Thinking of doing your PhD in the Life Sciences? The International PhD Programme (IPP) on Gene Regulation, Epigenetics & Genome Stability is offering talented students the chance to work at the cutting edge of research. 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.
Activities and responsibilities:
In the field of “RNA Biology”, the research group of Andreas Wachter offers the following 2 PhD projects:
Alternative splicing (AS) massively increases transcriptome complexity in higher eukaryotes, with critical implications in development and stress responses. Studying AS events in animals and plants 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 seedling photomorphogenesis is accompanied and supported by AS changes. Furthermore, 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 1: 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 & 2018; Saile et al., in revision).
Based on first reports connecting R-loop formation and AS (e.g., Conn et al., 2017), we would like to examine whether these two processes are more widely coupled. In the context of this PhD project and as part of the 4R RTG “R-loop Regulation in Robustness and Resilience”, we will address the following major questions: 1) Are R-loops overrepresented in regions displaying light-dependent AS? 2)
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 UV-B light, which can also cause genotoxicity? 3) Do mutants with altered expression of the nuclear RNH1A 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 at a later stage of the project.
This project will be part of the RTG on R-loop Regulation in Robustness and Resilience (4R), and is pending of this programme being supported by third part funding.
If you are interested in this project, please select Andreas Wachter (Rloop) as your group preference in the IPP application platform.
PhD project 2: Condensation of RS splicing regulators in light-dependent plant development
We have previously demonstrated the occurrence and functions of light-triggered AS in etiolated seedlings (Hartmann et al., 2016 and 2018). Moreover, treatment with external sucrose triggered similar AS changes as illumination and a role of the central energy sensor kinases SnRK1 and TOR in this process was revealed (Saile et al., in revision).
The rapid phosphorylation and condensate formation of RS proteins upon exposing etiolated seedlings to light or sucrose as well as altered photomorphogenesis of rs mutants suggest a key role of RS proteins in light-dependent development. In this project, we will use a combination of in vitro and in vivo experiments to study the molecular determinants and biological functions of RS condensates.
The RS proteins consist of two RNA recognition motifs (RRMs) and an arginine/serine-rich domain predicted to be intrinsically disordered and responsible for condensate formation. Based on our preliminary work for recombinant production of RS proteins, we will generate domain mutants and study their condensation using turbidity and sedimentation assays.
GFP-containing fusion proteins will be investigated with respect to droplet formation and dynamics. The most interesting RS protein versions will then be used to complement Arabidopsis thaliana mutants or generate overexpression lines to study RS functions and domain contributions in light-dependent speckle formation, AS, and seedling development.
Assuming that phase separation of RS41 is linked to altered molecular interactions, we will identify proteins and RNAs that are in contact or in complexes with RS41, by comparing etiolated seedlings before and after light/sucrose exposure. These experiments will involve in vivo labelling techniques established in the Wachter group such as TRIBE for RNAs (targets of RNA-binding proteins identified by editing; Loeser et al., in revision) and proximity labelling for proteins.
Candidate factors will be independently validated, e.g., by using iCLIP for RNA targets of the RS proteins, and will provide the basis for functional studies in follow-up projects. This project is part of the CRC 1551 on “Polymer concepts in cellular function” and will be conducted in collaboration with the group of Prof. Friederike Schmid from the Physics department, who will be providing theoretical and computer modelling approaches.
If you are interested in this project, please select Andreas Wachter (RS) as your group preference in the IPP application platform.
What we offer:
- Exciting, interdisciplinary projects in a fully 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 190 PhD students from 44 different countries
Are you an ambitious, young scientist looking to push the boundaries of science while interacting with colleagues from multiple disciplines and cultures? Then 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
The deadline for applications is 19 April 2023. Interviews will take place at IMB in Mainz on 19-21 June 2023.
Starting date: 1 August 2023 – 1 February 2024
Contact Details Prof. Dr. Andreas Wachter, Email: firstname.lastname@example.org