Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192 Japan.
Idemitsu Kosan Co., Ltd., Advanced Technology Research Laboratories, 1280 Kami-izumi, Sodegaura, Chiba, 299-0293 Japan.
Plant Cell Physiol. 2020 Jan 1;61(1):53-63. doi: 10.1093/pcp/pcz175.
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.
mRNA 降解是参与基因表达调控的一个重要的细胞机制。已经开发了几种全基因组分析方法来检测动植物中的 mRNA 降解。然而，由于这些技术中的许多方法都使用聚（A）mRNA 进行文库制备，因此降解中间体通常仅在转录本的 3'端附近检测到。以前，我们使用拟南芥开发了截断 RNA 末端测序（TREseq）方法，并证明该方法改善了 3'端偏倚。在使用 TREseq 的分析中，我们观察到降解中间体 5'端附近存在富含 G 的序列。然而，这一发现仍需要在其他植物物种中得到证实。因此，在本研究中，我们在生菜（莴苣）、水稻（水稻）和杂种玫瑰（玫瑰）中进行了 TREseq 分析。选择这些物种（包括拟南芥）涵盖了被子植物系统发育中的多种范围。结果表明，在所有四个物种中，降解中间体 5'端附近存在类似的序列特征，并涉及翻译过程。此外，在不同植物中，同源基因的 mRNA 降解效率相似，这表明 mRNA 降解的相似机制在植物物种中是保守的。在以前的不同植物物种的降解组分析中没有观察到这些强烈的序列特征。
