mRNA degradation is an important cellular mechanism involved in the control of gene expression. Several genome-wide profiling methods have been developed for detecting mRNA degradation in plants and animals. However, because many of these techniques use poly (A) mRNA for library preparation, degradation intermediates are often only detected near the 3'-ends of transcripts. Previously, we developed the Truncated RNA End Sequencing (TREseq) method using Arabidopsis thaliana, and demonstrated that this method ameliorates 3'-end bias. In analyses using TREseq, we observed G-rich sequences near the 5'-ends of degradation intermediates. However, this finding remained to be confirmed in other plant species. Hence, in this study, we conducted TREseq analyses in Lactuca sativa (lettuce), Oryza sativa (rice) and Rosa hybrida (rose). These species including A. thaliana were selected to encompass a diverse range in the angiosperm phylogeny. The results revealed similar sequence features near the 5'-ends of degradation intermediates, and involvement of translation process in all four species. In addition, homologous genes have similar efficiencies of mRNA degradation in different plants, suggesting that similar mechanisms of mRNA degradation are conserved across plant species. These strong sequence features were not observed in previous degradome analyses among different species in plants.

中文翻译：

---

不同植物物种具有与 mRNA 降解中间体相关的共同序列特征。


mRNA 降解是参与基因表达控制的重要细胞机制。已经开发了几种全基因组分析方法来检测植物和动物中的 mRNA 降解。然而，由于许多这些技术使用 Poly (A) mRNA 进行文库制备，因此通常仅在转录本的 3' 末端附近检测到降解中间体。此前，我们利用拟南芥开发了截短 RNA 末端测序 (TREseq) 方法，并证明该方法可改善 3' 末端偏差。在使用 TREseq 的分析中，我们观察到降解中间体 5' 端附近富含 G 的序列。然而，这一发现仍有待在其他植物物种中得到证实。因此，在本研究中，我们对 Lactuca sativa（生菜）、Oryza sativa（水稻）和 Rosa Hydra（玫瑰）进行了 TREseq 分析。包括拟南芥在内的这些物种被选择为涵盖被子植物系统发育中的不同范围。结果揭示了所有四个物种中降解中间体 5' 端附近的相似序列特征以及翻译过程的参与。此外，同源基因在不同植物中具有相似的 mRNA 降解效率，这表明相似的 mRNA 降解机制在植物物种中是保守的。在之前的植物不同物种的降解组分析中没有观察到这些强烈的序列特征。