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