We report an intriguing relationship between changes in mRNA abundance and changes in mRNA degradation in response to stress. We show that this relationship varies between conditions, and among genes with different kinetics within the same condition. In particular, among the transient genes, which attain maximal fold change, and begin relaxation within the first 60 min, it appears that the change in the mRNA abundance level is counteracted by the change in degradation rate.
Clearly, the destabilization of transiently induced genes has to be compensated by a large increase in transcription rates, otherwise a net increased level would not be obtained. Likewise, fast repressed transient genes must experience a decrease in production rate, as at the degradation level they are actually stabilized. Thus, although we deduce transcription rates indirectly, we can still conclude in this case, that transcription rate has increased among the induced destabilized genes and decreased among the repressed stabilized genes. A more direct indication that among destabilized genes transcription rates are predominantly increased, and that among stabilized genes transcription rates are most reduced, may be obtained from the measurements done recently by Molina-Navarro et al (2008)
. Reassuringly, re-analysis of their data strongly shows exactly that trend (Supplementary Figure S13
). Among genes that respond either by induction or repression of above twofold change, genes which, by our measurements, are destabilized show a mean increase in transcription rate of above 60% in most time points, whereas genes that we found to be stabilized show a general decrease in transcription rate of about 40%. An interesting conclusion regarding the fast transient responding genes is that changes in transcription rates alone (increase or decrease) determine the direction
of the response (induction or repression). Stability changes appear not to determine the direction of the net response as they actually occur in opposite directions. Yet our results ascribe a major role to changes in degradation—these, along with likely changes at the transcriptional level, appear to impact the speed and relaxation properties of the response. These conclusions are in line with the study of Perez-Ortin et al (2007)
who showed for the STL1
gene in yeast that the measured transcription rate profile was not sufficient to explain a transient mRNA abundance response after osmotic stress; an increase in degradation rate had to be assumed to achieve a rapid decrease back to the basal level. The combined increase in both production and degradation rates, observed at the transient induced genes, may thus represent an interesting strategy, as it allows the acceleration of the response, without compromise of the maximal expression level (see Box 1
On the other hand, for genes that display a high endurance response, both up- and downregulated, it is possible that the direction of the response is both due to transcriptional and degradation effects, as for these genes both factors do not counteract each other. A potential explanation for the behavior seen among the long endurance responsive genes could be that changes in mRNA stability are used to maintain and enhance the changes in transcription, i.e. induced genes are further stabilized, whereas repressed genes are also degraded faster.
Increase in both production and degradation can account for a transient response if the increase in degradation is slower than the increase in production. Under these assumptions, for a short time period, production rate may be higher than degradation rate. In this period, mRNA level may overshoot when compared with the final steady state, and the relaxation is attained when degradation rate exceeds the rate of production (Supplementary Figure S3
). Assuming that an external signal control both production and degradation rates, this model produces a relaxation of the response in mRNA even if the external signal (e.g. hydrogen peroxide in the present case) is still ON. Support to this idea is given by the fact that the levels of hydrogen peroxide are decreased only slightly throughout the experiment (not shown) in agreement with previous studies (Gasch et al, 2000
), whereas the mRNA response begins to relax after an hour. Although concomitant increase in both production and degradation rates is an energetically costly solution, it might have an important advantage as it accelerates both the response to the stress and the relaxation back toward fast growing mode.
Finally, the idea of counteraction between production and degradation suggests coordination of transcriptional and mRNA degradation in the cell. Recently, experimental evidence suggested one potential mechanism that could account for this interplay. Lotan et al (2005
) have shown that two subunits of RNA polymerase II, Rpb4p and Rpb7p, are involved in mRNA decay by enhancing both deadenylation and decapping. This suggests that counteraction could be achieved through direct coupling between transcription and degradation, namely that degradation rates are directly affected by changes in the rates of transcription. An alternative model is that the sensor of the stress activates a transcriptional response and, independently of that, it also induces a change in stability of the transcripts (). This latter model has a topology reminiscent of a feed-forward loop, a recurring motif in many regulatory networks (Milo et al, 2002
; Mangan et al, 2006
), which was curiously found to accelerate response time to nutrient changes (Mangan et al, 2006
). In this respect, it is noteworthy that recent observations made in the mammalian network spanned by microRNAs and transcription factors have proposed that similar coupling between transcription and post-transcription regulators may be implemented through similar in-coherent feed-forward loops (Shalgi et al, 2007
; Sinha et al, 2008
). Future work will be needed to determine the relative contribution of these models, or yet alternative ones, to the interplay seen here between the transcriptional and post-transcriptional regulation.
Figure 4 Two alternative models that might account for the observed coordination between transcription and degradation. Our results suggest coordination between changes in transcription to changes in mRNA degradation; this might be achieved by at least two alternative (more ...)