Genetic control of metabolism: the regulome of iron regulatory proteins

• Applicant: Bruno Galy, Ph.D.
• Subject Area: Biochemistry
• Term: from 2016 to 2019
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 317539369

Metabolic remodeling is emerging as a key process in the control of cellular fate, environmental responses, or tumorigenesis. Although posttranscriptional regulations play a key role in shaping proteomes, genetic control of metabolism has so far been mostly investigated at the level of transcription. Iron metabolism is ideally suited to study posttranscriptional regulation of metabolism. Indeed, iron homeostasis is maintained by two RNA binding factors called Iron Responsive Proteins (IRP)-1 and -2, which bind cis-regulatory iron responsive elements (IRE) and thereby modulate the translation or turnover of target mRNAs encoding proteins of iron transport or storage. Our current knowledge of the IRP regulon is limited to those few genes encoding core iron management proteins. However, iron is now recognized as a critical co-factor for numerous biological processes including DNA synthesis and repair, epigenetics, immunity, lipid and oxygen metabolism, etc. This indicates that iron metabolism is interconnected with multiple cellular pathways. We hypothesize that the IRPs could constitute a central link between iron metabolism and those other pathways. This implies that the regulatory scope of the IRP/IRE system expands beyond what we currently know, and raises the question of the identity of IRP targets. High-throughput technologies developed recently offer the possibility to explore posttranscriptional regulatory networks on a system-wide scale. This includes UV crosslinking and immunoprecipitation (CLIP) and deep sequencing for the mapping of native RNA-protein contacts. Combined with global investigation of mRNA translation and/or RNA dynamics, CLIP enables the thorough identification of functional binding sites for RNA binding proteins of interest. We propose to use these modern technologies and integrate CLIP with polysome profiling and global exploration of RNA turnover to establish a comprehensive repertoire of functional IRP binding sites in the transcriptome. This integrative approach will be carried out in vivo in cells within their natural context, using state-of-the-art IRP mouse models. With this work we wish to unveil new facets of the IRP/IRE regulatory network, and better understand the wiring of a key homeostatic circuit in the cell with other metabolic pathways. Because the IRP/IRE system is an archetypical posttranscriptional gene regulatory network, we believe our work will set a precedent for the in vivo study of gene control systems with similar properties.

• DFG Programme: Research Grants