Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
The Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
Nat Commun. 2024 Mar 28;15(1):2720. doi: 10.1038/s41467-024-46943-z.
RNA decay is vital for regulating mRNA abundance and gene expression. Existing technologies lack the spatiotemporal precision or transcript specificity to capture the stochastic and transient decay process. We devise a general strategy to inducibly recruit protein factors to modulate target RNA metabolism. Specifically, we introduce a Rapid Inducible Decay of RNA (RIDR) technology to degrade target mRNAs within minutes. The fast and synchronous induction enables direct visualization of mRNA decay dynamics in cells. Applying RIDR to endogenous ACTB mRNA reveals rapid formation and dissolution of RNA granules in pre-existing P-bodies. Time-resolved RNA distribution measurements demonstrate rapid RNA decay inside P-bodies, which is further supported by knocking down P-body constituent proteins. Light and oxidative stress modulate P-body behavior, potentially reconciling the contradictory literature about P-body function. This study reveals compartmentalized RNA decay kinetics, establishing RIDR as a pivotal tool for exploring the spatiotemporal RNA metabolism in cells.
RNA 衰变对于调节 mRNA 丰度和基因表达至关重要。现有的技术缺乏时空精度或转录特异性来捕捉随机和短暂的衰变过程。我们设计了一种通用策略，诱导蛋白因子来调节靶 RNA 代谢。具体来说，我们引入了一种快速诱导 RNA 降解（RIDR）技术，可在数分钟内降解靶 mRNA。快速且同步的诱导使我们能够直接观察细胞中 mRNA 衰变动力学。将 RIDR 应用于内源性 ACTB mRNA 揭示了在预先存在的 P 体中 RNA 颗粒的快速形成和溶解。时分辨析的 RNA 分布测量表明 P 体内部的 RNA 快速衰变，这进一步得到了敲低 P 体组成蛋白的支持。光和氧化应激调节 P 体行为，这可能调和了关于 P 体功能的矛盾文献。这项研究揭示了分隔的 RNA 衰变动力学，确立了 RIDR 作为探索细胞中时空 RNA 代谢的关键工具。
