European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany.
Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931, Cologne, Germany.
Nat Commun. 2023 Apr 12;14(1):2074. doi: 10.1038/s41467-023-37494-w.
System-wide approaches have unveiled an unexpected breadth of the RNA-bound proteomes of cultured cells. Corresponding information regarding RNA-binding proteins (RBPs) of mammalian organs is still missing, largely due to technical challenges. Here, we describe ex vivo enhanced RNA interactome capture (eRIC) to characterize the RNA-bound proteomes of three different mouse organs. The resulting organ atlases encompass more than 1300 RBPs active in brain, kidney or liver. Nearly a quarter (291) of these had formerly not been identified in cultured cells, with more than 100 being metabolic enzymes. Remarkably, RBP activity differs between organs independent of RBP abundance, suggesting organ-specific levels of control. Similarly, we identify systematic differences in RNA binding between animal organs and cultured cells. The pervasive RNA binding of enzymes of intermediary metabolism in organs points to tightly knit connections between gene expression and metabolism, and displays a particular enrichment for enzymes that use nucleotide cofactors. We describe a generically applicable refinement of the eRIC technology and provide an instructive resource of RBPs active in intact mammalian organs, including the brain.
系统方法揭示了培养细胞中 RNA 结合蛋白组的出人意料的广泛程度。关于哺乳动物器官的 RNA 结合蛋白（RBPs）的相应信息仍然缺失，这主要是由于技术挑战。在这里，我们描述了体外增强 RNA 相互作用组捕获（eRIC），以表征三种不同的小鼠器官的 RNA 结合蛋白组。由此产生的器官图谱包含了超过 1300 种在大脑、肾脏或肝脏中活跃的 RBPs。其中近四分之一（291 种）以前在培养细胞中没有被鉴定出来，其中 100 多种是代谢酶。值得注意的是，RBPs 的活性在器官之间存在差异，而与 RBP 的丰度无关，这表明存在器官特异性的控制水平。同样，我们在动物器官和培养细胞之间发现了 RNA 结合的系统差异。中间代谢酶在器官中的普遍 RNA 结合表明基因表达和代谢之间存在紧密的联系，并显示出对使用核苷酸辅助因子的酶的特别富集。我们描述了 eRIC 技术的通用改进，并提供了一个关于在完整的哺乳动物器官中活跃的 RBPs 的有指导意义的资源，包括大脑。
