Investigating Transcriptional Adaptation in the filamentous fungi Neurospora crassa

• Applicant: Dr. Hamzeh Haj Hammadeh
• Subject Area: General Genetics and Functional Genome Biology
• Term: since 2024
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 538665494

This study aims to investigate Transcriptional Adaptation (TA) in the filamentous fungus Neurospora crassa. Transcriptional Adaptation refers to the cellular response triggered by genetic perturbations whereby a mutation in one gene influences the transcription of other genes, termed "adapting genes”. This proposal aims to shed light on the mechanisms underlying TA in this fungal model organism. The overall objectives of this proposal are to address several unresolved questions: 1) Unveiling TA in Neurospora crassa: In this aim, the focus is on studying Transcriptional Adaptation (TA) in basal eukaryotes. Initial data suggests that certain genetic mutations lead to mRNA degradation. To confirm that these mutations don't diminish gene expression, pre-mRNA levels are assessed. Once equivalence with wild-type (WT) levels is established, comprehensive RNA sequencing is conducted. The aim aims to identify candidate-adapting genes and understand the RNA synthesis process underlying TA. 2) Deciphering Molecular Mechanisms in TA: The objective here is to uncover the molecular mechanisms driving TA. By genetically inactivating genes linked to RNA metabolism, their roles in transcriptional adaptation are explored. Knockout candidates will be positioned upstream or downstream of mRNA decay based on mRNA levels. Double mutants are generated to further probe the significance of these genes, with expected outcomes indicating their roles in mutant mRNA decay or downstream adaptation. 3) Exploring the Regulatory Role of Mutant mRNA Fragments: This aim delves into understanding the nature of RNAs synthesized from degrading mutant mRNA during transcriptional adaptation. Specific RNA binding proteins (RBPs) are screened for their roles in this process. Double mutants are generated to examine the effects on adapting gene mRNA levels. High-throughput sequencing of RBP-associated RNAs is conducted, with insights into sequences initiating TA. Collaboration and knowledge transfer enhance understanding of biological processes and techniques. These aims collectively contribute to unraveling the complex process of Transcriptional Adaptation, shedding light on its mechanisms and potential implications in biological adaptation.

• DFG Programme: WBP Position