Main conclusion

The combined transcriptome outcome provides an important clue to the regulatory cascade centering on lncRNA GARR2 and CPS2 gene in GA response.

Abstract

Long non-coding RNAs (lncRNAs) serve as regulatory components in transcriptional hierarchy governing multiple aspects of biological processes. Dissecting regulatory mechanisms underpinning tetracyclic diterpenoid gibberellin (GA) cascade holds both theoretical and applied significance. However, roles of lncRNAs in transcriptional modulation of GA pathway remain largely elusive. Gypsy retrotransposon-derived GIBBERELLIN RESPONSIVE lncRNA2 (GARR2) has been reported as GA-responsive maize lncRNA. Here a novel GARR2-edited line garr2-1 was identified, characteristic of GA-induced phenotype of increased seedling height and elongated leaf sheath. Transcriptome analysis indicated that transcriptional abundance of five genes [ent-copalyl diphosphate synthase2 (CPS2), ent-kaurene synthase4 (KS4), ent-kaurene synthase6 (KS6), ent-kaurene oxidase2 (KO2), and ent-kaurenoic acid oxidase1/Dwarf3 (KAO1/D3)] was elevated in garr2-1 for early steps of GA biosynthesis. Five GA biosynthetic genes as hub regulators were interlaced to shape regulatory network of GA response. Different transcriptome resources were integrated to discover common differentially expressed genes (DEGs) in the independent GARR2-edited lines GARR2KO and garr2-1. A total of 320 common DEGs were retrieved. These common DEGs were enriched in diterpenoid biosynthetic pathway. Integrative transcriptome analysis revealed the common CPS2 encoding the CPS enzyme that catalyzes the conversion of the precursor trans-geranylgeranyl diphosphate to ent-copalyl diphosphate. The up-regulated CPS2 supported the GA-induced phenotype of slender seedlings observed in the independent GARR2-edited lines GARR2KO and garr2-1. Our integrative transcriptome analysis uncovers common components of the GA pathway regulated by lncRNA GARR2. These common components, especially for the GA biosynthetic gene CPS2, provide a valuable resource for further delineating the underlying mechanisms of lncRNA GARR2 in GA response.

中文翻译：

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综合转录组分析揭示了赤霉素反应中受玉米 lncRNA GARR2 调节的含有 CPS2 的常见成分

主要结论

组合转录组结果为 GA 反应中以 lncRNA GARR2和CPS2基因为中心的调控级联提供了重要线索。

抽象的

长非编码 RNA (lncRNA) 作为转录层次结构中的调控组件，控制生物过程的多个方面。剖析支持四环二萜赤霉素（GA）级联的调节机制具有理论和应用意义。然而，lncRNA 在 GA 途径转录调节中的作用仍然很大程度上难以捉摸。据报道，吉普赛逆转录转座子衍生的赤霉素响应性 lncRNA2 ( GARR2 ) 是 GA 响应性玉米 lncRNA。这里鉴定了一个新的GARR2编辑品系garr2-1，其特征是 GA 诱导的幼苗高度增加和叶鞘延长的表型。转录组分析表明，五个基因的转录丰度[对映柯巴基二磷酸合酶2（CPS2）、对映贝壳杉烯合酶4（KS4）、对映贝壳杉烯合酶6（KS6）、对映贝壳杉烯氧化酶2（KO2）和对映贝壳杉烯酸氧化酶1 / Dwarf3 ( KAO1/D3 )]在 GA 生物合成的早期步骤中在garr2-1中升高。五个 GA 生物合成基因作为枢纽调节因子相互交织，形成 GA 反应的调节网络。整合不同的转录组资源以发现独立的GARR2编辑系GARR2 KO和garr2-1中常见的差异表达基因(DEG) 。共检索到320个常见DEG。这些常见的DEG在二萜生物合成途径中富集。综合转录组分析揭示了编码CPS酶的常见CPS2 ，该酶催化前体反式-香叶基香叶基二磷酸转化为对映-柯巴基二磷酸。上调的CPS2支持在独立的GARR2编辑系GARR2 KO和garr2-1中观察到的GA诱导的细长幼苗表型。我们的综合转录组分析揭示了受 lncRNA GARR2调节的 GA 途径的常见成分。这些共同成分，特别是 GA 生物合成基因CPS2 ，为进一步描述 lncRNA GARR2在 GA 反应中的潜在机制提供了宝贵的资源。