Mapping the indirect p53 gene regulatory network

• Applicant: Privatdozent Dr. Martin Fischer
• Subject Area: General Genetics and Functional Genome Biology
• Term: since 2022
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 498394458

Cancer is a group of age-related diseases that leads to more than 1.2 million deaths per year in the EU, and the transcription factor p53 serves as a central suppressor of carcinogenesis. It controls cell proliferation and apoptosis by regulating a plethora of target genes. Despite intensive efforts in the past decade, it is still unclear how p53 regulates many of its target genes, what co-factors are necessary for up or down-regulation, and what their regulation contributes to the suppression of carcinogenesis. Our incomplete picture of the molecular basis of gene regulation by p53 remains a critical barrier to our overall understanding of tumor suppression. We hypothesize that p53 employs several factors mediating gene regulation and control cell viability to suppress cancer growth; and that these pathways in the p53 gene regulatory network contribute independent, distinct, and essential gene regulatory activities. Using a meta-analysis approach that we developed earlier, we identified the novel p53-RFX7 signaling pathway. We found that the transcription factor RFX7 governs a tumor suppressor gene network in response to p53 and stress. In the case of RFX7, publicly available data on its sibling RFX5 enabled us to identify RFX7 as a critical transcriptional regulator that functions downstream of p53. However, this rather lucky circumstance cannot conceal that the discovery of new transcriptional regulators in p53’s network is difficult when working with public data alone. To overcome the limitation of our previous approach to identify novel candidate factors in the p53 gene regulatory network, we established methods to identify uncharted transcription factors and generated data that enables an informed screening approach. We will use CAGE-seq data to pinpoint promoter regions that mediate p53-dependent gene regulation and combine it with an established workflow of DNA-affinity purification followed by mass spectrometry to identify transcription factors that specifically bind the regulatory DNA fragments. Candidate transcription factors identified from the informed, comprehensive screening approach will subsequently be validated and characterized. The functional characterization of novel transcriptional regulators that operate downstream of p53 will provide insights into their contribution to p53-regulated processes as well as to their effect on target genes and biological processes irrespective of p53. Together, the goal of this project is to identify uncharted transcription factors contributing to p53-dependent transcriptional regulation. Thus, the project contributes to a better understanding of the p53 gene regulatory network and helps to determine the roles of the identified transcription factors in tumor suppression. In addition to acquiring new candidates for therapeutic intervention in the specific case of p53 malfunction, the project also serves as a blueprint for the genome-wide elucidation of other transcriptional networks.

• DFG Programme: Research Grants
• Co-Investigator: Professor Dr. Steve Hoffmann