The miRNAome of globe artichoke: conserved and novel micro RNAs and target analysis.
The miRNAome of globe artichoke: conserved and novel micro RNAs and target analysis.
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DOI：
10.1186/1471-2164-13-41
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发表时间：
2012-01-24
期刊：
影响因子：
4.4
通讯作者：
Sonnante G
中科院分区：
文献类型：
--
作者：
De Paola D;Cattonaro F;Pignone D;Sonnante G
植物微小RNA（miRNA）参与多个过程的转录后调节机制，包括对生物和非生物胁迫的响应，通常有助于植物对不利条件的适应性反应。除了在植物中发现的保守的miRNAs外，还发现了许多新的物种特异性miRNAs，它们的表达水平较低，但由于丰度低，非保守的miRNAs很难用常规方法进行鉴定和分离。相反，小RNA（sRNA）文库的深度测序可以检测甚至表达差的miRNA。迄今为止，还没有来自地球仪朝鲜蓟的miRNA被描述。我们通过对从NaCl胁迫和对照叶片和根获得的四个sRNA文库进行深度测序来分析来自朝鲜蓟的miRNA组。保守的和新的miRNA被发现使用公认的标准。通过定量实时PCR监测所选miRNA的表达水平。预测靶并验证其切割位点。共鉴定出122个朝鲜蓟miRNAs，其中98个（25个家族）与其他植物物种保守，24个是新的。根据组织或条件，一些miRNA差异表达，盐胁迫后的变化幅度在根中更明显。通过与拟南芥蛋白质的比较预测了靶功能;确定的43个靶点（23个为新型miRNA）包括转录因子和其他基因，其中大多数参与对各种胁迫的响应。检测到miR 393靶标的不寻常的切割转录物，转运抑制剂反应1。朝鲜蓟中的miRNAome，包括新的miRNAs，被揭开，提供了在不同器官和条件下表达的有用信息。鉴定了新的靶基因。我们认为，从miR 393靶产生二级短干扰RNA可能是植物界的一般规则。
Plant microRNAs (miRNAs) are involved in post-transcriptional regulatory mechanisms of several processes, including the response to biotic and abiotic stress, often contributing to the adaptive response of the plant to adverse conditions. In addition to conserved miRNAs, found in a wide range of plant species a number of novel species-specific miRNAs, displaying lower levels of expression can be found. Due to low abundance, non conserved miRNAs are difficult to identify and isolate using conventional approaches. Conversely, deep-sequencing of small RNA (sRNA) libraries can detect even poorly expressed miRNAs. No miRNAs from globe artichoke have been described to date. We analyzed the miRNAome from artichoke by deep sequencing four sRNA libraries obtained from NaCl stressed and control leaves and roots. Conserved and novel miRNAs were discovered using accepted criteria. The expression level of selected miRNAs was monitored by quantitative real-time PCR. Targets were predicted and validated for their cleavage site. A total of 122 artichoke miRNAs were identified, 98 (25 families) of which were conserved with other plant species, and 24 were novel. Some miRNAs were differentially expressed according to tissue or condition, magnitude of variation after salt stress being more pronounced in roots. Target function was predicted by comparison to Arabidopsis proteins; the 43 targets (23 for novel miRNAs) identified included transcription factors and other genes, most of which involved in the response to various stresses. An unusual cleaved transcript was detected for miR393 target, transport inhibitor response 1. The miRNAome from artichoke, including novel miRNAs, was unveiled, providing useful information on the expression in different organs and conditions. New target genes were identified. We suggest that the generation of secondary short-interfering RNAs from miR393 target can be a general rule in the plant kingdom.
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影响因子：
3.7
作者：
Harvey JJ;Lewsey MG;Patel K;Westwood J;Heimstädt S;Carr JP;Baulcombe DC
通讯作者：
Baulcombe DC
影响因子：
3.7
作者：
Fahlgren N;Howell MD;Kasschau KD;Chapman EJ;Sullivan CM;Cumbie JS;Givan SA;Law TF;Grant SR;Dangl JL;Carrington JC
通讯作者：
Carrington JC
影响因子：
5.1
作者：
Jia, Xiaoyun;Wang, Wang-Xia;Tang, Guiliang
通讯作者：
Tang, Guiliang
影响因子：
1.9
作者：
FRANCOIS, LE
通讯作者：
FRANCOIS, LE
影响因子：
5.2
作者：
Gavnholt, B;Larsen, K;Rasmussen, SK
通讯作者：
Rasmussen, SK