Systematic investigation of the role of the BAF complexes in genome stability

1 PhD project offered in the IPP winter call 2022

Scientific Background

BAF chromatin remodellers are polymorphic complexes, subdivided into three major subtypes (cBAF, PBAF, GBAF) that regulate the accessibility of chromatin by sliding or ejecting nucleosomes. BAF complexes are primarily known for their role in gene regulation. However, there is increasing evidence that BAF complexes are also actively implicated in genome stability processes, especially those that involve DNA double-strand breaks (DSBs), in ways that are also likely independent from their chromatin remodelling functions. However, we know very little about the putative differential roles of individual BAF subunits and BAF subtypes in the protection and repair of DSBs, where in the genome DSBs occur upon BAF perturbation and how genome instabilities caused by BAF perturbations are linked to cancerogenesis.

PhD Project: “Deciphering crosstalks between the BAF complexes and genome stability pathways using an integrative systems approach”

This project aims at providing computational expertise to a larger project conducted in close collaboration with the Schick lab for ‘omic data analysis, data integration, and hypothesis generation to investigate mechanisms by which the BAF chromatin remodelling complexes promote genome stability. We are looking for a computational PhD student that will work closely together with an experimental PhD student already working in the Schick lab. You will assist the experimental PhD student in the processing and analysis of generated genomic, proteomic, and imaging data. Vice versa, the experimental PhD student will validate the predictions you generated. The integration of various generated and published ‘omic datasets will be key in this project to gain a comprehensive and unbiased understanding of the role of the different BAF subtypes and individual BAF subunits in genome stability processes and to generate further hypotheses that we can test in the lab. We seek for a PhD candidate with expertise in programming and ‘omic data analysis with a strong interest to learn about the biological processes that are subject to study and with a high collaborative spirit. We offer working in a young, motivated, and dynamic team of researchers in a highly interdisciplinary environment with a good work-life balance.

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

Publications relevant to this project

Schick et al Nature Genetics 2019 https://doi.org/10.1038/s41588-019-0477-9
Luck et al Nature 2020 https://doi.org/10.1038/s41586-020-2188-x
Schick et al Nature Genetics 2021 https://doi.org/10.1038/s41588-021-00777-3
Varga et al Biochem Soc Trans 2021 https://doi.org/10.1042/BST20190960

Contact

Dr Katja Luck
Email
Website: www.imb.de/luck
               www.imb.de/schick
               www.sfb1361.de