Thinking of doing your PhD in the Life Sciences? The International PhD Programme (IPP) Mainz is offering talented, young scientists the chance to work on cutting edge research projects within the open call on “Molecular Mechanisms in Genome Stability & Gene Regulation”. As an IPP PhD student, you will join a community of exceptional scientists working on diverse topics ranging from how organisms age or how our DNA is repaired, to how epigenetics regulates cellular identity or neural memory. The research group of Andreas Wachter offers the following PhD project: 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 modulate seedling development in a light-dependent manner. PhD project: Regulation of alternative splicing by R-loop formation in Arabidopsis R-loops refer to RNA-DNA hybrid structures that have been linked to genotoxic stress. More recently, R-loops have also been shown to function in the regulation of gene expression. A previous study generating a genome-wide R-loop atlas for the model plant Arabidopsis thaliana using ssDRIP-seq (single-strand DNA ligation-based library preparation from DNA:RNA hybrid immunoprecipitation followed by sequencing) identified major changes in R-loop formation in the comparison of dark- and light-grown seedlings (Xu et al., 2020). Furthermore, the Wachter group has demonstrated rapid re-programming of alternative splicing (AS) upon exposing etiolated seedlings to light (Hartmann et al., 2016; Saile et al., 2023). In this project, we would like to examine whether the occurrence of R-loops and AS are more widely coupled and will address in the context of the 4R RTG “R-loop Regulation in Robustness and Resilience” the following major questions: i) Are R-loops overrepresented in regions displaying light-dependent AS? ii) Does light exposure of dark-grown seedlings alter R-loop formation as quickly as changes occur on the level of AS? Here, it is planned to test the effects of photosynthetically active white light and genotoxic UV-B light. iii) Do mutants with altered expression of nuclear RNase H1, including gene knockouts and inducible expression lines, show alterations in their light responses, considering R-loop formation, AS, and development? Resolving these questions will also provide a basis to further study the mechanistic link between R-loops and AS in the future. This project will be part of the RTG on R-loop Regulation in Robustness and Resilience (4R). If you are interested in this project, please select Wachter as your group preference in the IPP application platform. Are you an ambitious, young scientist looking to push the boundaries of research while interacting with colleagues from multiple disciplines and cultures? Then joining the IPP is your opportunity to give your scientific career a flying start All you need is: Master or equivalent Interactive personality & good command of English 2 letters of reference Exciting, interdisciplinary projects in a lively international environment, with English as our working language Advanced training in scientific techniques and professional skills Access to our state-of-the-art Core Facilities and their technical expertise Fully funded positions with financing until the completion of your thesis A lively community of more than 200 PhD students from 44 different countries