Dissecting protein-RNA and -DNA interactions in cells through crosslinking/mass spectrometry analyses (P04)

• Subject Area: Biochemistry
• Term: since 2023
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 469281184

Identifying the proteins involved in gene expression processes and their interactions with RNA and/or DNA, has long been a goal of research. Mass-spectrometry (MS)-driven approaches allow identification of such proteins after purification of RNA or DNA components. Here, we will apply chemical (and also UV) crosslinking to define direct protein–RNA/DNA interactions in selected eukaryotic cellular systems of different complexity: (i) mitochondria, a prime example of a cellular organelle, and (ii) cell nuclei with their chromatin and RNA content. We will integrate the MS-based detection of RNA/DNA-interacting proteins and subsequent data annotation and evaluation into a single workflow and also develop MS-based methods for identifying protein-nucleic acid crosslinks using ion-mobility settings with dedicated MS instruments. Importantly, our approaches will also allow the unbiased identification of the spectrum of RNA/DNA targets for multifunctional proteins in different gene expression processes.

• DFG Programme: Collaborative Research Centres
• Subproject of: SFB 1565: Molecular mechanisms and interplay of gene expression processes
• Applicant Institution: Georg-August-Universität Göttingen
• Project Head: Professor Dr. Henning Urlaub