Projects Offered

2 PhD projects offered in the IPP winter call Molecular Mechanisms in Genome Stability & Gene Regulation

Scientific Background Project 1

Alternative polyadenylation (APA) is a widespread and highly dynamic mechanism of gene regulation. It affects more than 70% of all genes, resulting in transcript isoforms with distinct 3’end termini (Derti et al. 2012). APA thereby considerably expands the diversity of the transcriptome 3' end, leading to mRNA isoforms with profoundly different physiological effects, by affecting protein output, production of distinct protein isoforms, or modulating protein localization (Mayer, 2017). APA is globally regulated in various conditions, including developmental and adaptive programs (Tian & Manley, 2017). Perturbations of APA can disrupt biological processes, ultimately resulting in devastating disorders including cancer (Ogorodnikov et al. 2018, Nourse et al. 2020). Although substantial evidence for an interplay between RNA cleavage and polyadenylation (CPA) and the maintenance of genome stability exists (Spada, Luke, Danckwardt 2022, Khan & Danckwardt 2022), little is known about the role APA and CPA have in R-loop formation, and vice versa.

PhD Project 1: Functional implications of the crosstalk between R-loop formation and alternative polyadenylation

In a systematic large-scale RNAi screening, we recently mapped the dynamic landscape of APA after depletion of >170 proteins involved in various facets of transcriptional, co- and post-transcriptional gene regulation, epigenetic modifications and further processes (Ogorodnikov et al. 2018, Marini et al. 2021). We observed that key components pervasively regulating CPA and APA (including RNA processing factors involved in the coupling of transcription termination and CPA such as PCF11) control processing of various components involved in the formation and resolution of R-loops (TREND-DB atlas http://shiny.imbei.uni-mainz.de:3838/trend-db/).

In this project, we aim to investigate the crosstalk between R-loop formation and alternative polyadenylation, and how this contributes to R-loop homeostasis and modulation of CPA and APA, respectively. Our primary goal is to elucidate the underlying molecular mechanism(s) and to explore how these affect disease phenotypes.

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 Danckwardt (Rloop) as your group preference in the IPP application platform.

Publications relevant to this project

Kargapolova Y, Levin M, Lackner K, Danckwardt S (2017) sCLIP-an integrated platform to study RNA-protein interactomes in biomedical research: identification of CSTF2tau in alternative processing of small nuclear RNAs. Nucleic Acids Res, 45(10):6074-6086 Link

Ogorodnikov A, Levin M, Tattikota S, Tokalov S, Hoque M, Scherzinger D, Marini F, Tian B, Schaefer M, Lackner KJ, Westermann F, Danckwardt S (2018) Transcriptome 3'end organization by PCF11 links alternative polyadenylation to formation and neuronal differentiation of neuroblastoma. Nature Comm, 9(1):5331 Link

Nourse J, Spada S, Danckwardt S (2020) Emerging roles of RNA 3’end cleavage and polyadenylation in pathogenesis, diagnosis and therapy of human disorders. Biomolecules, 10(6):915 Link

Marini F, Scherzinger D, Danckwardt S (2020) TREND-DB – A Transcriptome-wide Atlas of the Dynamic Landscape of Alternative Polyadenylation. Nucl Acid Res, 49(D1):D243-D253 Link

Spada S, Luke B and Danckwardt S (2022) The bidirectional link between RNA cleavage and polyadenylation and genome stability: recent insights from a systematic screen. Front Genet, 13:854907 Link

Khan ES, Danckwardt S. (2022) Pathophysiological role and diagnostic potential of R-loops in cancer and beyond. Genes, 13(12):2181 Link

Scientific Background Project 2

Proteins are macromolecules that carry out a wide range of functions, with most being specialized for a single role. However, an increasing number of proteins are being recognized as multifunctional. In addition, secretory proteins can display entirely distinct functional characteristics depending on their spatial and temporal context (Furukawa, et al. Nature 1992, Radisky et al. Nat Rev Mol Cell Biol 2009). Notable examples include enzymes that, beyond their catalytic roles, are also involved in entirely different processes such as autophagy, protein transport, or DNA maintenance (Mani et al. Nucleic Acids Res 2015).

PhD Project 2: Moonlighting functions of secretory proteins in genome stability

We recently obtained evidence that some secretory proteins govern genome integrity in a cell-autonomous manner by hitherto poorly defined mechanism(s). In this project we want to dissect the moonlighting function of select secretory proteins in genome integrity. Through the use of innovative genetic models that allow to study the tempospatial dynamics of secretory proteins systems-wide real-time combined with functional genetic tools and omics technologies, we will elucidate the functional mechanism(s) through which our target proteins regulate genome stability. Furthermore, we will explore whether this distinct moonlighting function can be leveraged to develop novel therapeutic strategies to prevent and treat devastating disorders such as cancer.

If you are interested in this project, please select Danckwardt (SP) as your group preference in the IPP application platform.

Publications relevant to this project

Nourse J, Tokalov S, Khokhar S, Khan E, Schott LK, Hinz L, Eder L, Arnold-Schild D, Satrapa J, Lackner KJ, Ten Cate H, Probst HC, Danckwardt S (2022) Non-invasive imaging of gene expression and protein secretion dynamics in living mice. BioRxivLink

Contact Details

Prof. Sven Danckwardt
Email
Website IMB
Website 4R
Website UMC

Website Optical Imaging Mainz