Profiling of short RNAs during fleshy fruit development reveals stage-specific sRNAome expression patterns
Profiling of short RNAs during fleshy fruit development reveals stage-specific sRNAome expression patterns
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DOI：
10.1111/j.1365-313x.2011.04586.x
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发表时间：
2011-07-01
期刊：
影响因子：
7.2
通讯作者：
Dalmay, Tamas
中科院分区：
文献类型：
--
作者：
Mohorianu, Irina;Schwach, Frank;Dalmay, Tamas
植物具有特别多样化的短 RNA 群体，是所有 RNA 沉默途径的核心组成部分。下一代测序技术可以更深入地了解这种复杂且高度保守的机制，并可以对 sRNA 进行识别和定量。我们采用深度测序技术，通过对 10 个时间点的 sRNA 进行分析，监测发育中的番茄果实的 sRNA 组，涵盖开花期和果实成熟之间的时期。众所周知，microRNA (miRNA) 在发育中发挥着重要作用，但有关大多数非 miRNA 的 sRNA 的信息却很少。在这里，我们展示了 sRNA 表达的独特模式，这些模式通常与发育过程的阶段一致，例如开花、果实成熟早期和晚期。此外，数以千计的非 miRNA sRNA 在果实发育和成熟过程中差异表达。其中一些差异表达的 sRNA 源自转座子，但许多源自蛋白质编码基因或与蛋白质编码基因显示同源性的区域，其中一些已知在花和果实发育中发挥作用。这些发现提出了这些 sRNA 在作物品种的果实萌发和成熟过程中发挥调节作用的可能性。我们还鉴定了 6 个新的 miRNA，并通过实验验证了两个目标 mRNA。这两个 mRNA 被相同的 miRNA 靶向，但不属于同一基因家族，这对于植物 miRNA 来说是罕见的。这些靶标的表达模式和假定功能表明在谷氨酸积累中可能发挥作用，谷氨酸积累有助于确定水果的味道。
Plants feature a particularly diverse population of short (s) RNAs, the central component of all RNA silencing pathways. Next generation sequencing techniques enable deeper insights into this complex and highly conserved mechanism and allow identification and quantification of sRNAs. We employed deep sequencing to monitor the sRNAome of developing tomato fruits covering the period between closed flowers and ripened fruits by profiling sRNAs at 10 time-points. It is known that microRNAs (miRNAs) play an important role in development but very little information is available about the majority of sRNAs that are not miRNAs. Here we show distinctive patterns of sRNA expression that often coincide with stages of the developmental process such as flowering, early and late fruit maturation. Moreover, thousands of non-miRNA sRNAs are differentially expressed during fruit development and ripening. Some of these differentially expressed sRNAs derived from transposons but many derive from protein coding genes or regions that show homology to protein coding genes, several of which are known to play a role in flower and fruit development. These findings raise the possibility of a regulative role of these sRNAs during fruit onset and maturation in a crop species. We also identified six new miRNAs and experimentally validated two target mRNAs. These two mRNAs are targeted by the same miRNA but do not belong to the same gene family, which is rare for plant miRNAs. Expression pattern and putative function of these targets indicate a possible role in glutamate accumulation, which contributes to establishing the taste of the fruit.