Castello Alfredo, Fischer Bernd, Frese Christian K, Horos Rastislav, Alleaume Anne-Marie, Foehr Sophia, Curk Tomaz, Krijgsveld Jeroen, Hentze Matthias W
European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany; Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany; German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
Mol Cell. 2016 Aug 18;63(4):696-710. doi: 10.1016/j.molcel.2016.06.029. Epub 2016 Jul 21.
Mammalian cells harbor more than a thousand RNA-binding proteins (RBPs), with half of these employing unknown modes of RNA binding. We developed RBDmap to determine the RNA-binding sites of native RBPs on a proteome-wide scale. We identified 1,174 binding sites within 529 HeLa cell RBPs, discovering numerous RNA-binding domains (RBDs). Catalytic centers or protein-protein interaction domains are in close relationship with RNA-binding sites, invoking possible effector roles of RNA in the control of protein function. Nearly half of the RNA-binding sites map to intrinsically disordered regions, uncovering unstructured domains as prevalent partners in protein-RNA interactions. RNA-binding sites represent hot spots for defined posttranslational modifications such as lysine acetylation and tyrosine phosphorylation, suggesting metabolic and signal-dependent regulation of RBP function. RBDs display a high degree of evolutionary conservation and incidence of Mendelian mutations, suggestive of important functional roles. RBDmap thus yields profound insights into native protein-RNA interactions in living cells.
哺乳动物细胞含有一千多种RNA结合蛋白（RBP），其中一半采用未知的RNA结合模式。我们开发了RBDmap，以在全蛋白质组范围内确定天然RBP的RNA结合位点。我们在529个HeLa细胞RBP中鉴定出1174个结合位点，发现了许多RNA结合结构域（RBD）。催化中心或蛋白质-蛋白质相互作用结构域与RNA结合位点密切相关，这表明RNA在控制蛋白质功能中可能发挥效应作用。近一半的RNA结合位点定位于内在无序区域，揭示了无结构结构域是蛋白质-RNA相互作用中普遍存在的伙伴。RNA结合位点是特定翻译后修饰（如赖氨酸乙酰化和酪氨酸磷酸化）的热点，这表明RBP功能存在代谢和信号依赖性调节。RBD显示出高度的进化保守性和孟德尔突变发生率，提示其具有重要的功能作用。因此，RBDmap对活细胞中天然蛋白质-RNA相互作用产生了深刻的见解。
