Plant Genome. 2019 Mar;12(1). doi: 10.3835/plantgenome2018.04.0022.
Epigenetic regulations in the form of changes in differential expression of noncoding RNAs (ncRNAs) are an essential mechanism of stress response in plants. Previously we showed that heat treatment in L. results in the differential processing and accumulation of ncRNA fragments (ncRFs) stemming from transfer RNAs (tRNAs), ribosomal RNAs (rRNAs), small nuclear RNAs (snRNAs), and small nucleolar RNAs (snoRNAs). In this work, we analyzed whether ncRFs are differentially expressed in the progeny of heat-stressed plants. We found significant changes in the size of tRF reads and a significant decrease in the percentage of tRFs mapping to tRNA-Ala, tRNA-Arg, and tRNA-Tyr and an increase in tRFs mapping to tRNA-Asp. The enrichment analysis showed significant differences in processing of tRFs from tRNA, tRNA, tRNA, tRNA, tRNA, and tRNA isoacceptors. Analysis of potential targets of tRFs showed that they regulate brassinosteroid metabolism, the proton pump ATPase activity, the antiporter activity, the mRNA decay activity as well as nucleosome positioning and the epigenetic regulation of transgenerational response. Gene ontology term analysis of potential targets demonstrated a significant enrichment in tRFs that potentially targeted a cellular component endoplasmic reticulum (ER) and in small nucleolar RNA fragments (snoRFs), the molecular function protein binding. To summarize, our work demonstrated that the progeny of heat-stressed plants exhibit changes in the expression of tRFs and snoRFs but not of small nuclear RNA fragments (snRFs) or ribosomal RNA fragments (rRFs) and these changes likely better prepare the progeny of stressed plants to future stress encounters.
植物应激反应的重要机制之一是表观遗传调控，即通过非编码 RNA（ncRNA）的差异表达实现。此前我们发现，热激处理会导致 L. 中 ncRNA 片段（ncRFs）的差异加工和积累，这些片段源自转移 RNA（tRNA）、核糖体 RNA（rRNA）、小核 RNA（snRNA）和小核仁 RNA（snoRNA）。在这项工作中，我们分析了热激植物后代中 ncRFs 是否存在差异表达。我们发现 tRF 读长大小发生显著变化，tRNA-Ala、tRNA-Arg 和 tRNA-Tyr 的 tRF 比例显著降低，而 tRNA-Asp 的 tRF 比例增加。富集分析显示，tRNA、tRNA、tRNA、tRNA、tRNA 和 tRNA 同工受体的 tRF 加工存在显著差异。对 tRF 潜在靶标的分析表明，它们调控油菜素内酯代谢、质子泵 ATP 酶活性、反向转运体活性、mRNA 降解活性以及核小体定位和跨代反应的表观遗传调控。潜在靶标基因本体论术语分析表明，tRF 可能靶向细胞成分内质网（ER）和小核仁 RNA 片段（snoRFs），以及分子功能蛋白结合，存在显著富集。总之，我们的工作表明，热激植物的后代表现出 tRF 和 snoRF 表达的变化，但 snRF 和 rRF 表达没有变化，这些变化可能使受胁迫植物的后代更好地为未来的胁迫做好准备。
