初生 RNA 分析：追踪转录及其调控。
Nascent RNA analyses: tracking transcription and its regulation.
机构信息
Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, USA.
出版信息
Nat Rev Genet. 2019 Dec;20(12):705-723. doi: 10.1038/s41576-019-0159-6. Epub 2019 Aug 9.
Abstract
The programmes that direct an organism's development and maintenance are encoded in its genome. Decoding of this information begins with regulated transcription of genomic DNA into RNA. Although transcription and its control can be tracked indirectly by measuring stable RNAs, it is only by directly measuring nascent RNAs that the immediate regulatory changes in response to developmental, environmental, disease and metabolic signals are revealed. Multiple complementary methods have been developed to quantitatively track nascent transcription genome-wide at nucleotide resolution, all of which have contributed novel insights into the mechanisms of gene regulation and transcription-coupled RNA processing. Here we critically evaluate the array of strategies used for investigating nascent transcription and discuss the recent conceptual advances they have provided.
摘要
指导生物体发育和维持的程序编码在其基因组中。该信息的解码始于受调控的基因组 DNA 转录为 RNA。尽管转录及其调控可以通过测量稳定的 RNA 来间接追踪，但只有通过直接测量新生 RNA，才能揭示对发育、环境、疾病和代谢信号的即时调控变化。已经开发了多种互补的方法来定量跟踪全基因组核苷酸分辨率的新生转录，所有这些方法都为基因调控和转录偶联的 RNA 处理机制提供了新的见解。在这里，我们批判性地评估了用于研究新生转录的一系列策略，并讨论了它们最近提供的概念性进展。
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3
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