1 PhD project offered in the IPP summer call Molecular Mechanisms in Genome Stability & Gene Regulation

Scientific Background

Alternative splicing (AS) massively increases transcriptome complexity in higher eukaryotes, with critical implications in developmental processes and stress responses. Studying AS events in model systems revealed the existence of diverse regulatory principles, however, the mechanisms by which rapid and coordinated changes in the AS output can be achieved are still poorly understood. The Wachter group and others have previously shown that early seedling photomorphogenesis is accompanied and driven by AS changes. Furthermore, several splicing regulatory proteins involved in light-dependent AS and seedling development have been identified. In our ongoing research, we examine the molecular mechanisms and signaling pathways underlying rapid re-programming of the transcriptome via AS to steer seedling development in a light-dependent manner.

PhD Project: Light-dependent localization and interactions of RS splicing regulators in plant development

Illumination of etiolated seedlings triggers an extensive developmental re-programming from skoto- to photomorphogenesis, involving massive changes on the level of gene expression, metabolism, and growth. In our previous studies, we have identified light-triggered AS in etiolated Arabidopsis thaliana seedlings as a critical component of photomorphogenesis (Hartmann et al., 2016). Moreover, we have demonstrated an important role of the central energy sensor kinases SnRK1 and TOR in the upstream signaling (Saile et al., 2023). Transducing light signals into an AS response involves RS splicing regulators, which are differentially phosphorylated upon illumination of dark-grown seedlings. Altered photomorphogenesis of A. thaliana mutants with elevated or diminished RS protein levels corroborated their functional relevance in this process. Interestingly, RS proteins mainly localize in the nucleoplasm of etiolated seedlings, while light exposure can trigger their altered sub-nuclear distribution in speckles. Studying the underlying mechanisms and functional consequences of these sub-cellular localization patterns are the key goals of this PhD project. In the first experimental strategy, reporter lines for determining the dynamic localization patterns of RS proteins in a light- and tissue-specific manner will be established and analyzed. These experiments will also address the underlying mechanisms, such as the impact of RS phosphorylation and other protein features, which are studied in vitro by our group as part of the SFB 1551 on biomolecular condensates. The second line of research will identify in vivo interactors of RS proteins. Here, interacting proteins will be captured mainly using proximity labelling, while RNA targets can be searched for using TRIBE, an editing-based detection system recently optimized in our group (Loeser et al., accepted).

If you are interested in this project, please select Wachter as your group preference in the IPP application platform.

Publications relevant to this project

Hartmann L, Drewe-Boß P, Wießner T, Wagner G, Geue S, Lee HC, Obermüller DM, Kahles A, Behr J, Sinz FH, Rätsch G, Wachter A (2016) Alternative Splicing Substantially Diversifies the Transcriptome during Early Photomorphogenesis and Correlates with the Energy Availability in Arabidopsis. Plant Cell, 28:2715-2734 Link

Saile J, Wießner-Kroh T, Erbstein K, Obermüller DM, Pfeiffer A, Janocha D, Lohmann J, Wachter A (2023). SNF1-RELATED KINASE 1 and TARGET OF RAPAMYCIN control light-responsive splicing events and developmental characteristics in etiolated Arabidopsis seedlings. Plant Cell 35: 3413-3428. Link

Loeser J, Bauer J, Janßen K, Rockenbach K, Wachter A. A transient in planta editing assay identifies specific binding of the splicing regulator PTB as a prerequisite for cassette exon inclusion. accepted