Somalraju Sahiti, Salem Doaa Hassan, Janga Sarath Chandra
Department of Biomedical Engineering and Informatics, Luddy School of Informatics, Computing and Engineering, Indiana University Indianapolis (IUI), Indianapolis, IN, USA.
Department of Biomedical Engineering and Informatics, Luddy School of Informatics, Computing and Engineering, Indiana University Indianapolis (IUI), Indianapolis, IN, USA; Computers and Systems Department, National Telecommunication Institute, Cairo, Egypt.
Trends Genet. 2025 Jun 4. doi: 10.1016/j.tig.2025.05.001.
Investigating RNA dynamics is crucial for uncovering fundamental mechanisms, such as alternative splicing, RNA stability, and post-transcriptional modifications, all processes with implications for identifying therapeutic targets and advancing knowledge of cellular function and regulation. Advances in long-read sequencing technologies, particularly from Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT), offer unprecedented insights into RNA dynamics at single molecule and single nucleotide resolutions. In this review, we examine protocols and methods for analyzing RNA dynamics, focusing on isoform detection, poly(A) tail length quantification, and mapping of RNA modifications. We envision that these high-throughput, transcriptome-wide data sets, combined with integrated software systems, will transform workflows for studying single molecule RNA dynamics. Such advances will help unravel the complexities of gene regulation and deepen our understanding of cellular processes.
研究RNA动态对于揭示诸如可变剪接、RNA稳定性和转录后修饰等基本机制至关重要，所有这些过程都对确定治疗靶点以及推进细胞功能和调控知识具有重要意义。长读长测序技术的进步，特别是来自太平洋生物科学公司（PacBio）和牛津纳米孔技术公司（ONT）的技术，提供了前所未有的单分子和单核苷酸分辨率下的RNA动态见解。在本综述中，我们研究了分析RNA动态的方案和方法，重点关注异构体检测、聚腺苷酸（poly(A)）尾长度定量以及RNA修饰图谱绘制。我们设想，这些高通量、全转录组数据集与集成软件系统相结合，将改变研究单分子RNA动态的工作流程。这些进展将有助于揭示基因调控的复杂性，并加深我们对细胞过程的理解。
