Proximity-CLIP provides a snapshot of protein-occupied RNA elements in subcellular compartments.
Proximity-CLIP provides a snapshot of protein-occupied RNA elements in subcellular compartments.
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DOI：
10.1038/s41592-018-0220-y
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发表时间：
2018-12
期刊：
影响因子：
48
通讯作者：
Hafner M
中科院分区：
文献类型：
--
作者：
Benhalevy D;Anastasakis DG;Hafner M
系统地研究亚细胞RNA定位的方法是有限的，落后于蛋白质组学工具。在这里，我们结合APEX 2介导的蛋白质的邻近生物素化与光活化核糖核苷增强交联，同时分析蛋白质组，以及在任何给定的亚细胞区室中RNA结合蛋白结合的转录组。我们的方法是分馏独立的，能够研究RNA加工中间体的本地化，以及在细胞隔室特异性的方式由蛋白质占据的调节RNA顺式作用元件的识别。我们应用Proximity-CLIP研究细胞核、细胞质和细胞-细胞界面的RNA和蛋白质。在其他见解中，我们观察到频繁的转录通读继续为几个酶下游的典型切割和多聚腺苷酸化位点和差异RBP占用模式的mRNA在细胞核和细胞质中。令人惊讶的是，定位于细胞-细胞界面的mRNA通常编码调节蛋白，并且在其3'非翻译区中含有蛋白质占据的CUG序列元件。
Methods to systematically study subcellular RNA localization are limited and lagging behind proteomic tools. Here, we combined APEX2-mediated proximity biotinylation of proteins with photoactivatable ribonucleoside-enhanced crosslinking to simultaneously profile the proteome, as well as the transcriptome bound by RNA-binding proteins in any given subcellular compartment. Our approach is fractionation-independent and enables to study the localization of RNA processing intermediates, as well as the identification of regulatory RNA cis-acting elements occupied by proteins in a cellular compartment-specific manner. We applied Proximity-CLIP to study RNA and protein in the nucleus, cytoplasm and at cell-cell interfaces. Among other insights, we observed frequent transcriptional readthrough continuing for several kilobases downstream of the canonical cleavage and polyadenylation site and a differential RBP occupancy pattern for mRNAs in the nucleus and cytoplasm. Surprisingly, mRNAs localized to cell-cell interfaces often encoded regulatory proteins and contained protein-occupied CUG sequence elements in their 3’ untranslated region.
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影响因子：
14.8
作者：
Hung V;Udeshi ND;Lam SS;Loh KH;Cox KJ;Pedram K;Carr SA;Ting AY
通讯作者：
Ting AY
影响因子：
7.3
作者：
Guo Z;Neilson LJ;Zhong H;Murray PS;Zanivan S;Zaidel-Bar R
通讯作者：
Zaidel-Bar R
影响因子：
64.5
作者：
Hafner M;Landthaler M;Burger L;Khorshid M;Hausser J;Berninger P;Rothballer A;Ascano M Jr;Jungkamp AC;Munschauer M;Ulrich A;Wardle GS;Dewell S;Zavolan M;Tuschl T
通讯作者：
Tuschl T
DOI：
10.1002/wdev.272
发表时间：
2017-07
期刊：
Wiley interdisciplinary reviews. Developmental biology
影响因子：
--
作者：
Chen CL;Perrimon N
通讯作者：
Perrimon N
DOI：
10.4161/cl.1.1.14465
发表时间：
2011-01-01
期刊：
Cellular logistics
影响因子：
--
作者：
Choder, Mordechai
通讯作者：
Choder, Mordechai