Genetic control of metabolism: the regulome of iron regulatory proteins

代谢重塑是控制细胞命运、环境反应或肿瘤发生的关键过程。虽然转录后调控在蛋白质组的形成中起着关键作用，但迄今为止，代谢的遗传控制主要在转录水平上进行研究。铁代谢非常适合研究代谢的转录后调控。事实上，铁稳态由两种称为铁响应蛋白（IRP）-1和-2的RNA结合因子维持，其结合顺式调节铁响应元件（IRE），从而调节编码铁转运或储存蛋白的靶mRNA的翻译或周转。我们目前对IRP调节子的了解仅限于编码核心铁管理蛋白的少数基因。然而，铁现在被认为是许多生物过程的关键辅因子，包括DNA合成和修复，表观遗传学，免疫，脂质和氧代谢等，这表明铁代谢与多种细胞途径相互关联。我们推测IRP可能构成铁代谢和其他途径之间的中心环节。这意味着IRP/IRE系统的监管范围超出了我们目前所知的范围，并提出了IRP目标身份的问题。最近发展的高通量技术提供了在系统范围内探索转录后调控网络的可能性。这包括UV交联和免疫沉淀（CLIP）以及用于绘制天然RNA-蛋白质接触的深度测序。结合mRNA翻译和/或RNA动力学的全球调查，CLIP能够彻底识别感兴趣的RNA结合蛋白的功能结合位点。我们建议使用这些现代技术，并将CLIP与多核糖体分析和RNA周转的全球探索相结合，以建立转录组中功能性IRP结合位点的全面库。这种整合方法将使用最先进的IRP小鼠模型在其自然环境中的细胞中体内进行。通过这项工作，我们希望揭示IRP/IRE调控网络的新方面，并更好地了解细胞中关键稳态回路与其他代谢途径的连接。由于IRP/IRE系统是一个典型的转录后基因调控网络，我们相信我们的工作将为具有类似性质的基因调控系统的体内研究开创先例。

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.