Decapping is a crucial step in mRNA degradation in eucaryotes and requires the formation of a holoenzyme complex between the decapping enzyme DECAPPING 2 (DCP2) and the decapping enhancer DCP1. In Arabidopsis (Arabidopsis thaliana), DCP1-ASSOCIATED NYN ENDORIBONUCLEASE 1 (DNE1) is a direct protein partner of DCP1. The function of both DNE1 and decapping are necessary to maintain phyllotaxis, the regularity of organ emergence in the apex. In this study, we combined in vivo mRNA editing, RNA degradome sequencing, transcriptomics and small RNA-omics to identify targets of DNE1 and study how DNE1 and DCP2 cooperate in controlling mRNA fate. Our data reveal that DNE1 mainly contacts and cleaves mRNAs in the coding sequence and has sequence cleavage preferences. DNE1 targets are also degraded through decapping, and both RNA degradation pathways influence the production of mRNA-derived small interfering RNAs. Finally, we detected mRNA features enriched in DNE1 targets including RNA G-quadruplexes and translated upstream open reading frames. Combining these four complementary high-throughput sequencing strategies greatly expands the range of DNE1 targets and allowed us to build a conceptual framework describing the influence of DNE1 and decapping on mRNA fate. These data will be crucial to unveil the specificity of DNE1 action and understand its importance for developmental patterning.

中文翻译：

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多转录组学鉴定核糖核酸内切酶 DNE1 的靶标并强调其与脱帽的协调


脱帽是真核生物中 mRNA 降解的关键步骤，需要在脱帽酶 DECAPPING 2 (DCP2) 和脱帽增强子 DCP1 之间形成全酶复合物。在拟南芥 (Arabidopsis thaliana) 中，DCP1 相关的 NYN 内切核糖核酸酶 1 (DNE1) 是 DCP1 的直接蛋白质伴侣。 DNE1 和脱盖功能对于维持叶序（顶端器官出现的规律性）是必需的。在本研究中，我们结合体内mRNA编辑、RNA降解组测序、转录组学和小RNA组学来鉴定DNE1的靶标，并研究DNE1和DCP2如何合作控制mRNA命运。我们的数据表明，DNE1 主要接触并切割编码序列中的 mRNA，并具有序列切割偏好。 DNE1 靶标也会通过脱帽降解，两种 RNA 降解途径都会影响 mRNA 衍生的小干扰 RNA 的产生。最后，我们检测到 DNE1 靶标中富集的 mRNA 特征，包括 RNA G 四链体和翻译的上游开放阅读框。结合这四种互补的高通量测序策略极大地扩展了 DNE1 靶标的范围，并使我们能够构建一个概念框架来描述 DNE1 和脱帽对 mRNA 命运的影响。这些数据对于揭示 DNE1 作用的特异性并了解其对发育模式的重要性至关重要。