Sorenson Reed S, Sieburth Leslie E
School of Biological Sciences, University of Utah, Salt Lake City, Utah 84112.
bioRxiv. 2025 Jun 2:2025.05.09.653099. doi: 10.1101/2025.05.09.653099.
RNA decay is essential for maintenance of normal RNA abundances; however how RNA decay is regulated to contribute to changes in RNA abundances is poorly understood. Here, we addressed this question by analyzing rates of RNA abundance change, RNA halflives ( s), and transcription rates in stimulated Arabidopsis leaf cells. This revealed three mechanisms by which decay influenced RNA abundance changes. First, the biggest changes in RNA abundances resulted from changes that reinforced transcriptional regulation (synergistic). Modest RNA abundance changes arose from a second mechanism in which changes opposed transcriptional regulation (oppositional). Finally, RNA decay alone also contributed to RNA abundance change, and RNA decay's measured capacity influence RNA abundances was similar to that of transcription. RNA decay also contributed to transcriptome homeostasis through stimulus-induced RNA buffering. Oppositional and buffering regulation shared key features, including excessive and commensurate rate changes, which suggested use of a shared regulatory mechanism which we call countercyclical regulation. In this study, countercyclical regulation was widespread and used for regulation of 90% of the RNAs with regulation.
RNA降解对于维持正常的RNA丰度至关重要；然而，人们对RNA降解如何被调控以促成RNA丰度的变化却知之甚少。在此，我们通过分析拟南芥叶细胞受到刺激后的RNA丰度变化率、RNA半衰期（s）和转录率来解决这个问题。这揭示了降解影响RNA丰度变化的三种机制。首先，RNA丰度的最大变化源于强化转录调控的变化（协同作用）。适度的RNA丰度变化源于第二种机制，即变化与转录调控相反（对抗作用）。最后，仅RNA降解也促成了RNA丰度变化，并且所测得的RNA降解影响RNA丰度的能力与转录相似。RNA降解还通过刺激诱导的RNA缓冲作用促成转录组稳态。对抗作用和缓冲作用调控具有共同的关键特征，包括过度和相应的速率变化，这表明使用了一种我们称为反周期调控的共同调控机制。在本研究中，反周期调控广泛存在，并用于调控90%受到调控的RNA。
