Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins

RNA-binding proteins (RBPs) determine RNA fate from synthesis to decay. Employing two complementary protocols for covalent UV crosslinking of RBPs to RNA, we describe a systematic, unbiased, and comprehensive approach, termed ‘‘interactome capture,’’ to define the mRNA interactome of proliferating human HeLa cells. We identify 860 proteins that qualify as RBPs by biochemical and statistical criteria, adding more than 300 RBPs to those previously known and shedding light on RBPs in disease, RNA-binding enzymes of intermediary metabolism, RNA-binding kinases, and RNA-binding architectures. Unexpectedly, we find that many proteins of the HeLa mRNA interactome are highly intrinsically disordered and enriched in short repetitive amino acid motifs. Interactome capture is broadly applicable to study mRNA interactome composition and dynamics in varied biological settings.

RNA结合蛋白（RNA-binding proteins, RBPs）调控RNA从合成到降解的全部命运进程。本研究采用两种互补的共价紫外（UV）交联RBP与RNA的实验方案，报道了一种系统性、无偏倚且覆盖全面的实验方法，命名为交互组捕获（interactome capture），用于解析增殖状态的人类HeLa细胞的mRNA交互组。我们通过生化与统计学判定标准筛选出860个符合RNA结合蛋白定义的蛋白质，相较于此前已报道的RNA结合蛋白，新增了300余个新成员，并为疾病相关RBPs、中间代谢通路的RNA结合酶、RNA结合激酶以及RNA结合结构域的研究提供了全新视角。出乎意料的是，我们发现HeLa细胞mRNA交互组中的诸多蛋白质具有高度内在无序性，且富含短串联重复氨基酸基序。交互组捕获技术可广泛应用于不同生物学场景下的mRNA交互组组成与动态变化研究。