Hybridization-proximity labeling reveals spatially ordered interactions of nuclear RNA compartments.
Hybridization-proximity labeling reveals spatially ordered interactions of nuclear RNA compartments.
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杂交接近标记揭示了核RNA室的空间有序相互作用。
DOI：
10.1016/j.molcel.2021.10.009
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发表时间：
2022-01-20
期刊：
影响因子：
16
通讯作者：
Makeyev EV
中科院分区：
文献类型：
--
作者：
Yap K;Chung TH;Makeyev EV
RNA与其他大分子形成特异性接触的能力为亚细胞区室化提供了重要机制。在这里，我们描述了一套杂交-邻近（HyPro）标记技术，用于无偏地发现与基因未受干扰的细胞中感兴趣的RNA相关的蛋白质（HyPro-MS）和转录本（HyPro-seq）。作为原理的证明，我们表明HyPro-MS和HyPro-seq可以识别已知的和以前未探索的非编码RNA 45 S，NEAT 1和PNCTR的空间邻居，这些非编码RNA以明显不同的水平表达。值得注意的是，HyPro-seq揭示了一个广泛的未完全加工的，腺苷到肌苷编辑的转录本库，这些转录本在其编码染色体区域和含有NEAT 1的paraspeckle区室之间的界面处积累。这些靶点中至少有一些需要NEAT 1来实现其最佳表达。总的来说，这项研究提供了一个多功能的工具包，解剖RNA相互作用在不同的生物医学背景下，扩大了我们的理解哺乳动物细胞核的功能结构。HyPro标记揭示了目标RNA的相互作用子和空间邻居蛋白质和RNA伴侣通过质谱法和深度测序鉴定不需要遗传修饰，允许更广泛的生物医学用途含有RNA的核体的相互作用组被映射作为原理证明雅普et al.开发了一种空间相互作用组作图方法，该方法依赖于在固定的遗传未受干扰的细胞中将紧凑的过氧化物酶试剂募集到感兴趣的RNA和邻近生物素化。作者表明，这项技术可以识别RNA区室特异性蛋白质组和转录组，并揭示转录基因组区域的更高级接触。
The ability of RNAs to form specific contacts with other macromolecules provides an important mechanism for subcellular compartmentalization. Here we describe a suite of hybridization-proximity (HyPro) labeling technologies for unbiased discovery of proteins (HyPro-MS) and transcripts (HyPro-seq) associated with RNAs of interest in genetically unperturbed cells. As a proof of principle, we show that HyPro-MS and HyPro-seq can identify both known and previously unexplored spatial neighbors of the noncoding RNAs 45S, NEAT1, and PNCTR expressed at markedly different levels. Notably, HyPro-seq uncovers an extensive repertoire of incompletely processed, adenosine-to-inosine-edited transcripts accumulating at the interface between their encoding chromosomal regions and the NEAT1-containing paraspeckle compartment. At least some of these targets require NEAT1 for their optimal expression. Overall, this study provides a versatile toolkit for dissecting RNA interactomes in diverse biomedical contexts and expands our understanding of the functional architecture of the mammalian nucleus. HyPro labeling uncovers interactors and spatial neighbors of RNAs of interest Protein and RNA partners are identified by mass spectrometry and deep sequencing No genetic modifications are required, allowing wider biomedical use Interactomes of RNA-containing nuclear bodies are mapped as a proof of principle Yap et al. developed a spatial interactome mapping approach relying on recruitment of a compact peroxidase reagent to RNAs of interest and proximity biotinylation in fixed genetically unperturbed cells. The authors show that this technology can identify RNA compartment-specific proteomes and transcriptomes and reveal higher order contacts of transcribed genomic regions.
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DOI：
10.1093/bioinformatics/btx346
发表时间：
2017-10-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Gel B;Serra E
通讯作者：
Serra E
影响因子：
64.5
作者：
Bhatt DM;Pandya-Jones A;Tong AJ;Barozzi I;Lissner MM;Natoli G;Black DL;Smale ST
通讯作者：
Smale ST
影响因子：
48
作者：
Bar DZ;Atkatsh K;Tavarez U;Erdos MR;Gruenbaum Y;Collins FS
通讯作者：
Collins FS
影响因子：
7
作者：
Floutsakou I;Agrawal S;Nguyen TT;Seoighe C;Ganley AR;McStay B
通讯作者：
McStay B
影响因子：
4.6
作者：
Anantharaman A;Jadaliha M;Tripathi V;Nakagawa S;Hirose T;Jantsch MF;Prasanth SG;Prasanth KV
通讯作者：
Prasanth KV