Rose Rebecca E, Pazos Manuel A, Curcio M Joan, Fabris Daniele
From the ‡The RNA Institute, University at Albany (SUNY), Albany, New York 12222;
From the ‡The RNA Institute, University at Albany (SUNY), Albany, New York 12222; ‖Laboratory of Molecular Genetics, Wadsworth Center, Albany, New York 12208.
Mol Cell Proteomics. 2016 Mar;15(3):932-44. doi: 10.1074/mcp.M115.054718. Epub 2016 Jan 5.
The simultaneous detection of all the post-transcriptional modifications (PTMs) that decorate cellular RNA can provide comprehensive information on the effects of changing environmental conditions on the entire epitranscriptome. To capture this type of information, we performed the analysis of ribonucleotide mixtures produced by hydrolysis of total RNA extracts from S. cerevisiae that was grown under hyperosmotic and heat shock conditions. Their global PTM profiles clearly indicated that the cellular responses to these types of stresses involved profound changes in the production of specific PTMs. The observed changes involved not only up-/down-regulation of typical PTMs, but also the outright induction of new ones that were absent under normal conditions, or the elimination of others that were normally present. Pointing toward the broad involvement of different classes of RNAs, many of the newly observed PTMs differed from those engaged in the known tRNA-based mechanism of translational recoding, which is induced by oxidative stress. Some of the expression effects were stress-specific, whereas others were not, thus suggesting that RNA PTMs may perform multifaceted activities in stress response, which are subjected to distinctive regulatory pathways. To explore their signaling networks, we implemented a strategy based on the systematic deletion of genes that connect established response genes with PTM biogenetic enzymes in a putative interactomic map. The results clearly identified PTMs that were under direct HOG control, a well-known protein kinase pathway involved in stress response in eukaryotes. Activation of this signaling pathway has been shown to result in the stabilization of numerous mRNAs and the induction of selected lncRNAs involved in chromatin remodeling. The fact that PTMs are capable of altering the activity of the parent RNAs suggest their possible participation in feedback mechanisms aimed at modulating the regulatory functions of such RNAs. This tantalizing hypothesis will be the object of future studies.
同时检测修饰细胞RNA的所有转录后修饰（PTM），可以提供关于环境条件变化对整个表观转录组影响的全面信息。为了获取这类信息，我们对在高渗和热休克条件下生长的酿酒酵母总RNA提取物水解产生的核糖核苷酸混合物进行了分析。它们的整体PTM谱清楚地表明，细胞对这些类型应激的反应涉及特定PTM产生的深刻变化。观察到的变化不仅包括典型PTM的上调/下调，还包括正常条件下不存在的新PTM的直接诱导，或正常存在的其他PTM的消除。指向不同类RNA的广泛参与，许多新观察到的PTM与参与已知基于tRNA的翻译重编码机制（由氧化应激诱导）的PTM不同。一些表达效应是应激特异性的，而其他的则不是，因此表明RNA PTM可能在应激反应中发挥多方面的作用，且受到独特的调控途径的影响。为了探索它们的信号网络，我们实施了一种基于系统删除基因的策略，这些基因在一个假定的相互作用组图谱中将已建立的反应基因与PTM生物发生酶连接起来。结果清楚地鉴定出了直接受HOG控制的PTM，HOG是真核生物中参与应激反应的一种著名的蛋白激酶途径。已证明该信号通路的激活会导致许多mRNA的稳定以及参与染色质重塑的选定lncRNA的诱导。PTM能够改变亲本RNA的活性这一事实表明它们可能参与了旨在调节此类RNA调控功能的反馈机制。这个诱人的假设将是未来研究的对象。
