Monitoring Protein-RNA Interaction Dynamics in vivo at High Temporal Resolution using χCRAC

被引:2
|
作者
McKellar, Stuart W. [1 ]
Ivanova, Ivayla [1 ]
van Nues, Robert W. [2 ]
Cordiner, Ross A. [3 ]
Worboys, Will [4 ]
Langford, Andrew [4 ]
Jensen, Torben Heick [3 ]
Granneman, Sander [1 ]
机构
[1] Univ Edinburgh, Ctr Synthet & Syst Biol, Edinburgh, Midlothian, Scotland
[2] Univ Edinburgh, Inst Cell Biol, Edinburgh, Midlothian, Scotland
[3] Aarhus Univ, Dept Mol Biol & Genet, Aarhus, Denmark
[4] UVO3 Ltd, St Ives, England
来源
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS | 2020年 / 159期
基金
英国惠康基金; 英国医学研究理事会;
关键词
Biochemistry; Issue; 159; CRAC; CLIP; RNA-protein interaction; UV cross-linking; engineering; stress response; time-resolved; TRANSCRIPTOME-WIDE IDENTIFICATION; PRE-RIBOSOMAL-RNA; GENE-EXPRESSION; BINDING-SITES; CROSS-LINKING; CLIP; REVEALS; YEAST; CHROMATIN; PLATFORM;
D O I
10.3791/61027
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
The interaction between RNA-binding proteins (RBPs) and their RNA substrates exhibits fluidity and complexity. Within its lifespan, a single RNA can be bound by many different RBPs that will regulate its production, stability, activity, and degradation. As such, much has been done to understand the dynamics that exist between these two types of molecules. A particularly important breakthrough came with the emergence of 'cross-linking and immunoprecipitation' (CLIP). This technique allowed stringent investigation into which RNAs are bound by a particular RBP. In short, the protein of interest is UV cross-linked to its RNA substrates in vivo, purified under highly stringent conditions, and then the RNAs covalently cross-linked to the protein are converted into cDNA libraries and sequenced. Since its conception, many derivative techniques have been developed in order to make CLIP amenable to particular fields of study. However, cross-linking using ultraviolet light is notoriously inefficient. This results in extended exposure times that make the temporal study of RBP-RNA interactions impossible. To overcome this issue, we recently designed and built much-improved UV irradiation and cell harvesting devices. Using these new tools, we developed a protocol for time-resolved analyses of RBP-RNA interactions in living cells at high temporal resolution: Kinetic CRoss-linking and Analysis of cDNAs (chi CRAC). We recently used this technique to study the role of yeast RBPs in nutrient stress adaptation. This manuscript provides a detailed overview of the chi CRAC method and presents recent results obtained with the Nrd1 RBP.
引用
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页数:19
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