Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening
Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening
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DOI：
10.1101/gr.080127.108
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发表时间：
2008-10-01
期刊：
影响因子：
7
通讯作者：
Dalmay, Tamas
中科院分区：
文献类型：
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作者：
Moxon, Simon;Jing, Runchun;Dalmay, Tamas
在植物中，有几类21-24-nt的短RNA调节基因表达。最保守的一类是microRNA（miRNAs），尽管一些miRNAs仅在特定物种中发现。我们使用高通量焦磷酸测序来鉴定番茄果实和叶片中保守和非保守的miRNA和其他短RNA。一些保守的miRNAs表现出组织特异性表达，结合靶基因验证结果，表明miRNAs可能在肉质果实发育中发挥作用。我们还发现了四种新的非保守性miRNAs。新型miRNA的经验证的靶点之一是参与水果成熟的CTR家族的成员。然而，62个预测的目标显示出接近完美的互补性，以潜在的新的miRNA没有验证实验。这表明植物短RNA的靶预测可能具有高的假阳性率，因此必须通过实验验证。我们还发现了来自茄科特异性折返转座子的短RNA，其显示出miRNA/ miRNA* 样分布，这表明该元件可能作为miRNA基因祖先发挥作用。另一类茄科特有的短RNA来自插入番茄染色体的内源性副逆转录病毒序列。这项研究通过提高果实发育和成熟可能受miRNA调控的可能性，在肉质果实生物学领域开辟了一条新的途径。
In plants there are several classes of 21-24-nt short RNAs that regulate gene expression. The most conserved class is the microRNAs (miRNAs), although some miRNAs are found only in specific species. We used high-throughput pyrosequencing to identify conserved and nonconserved miRNAs and other short RNAs in tomato fruit and leaf. Several conserved miRNAs showed tissue-specific expression, which, combined with target gene validation results, suggests that miRNAs may play a role in fleshy fruit development. We also identified four new nonconserved miRNAs. One of the validated targets of a novel miRNA is a member of the CTR family involved in fruit ripening. However, 62 predicted targets showing near perfect complementarity to potential new miRNAs did not validate experimentally. This suggests that target prediction of plant short RNAs could have a high false-positive rate and must therefore be validated experimentally. We also found short RNAs from a Solanaceae-specific foldback transposon, which showed a miRNA/ miRNA*-like distribution, suggesting that this element may function as a miRNA gene progenitor. The other Solanaceae-specific class of short RNA was derived from an endogenous pararetrovirus sequence inserted into the tomato chromosomes. This study opens a new avenue in the field of fleshy fruit biology by raising the possibility that fruit development and ripening may be under miRNA regulation.