2 PhD projects offered in the IPP summer call 2021
Our lab’s interests are two-fold: on one hand, we study the mechanisms that ensure the complete and accurate duplication of a cell’s genetic information in every cell cycle, especially in the face of DNA damage. We are particularly interested in the pathways of DNA damage tolerance that allow cells to bypass lesions in the replication template. These systems control not only the efficiency of replication, but also its accuracy. As a result, their activities have the potential to either prevent or cause genome instability and are therefore implicated in problems related to cancer and ageing.
On the other hand, our lab investigates the signaling functions of posttranslational protein modifiers of the ubiquitin family, such as ubiquitin itself and the ubiquitin-related protein SUMO. Here we focus on the assembly, structures and recognition of polyubiquitin chains, whose enormous complexity, defined as the ‘ubiquitin code’, governs protein homeostasis, quality control and a variety of other biological functions. By characterizing the enzymatic machinery involved in ubiquitin and SUMO conjugation and deconjugation we are shining light onto the manifold ways in which these modifiers modulate molecular interactions in the cell.
These two research areas come together at several key regulatory nodes controlling essential genome maintenance pathways. We are therefore exploring the functions of ubiquitin and SUMO modifications on a range of DNA replication and repair factors, using biochemical, cell biological, genetic and genomic approaches.
PhD project 1: Replication of damaged chromatin
This project focuses on understanding the impact of chromatin on the replication of damaged DNA. We aim for a mechanistic analysis of the functions of histone modifications, chromatin remodelers and other regulatory factors as well as a characterization of damaged loci at the different stages of lesion processing via proteomics. Using tools like chromatin immunoprecipitation (ChIP), next-generation sequencing, fluorescence microscopy and quantitative mass spectrometry, we will examine the influence of chromatin structure, cell cycle and replication timing on damage processing and determine the interdependencies and hierarchies of the proteins involved in lesion bypass. Dedicated candidates with a strong background in molecular biology and an interest in DNA replication and chromatin-related techniques such as chromatin immunoprecipitation or next-generation sequencing, are encouraged to apply. We also welcome applicants with experience in the bioinformatic analysis of genomic data.
PhD project 2: Re-programming the ubiquitin code
In this project we will explore the signaling properties of polyubiquitin chains and SUMO conjugates. Depending on how the ubiquitin units are linked with each other, polyubiquitin chains can adopt a variety of geometries, including mixed linkages and even branching. How such structural variations translate into different biological signals is not well understood. Although a range of analytical methods exist for the characterization of polyubiquitin chains, it has until now been impossible to manipulate their features deliberately. In our lab, we have developed a series of analytical as well as engineering tools for the detection, inhibition and manipulation of ubiquitin and/or SUMO conjugation in vivo. We will apply these to investigate the contributions of ubiquitylation or sumoylation to genome maintenance, cellular quality control and protein turnover. Candidates with a strong background in protein biochemistry are welcome to apply.
Publications relevant to these projects
Sriramachandran AM, Petrosino G, Mendez-Lago M, Schafer AJ, Batista-Nascimento LS, Zilio N and Ulrich HD (2020) Genome-wide nucleotide-resolution mapping of DNA replication patterns, single-strand breaks, and lesions by GLOE-Seq. Mol Cell, 78:975-985 [Research Highlight in Nature Methods 17:559–565]
Wong RP, Garcia-Rodriguez N, Zilio N, Hanulova M and Ulrich HD (2020) Processing of DNA polymerase-blocking lesions during genome replication is spatially and temporally segregated from replication forks. Mol Cell, 77:3-16 [Featured Article & Cover Image]
Takahashi TS, Wollscheid H-P, Lowther J and Ulrich HD (2020) Effects of chain length and geometry on the activation of DNA damage bypass by polyubiquitylated PCNA. Nucleic Acids Res, 48:3042–3052
Renz C, Albanèse V, Tröster V, Albert TK, Santt O, Jacobs SC, Khmelinskii A, Léon S and Ulrich HD (2020) Ubc13-Mms2 cooperates with a family of RING E3s in membrane protein sorting. J Cell Sci, 133:jcs244566
García-Rodríguez N, Morawska M, Wong RP, Daigaku Y and Ulrich HD (2018) Spatial separation between replisome- and template-induced replication stress signaling. EMBO J, 37:e98369