Discussion

A high resolution time series is required to capture fast transcriptional dynamics

While previous researchers have noted that there is a peculiar burst of gene expression in the early morning, they were unable to fully characterise the transcriptional dynamics in this time period because the time points were not sampled frequently enough.  We were able to identify multiple coordinated waves of gene expression (Figure 5A) .  This included a cluster containing HSF1A (cluster 7-8) that had elevated expression at 27oC and a second cluster that had a large number of light induced genes and that decreased its expression levels at the higher ambient temperature (cluster 5-6).  In general, it is a useful strategy to conduct a few high resolution time course experiments, and then use this data to select informative time point experiments for future experiments.

Perturbed clock and light insensitive mutants use different pathways but produce the same transcriptomic responses

A large proportion of transcription factors have perturbed expression in the early morning, and most of these genes are perturbed in similar ways  in both the circadian and light sensing mutants (Figure 5B ).  Specifically, we observed (i) elevated levels of temperature-responsive genes and (ii) a time delay in the expression in most clusters.
However, we found that these mutants differentially regulate certain gene regulatory networks (Figure 5B ).  For instance, while we found that both mutants have elevated expression of temperature-responsive clusters, prr5prr7prr9 has elevated expression of a subnetwork including CBF2 and SVP, whilephyAphyBcry1cry2 has elevated expression of a subnetwork including HSFB2B, HSP90, and HSP60.  We also saw that the mutants upregulated two different pathways that both increased ABA sensitivity.
Having two different pathways that can lead to the same outcome is one strategy for increasing the robustness of the system.  We know that prr5prr7prr9 has cyclical gene expression, but only in the presence of cyclical light or temperature signals.  Meanwhile, phyAphyBcry1cry2  has a robust circadian clock and can even be partially entrained by light signals, but the period length increases…
Light and temperature signals in the early morning can bypass a ‘blockage’ in the circadian clock.  Here we show that this is true at a molecular level as well.

A detailed map of gene regulation at dawn

This work is consistent with the prr–> CBF2 link that was previously described.  This also suggests a mechanism by which the phyB/EC driven temperature sensing <–> HSF/H2A.Z temperature sensing might be related.
Discuss the delay in both prr5prr7prr9 mutants–> site the Knight/Davis paper about how a circadian clock might have the same period– but the pattern of expression might be stretched or squished.  This further emphasises the importance of sampling at a high resolution–> you might miss a shift in gene expression.
Discuss the ABA thing…

Robust responses to dawn

Conclusions:
From an agricultural perspective, it is important to understand how environmental signalling and the circadian clock is integrated in the early morning.  Researchers have developed lighting systems that maximise yields and photosynthetic efficiency in indoor farms, using either pulsed or continuous exposure to LED lights (CITE: ErnestoOlvera-Gonzalez 2013), but these studies are not considering other factors, such as the resilience of the plant to unexpected conditions.  Additionally, climate change will require crops to be grown in conditions