Acrylonitrile‐Mediated Nascent RNA Sequencing for Transcriptome‐Wide Profiling of Cellular RNA Dynamics
| Autor: | Weiwu Zeng, Xiang Zhou, Xiaocheng Weng, Fan Wu, Yuqi Chen, Zhiyong He, Yushu Yuan, Qi Wei, Feng Xiao, Yu Zhou, Kun Chen, Zonggui Chen |
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| Rok vydání: | 2020 |
| Předmět: |
RNA polyadenylation
Guanine General Chemical Engineering General Physics and Astronomy Medicine (miscellaneous) 02 engineering and technology Computational biology 010402 general chemistry G-quadruplex 01 natural sciences Biochemistry Genetics and Molecular Biology (miscellaneous) Transcriptome chemistry.chemical_compound Gene expression nascent RNA sequencing General Materials Science lcsh:Science RNA dynamics transcriptome‐wide profiling Gene Messenger RNA Full Paper Chemistry General Engineering RNA Full Papers acrylonitrile 021001 nanoscience & nanotechnology 0104 chemical sciences G‐quadruplex uridine‐to‐cytidine conversion lcsh:Q 0210 nano-technology |
| Zdroj: | Advanced Science Advanced Science, Vol 7, Iss 8, Pp n/a-n/a (2020) |
| ISSN: | 2198-3844 |
| DOI: | 10.1002/advs.201900997 |
| Popis: | RNA sequencing has greatly facilitated gene expression studies but is weak in studying temporal RNA dynamics; this issue can be addressed by analyzing nascent RNAs. A famous method for nascent RNA analysis is metabolic labeling with noncanonic nucleoside followed by affinity purification, however, purification processes can always introduce biases into data analysis. Here, a chemical method for nascent RNA sequencing that avoids affinity purification based on acrylonitrile‐mediated uridine‐to‐cytidine (U‐to‐C) conversion (AMUC‐seq) via 4‐thiouridine (s4U) cyanoethylation is presented. This method converts s4U base‐pairing with guanine through the nucleophilic addition of s4U to acrylonitrile. The high reaction efficiency permits AMUC‐seq directly and efficiently to recover nascent RNA information from total RNAs. AMUC‐seq is validated by being used to detect mRNA half‐lives and investigating the direct gene targets of a G‐quadruplex stabilizer, which can be regarded as potential anticancer drug, in human cells. Thousands of direct gene targets of this drug are verified (these genes are significantly enriched in cancer such as SRC and HRAS). AMUC‐seq also confirms G‐quadruplex stabilization that impacts RNA polyadenylation. These results show AMUC‐seq is qualified for the study of temporal RNA dynamics, and it can be a promising strategy to study the therapeutic mechanism of transcription‐modulating drugs. 4‐thiouridine (s4U) cyanoethylation converts in the nascent RNA to cytidine in a base‐pairing manner, representing a promising strategy for enrichment‐free nascent RNA detection that further benefits transcriptome‐wide analysis of temporal RNA dynamics. |
| Databáze: | OpenAIRE |
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