Comprehensive Identification of RNA-Binding Domains in Human Cells.
Comprehensive Identification of RNA-Binding Domains in Human Cells.
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DOI：
10.1016/j.molcel.2016.06.029
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发表时间：
2016-08-18
期刊：
影响因子：
16
通讯作者：
Hentze, Matthias W.
中科院分区：
文献类型：
--
作者：
Castello, Alfredo;Fischer, Bernd;Frese, Christian K.;Horos, Rastislav;Alleaume, Anne-Marie;Foehr, Sophia;Curk, Tomaz;Krijgsveld, Jeroen;Hentze, Matthias W.
哺乳动物细胞中含有超过1000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来确定天然rbp在蛋白质组范围内的rna结合位点。我们在529个HeLa细胞rbp中鉴定了1174个结合位点，发现了许多rna结合域（rbd）。催化中心或蛋白-蛋白相互作用结构域与RNA结合位点密切相关，可能调用RNA在控制蛋白质功能中的效应作用。近一半的rna结合位点映射到内在无序的区域，揭示了在蛋白质- rna相互作用中普遍存在的非结构化结构域。rna结合位点是定义的翻译后修饰的热点，如赖氨酸乙酰化和酪氨酸磷酸化，提示RBP功能的代谢和信号依赖性调节。rbd表现出高度的进化保守性和孟德尔突变的发生率，表明其具有重要的功能作用。因此，RBDmap对活细胞中天然蛋白- rna相互作用产生了深刻的见解。人类细胞中RNA结合位点（RBS）图谱的实验生成与酶核心和蛋白-蛋白相互作用位点重叠的RNA结合位点（RBS）总数中约有一半映射到无序的蛋白质区域，RBS富含磷酸化、乙酰化和甲基化位点。许多最近发现的RNA结合蛋白（RBS）与经典的RNA结合蛋白在结构上没有相似之处，它们与RNA的相互作用模式也不清楚。我们开发并使用RBDmap作为一种方法来全面确定rbp的rna相互作用位点，确定了1000多个这样的位点。这些数据对细胞中rna -蛋白相互作用产生了前所未有的见解，并对许多生物学背景产生了影响。
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. Experimental generation of an atlas of RNA-binding sites (RBS) in human cells RBS overlap with enzymatic cores and protein-protein interaction sites About half of the total RBS map to disordered protein regions RBS are enriched for phosphorylation, acetylation, and methylation sites Many recently discovered RNA-binding proteins (RBPs) do not show architectural similarities with classical RBPs, and their modes of interaction with RNA were unclear. We developed and employed RBDmap as a method for the comprehensive determination of the RNA-interacting sites of RBPs, identifying more than a thousand such sites. These data yield unprecedented insight into RNA-protein interactions in cells with implications for numerous biological contexts.
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DOI：
10.1016/j.tem.2015.09.012
发表时间：
2015-12
期刊：
Trends in endocrinology and metabolism: TEM
影响因子：
--
作者：
Castello A;Hentze MW;Preiss T
通讯作者：
Preiss T
影响因子：
3.4
作者：
Boersema, Paul J.;Aye, Thin Thin;Mohammed, Shabaz
通讯作者：
Mohammed, Shabaz
影响因子：
16.6
作者：
Beckmann BM;Horos R;Fischer B;Castello A;Eichelbaum K;Alleaume AM;Schwarzl T;Curk T;Foehr S;Huber W;Krijgsveld J;Hentze MW
通讯作者：
Hentze MW
影响因子：
14.8
作者：
Castello, Alfredo;Horos, Rastislav;Hentze, Matthias W.
通讯作者：
Hentze, Matthias W.
影响因子：
5.6
作者：
Brown, Christopher J.;McNae, Iain;Walkinshaw, Malcolm D.
通讯作者：
Walkinshaw, Malcolm D.