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光活化核苷酸标记碱基特异性的 RNA 结合位点。

Photoactivatable ribonucleosides mark base-specific RNA-binding sites.

机构信息

Center for RNA Research, Institute for Basic Science, Seoul, 08826, Korea.

School of Biological Sciences, Seoul National University, Seoul, 08826, Korea.

出版信息

Nat Commun. 2021 Oct 15;12(1):6026. doi: 10.1038/s41467-021-26317-5.

Abstract

RNA-protein interaction can be captured by crosslinking and enrichment followed by tandem mass spectrometry, but it remains challenging to pinpoint RNA-binding sites (RBSs) or provide direct evidence for RNA-binding. To overcome these limitations, we here developed pRBS-ID, by incorporating the benefits of UVA-based photoactivatable ribonucleoside (PAR; 4-thiouridine and 6-thioguanosine) crosslinking and chemical RNA cleavage. pRBS-ID robustly detects peptides crosslinked to PAR adducts, offering direct RNA-binding evidence and identifying RBSs at single amino acid-resolution with base-specificity (U or G). Using pRBS-ID, we could profile uridine-contacting RBSs globally and discover guanosine-contacting RBSs, which allowed us to characterize the base-specific interactions. We also applied the search pipeline to analyze the datasets from UVC-based RBS-ID experiments, altogether offering a comprehensive list of human RBSs with high coverage (3,077 RBSs in 532 proteins in total). pRBS-ID is a widely applicable platform to investigate the molecular basis of posttranscriptional regulation.

摘要

RNA-蛋白质相互作用可以通过交联和富集,然后进行串联质谱分析来捕获,但确定 RNA 结合位点(RBS)或提供 RNA 结合的直接证据仍然具有挑战性。为了克服这些限制,我们在这里开发了 pRBS-ID,它结合了基于 UVA 的光活化核苷酸(PAR;4-硫代尿嘧啶和 6-硫代鸟嘌呤)交联和化学 RNA 切割的优点。pRBS-ID 可以可靠地检测与 PAR 加合物交联的肽,提供直接的 RNA 结合证据,并以单个氨基酸分辨率识别具有碱基特异性(U 或 G)的 RBS。使用 pRBS-ID,我们可以全局分析尿嘧啶接触的 RBS,并发现与鸟嘌呤接触的 RBS,这使我们能够描述碱基特异性相互作用。我们还应用搜索管道分析基于 UVC 的 RBS-ID 实验的数据集,总共提供了具有高覆盖率的全面人类 RBS 列表(总共 532 个蛋白质中有 3077 个 RBS)。pRBS-ID 是一个广泛适用的平台,可以研究转录后调控的分子基础。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d3be/8519950/1b01c17ee94a/41467_2021_26317_Fig1_HTML.jpg

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本文引用的文献

1
Inhibition of RNA-binding proteins with small molecules.
Nat Rev Chem. 2020 Sep;4(9):441-458. doi: 10.1038/s41570-020-0201-4. Epub 2020 Jul 15.
2
Accurate prediction of protein structures and interactions using a three-track neural network.
Science. 2021 Aug 20;373(6557):871-876. doi: 10.1126/science.abj8754. Epub 2021 Jul 15.
3
Highly accurate protein structure prediction with AlphaFold.
Nature. 2021 Aug;596(7873):583-589. doi: 10.1038/s41586-021-03819-2. Epub 2021 Jul 15.
4
Global analysis of protein-RNA interactions in SARS-CoV-2-infected cells reveals key regulators of infection.
Mol Cell. 2021 Jul 1;81(13):2851-2867.e7. doi: 10.1016/j.molcel.2021.05.023. Epub 2021 May 24.
5
FAX-RIC enables robust profiling of dynamic RNP complex formation in multicellular organisms in vivo.
Nucleic Acids Res. 2021 Mar 18;49(5):e28. doi: 10.1093/nar/gkaa1194.
6
RNA-binding proteins in human genetic disease.
Nat Rev Genet. 2021 Mar;22(3):185-198. doi: 10.1038/s41576-020-00302-y. Epub 2020 Nov 24.
7
Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry.
Nat Commun. 2020 Oct 16;11(1):5250. doi: 10.1038/s41467-020-19047-7.
8
EDF1 coordinates cellular responses to ribosome collisions.
Elife. 2020 Aug 3;9:e58828. doi: 10.7554/eLife.58828.
9
Chemical RNA digestion enables robust RNA-binding site mapping at single amino acid resolution.
Nat Struct Mol Biol. 2020 Jul;27(7):678-682. doi: 10.1038/s41594-020-0436-2. Epub 2020 Jun 8.
10
Discovery of Widespread Host Protein Interactions with the Pre-replicated Genome of CHIKV Using VIR-CLASP.
Mol Cell. 2020 May 21;78(4):624-640.e7. doi: 10.1016/j.molcel.2020.04.013. Epub 2020 May 6.

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