether phyB plays a role in temperature entrainment of the circadian clock.  However, there is evidence that heat shock protein 90 (HSP90) may be responsible for temperature entrainment \cite{Davis2018}.  
NEW PARAGRAPH, NOT REFERENCED YET:  Intriguingly, many of the genes that are involved in entraining the circadian clock are also key genes in photoperiodism and photomorphogenesis, including the phytochromes/cryptochromes and ZTL.  It makes sense that there should be a mechanistic link between photoperiod-dependent processes and circadian entrainment, since both depend on day length.   However, it is unclear how entrainment genes (such as phytochromes and cryptochromes) relay information to photomorphogenesis pathways and the circadian clock.  
In this manuscript, we characterise the 'dawn burst' of expression with an unprecedented level of detail, and then map the specific sub-network that links phytochromes and cryptochromes with photomorphogenesis.
Although there have been a number of studies that demonstrate that there is a burst of gene expression after light stimulus in the morning, the dynamics of this burst have not been fully characterised because time points were not sampled frequently enough.  Through a high resolution RNA-seq time series, we find five distinct transcriptional waves within the first two hours of the morning.  We characterise how each wave of expression responds to temperature elevation and light signals during the night and subjective day, and how these waves are affected by a light signalling mutant (phyAphyBcry1cry2), a circadian clock mutant (prr5prr7prr9), and a temperature response mutant (hsfa1Q).  Furthermore, we infer a gene regulatory network and validate edges using DNA binding data.  We find that HY5 and BBX31 are among the TFs that are predicted to regulate multiple expression waves.  Phytochromes and cryptochromes are required for a burst of expression of HY5 and BBX family proteins that fine-tune hypocotyl elongation and photomorphogenesis, suggesting that the dawn bursts may play a role in time-of-day dependent growth response to light stimulus.  This work provides unprecedented detail as to how light, temperature, and circadian genes are regulated at dawn, as well as providing evidence of a mechanistic link between morning entrainment and photomorphogenesis.

Results

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

While previous research found groups of genes that had peak expression at dawn, we wondered whether the dawn burst was a more widespread phenomenon and whether regulatory proteins also exhibited a peak in expression (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)-- see Figure 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 \cite{Michael2008}, we observe that DNA binding factors that have peak expression immediately 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 suggests that phyABCDE may play a more important role in inhibiting nighttime genes than activating morning genes.  We observe the same trends in elf3-1, which is consistent with evidence that phytochromes interact with ELF3 \cite{Ezer2017} (Figure S2).