RNA half-life regulation reveals countercyclical regulation of buffered RNAs and RNAs undergoing changes in abundance [trim-Qfilt]. RNA half-life regulation reveals countercyclical regulation of buffered RNAs and RNAs undergoing changes in abundance [trim-Qfilt]

mRNA abundances are regulated by the opposing forces of transcription and decay, and yet how decay contributes to mRNA abundance regulation is largely unexplored. We addressed this question using genome-wide data on mRNA rates of abundance change, half-lives, and transcription rates of leaf cells responding to a transdifferentiation stimulusulus. Half-life regulation was common (22% of mRNAs underwent changes in half-life), but RNA abundance regulation by decay alone or by decay that supported transcriptional regulation was rare. Instead, most altered RNA half-lives opposed changes in transcription. Oppositionally regulated mRNAs were characterized by large changes in transcription and decay rates yet changes in mRNA abundances were either modest or undetectable, suggestive of RNA buffering. Oppositionally-regulated and buffered RNAs showed very similar dynamics, suggesting use of a common mechanism. The strongest contributions of RNA decay to RNA abundance regulation was in synergistically regulated transcripts, where rate changes in decay and transcription rates worked together to change RNA abundances. Overall design: To investigate rates of RNA abundance change for comparison with RNA decay rates following a stimulusulus response, we preformed a time course experiment of mock and stimulusulus. Detached leaves of 10 d old Arabidopsis thaliana seedlings were treated with mock conditions or with a transdifferentiation treatment for 5, 6, 7, 8, 9, or 10 h. Tissue was collected for RNA extraction and RNA seq analysis.

信使RNA（mRNA）的丰度由转录与降解这两股拮抗作用力共同调控，然而目前学界对降解过程如何参与mRNA丰度调控的机制仍鲜有探索。本研究借助全基因组水平的转录组数据——涵盖响应转分化刺激的叶细胞中mRNA丰度变化速率、半衰期以及转录速率——解答了上述问题。研究发现，半衰期调控现象较为普遍（22%的mRNA出现了半衰期变化），但仅通过降解调控RNA丰度，或是借助降解辅助转录调控的方式则较为罕见。与之相反，多数发生变化的RNA半衰期与转录水平变化呈拮抗关系。呈拮抗调控的mRNA具有转录与降解速率发生大幅变化的特征，但对应的mRNA丰度变化却较为微弱甚至无法检测到，这提示存在RNA缓冲机制。呈拮抗调控的RNA与受缓冲调控的RNA展现出高度相似的动态变化特征，提示二者共享同一调控机制。RNA降解对RNA丰度调控的最强贡献体现在协同调控转录本中：降解与转录的速率变化协同作用，共同改变RNA丰度。整体实验设计：为探究刺激响应后RNA丰度变化速率以与RNA降解速率进行对比分析，我们开展了对照组与刺激组的时间序列实验。将10日龄拟南芥（Arabidopsis thaliana）幼苗的离体叶片置于模拟对照条件，或施加转分化处理，分别培养5、6、7、8、9或10小时后收集组织样本，用于RNA提取与RNA测序（RNA-seq）分析。