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Environmental cues, such as temperature and light, are central developmental signals for plants. Due to their sessile lifestyle, they must constantly surveil the environment and adapt accordingly. Ambient temperature fluctuations and light quality can cause abiotic stress and significantly influence plant physiological processes. Consequently, an appropriate response to the environment is pivotal for plant survival.

A central mechanism for environmental adaptation, and the appropriate response to abiotic stresses, is based on transcriptomic adjustments, through the regulation of RNA polymerase II and co-transcriptional alternative splicing. One mechanism for the regulation of transcription is the dynamic phosphorylation of the RNA polymerase II C-terminal domain by Cyclin-Dependent Kinases. Co-transcriptional alternative splicing, which describes the dynamic processing of primary RNA transcripts into multiple messenger RNAs, is tightly linked to the regulation of RNA polymerase II. Intriguingly, both processes have been shown to play essential roles in plants’ environmental responses. However, mechanistic insights for many of these processes are still lacking, and it remains unclear how environmental signalling is translated into transcriptomic changes. Additionally, many studies focus on the temperature response of above-ground tissue, while root-specific responses are only poorly studied.

By assessing the transcriptomic response, as well as phenotypic alterations, of multiple splicing mutants across a temperature range from 16 °C to 27 °C, we show that alternative splicing reacts to moderated changes in ambient temperature, resulting in extensive transcriptomic changes. Among these, we find many adjustments related to light signalling, regulation of the circadian clock, and temperature signalling. We furthermore find that the loss of a central splicing component (PORCUPINE/SmEb) in Arabidopsisthaliana causes severe defects in root meristem architecture through the disruption of auxin homeostasis and misregulation of meristematic activity. Finally, we show that the inhibition of RNA polymerase II CTD phosphorylation by the Cyclin-Dependent Kinase Group C2 attenuates the low-temperature sensivity of multiple splicing mutants.

In summary, these results highlight the complexity of plant transcriptional regulation in response to the environment. Our results underscore the crosstalk of many regulatory mechanisms, which together ensure correct plant development under varying environmental conditions.

Temperature is an important signal that informs plants about their surroundings and daily and seasonal changes. In temperate climates, temperature variation throughout the year can reach up to 40°C, and usually, it is the cold that acts as a limiting factor for successful growth and development. The cold response is a multifaceted process that affects all levels of the organization, from molecular to organismal. There is an intertwined network of transcriptional changes, cold-triggered splicing events, and unspecific stress responses.

The aim of this thesis was to investigate the role of PORCUPINE (PCP/SmE1), a component of the core splicing complex called Sm-ring, in cold signaling and its connection to co-occurring events in the model plant Arabidopsis thaliana. Despite the functional redundancy of PCP and its homolog PORCUPINE-LIKE (PCPL/SmE2), their roles diverge due to the differential gene regulation in response to temperature. We showed a correlation between the level of the PCP transcript and plant phenotype and linked PCP expression to its introns. Then, we compared the transcriptome of the knockout PCP mutant, pcp-1, to other temperature-sensitive splicing mutants and showed a pool of differential splicing events that were PCP-specific. Some of these events were linked to the core components of the cold response. We hypothesized that at least part of the pleiotropic effects of the PCP loss in A. thaliana occur due to the misregulated splicing of these genes. We also identified a plausible connection between splicing and transcription through PCP as a component of the Sm-ring and an RNA Polymerase II regulator, CDKC;2. Here we found that the loss of CDKC;2 in the pcp-1 background rescued the cold-sensitive pcp-1 phenotype and restored transcriptional kinetics to the wild-type levels. Finally, we hypothesize that a broken Sm-ring requires an appropriate attenuation of the transcription rates to perform the splicing successfully.

Taken together, the work in this thesis demonstrates the complexity of the cold response mechanisms in A. thaliana and the central role of splicing components, such as PCP, for temperature acclimatization.