Identification, Expression Analysis, and Target Prediction of Flax Genotroph MicroRNAs Under Normal and Nutrient Stress Conditions.
Identification, Expression Analysis, and Target Prediction of Flax Genotroph MicroRNAs Under Normal and Nutrient Stress Conditions.
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DOI：
10.3389/fpls.2016.00399
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发表时间：
2016
影响因子：
5.6
通讯作者：
Kudryavtseva AV
中科院分区：
文献类型：
--
作者：
Melnikova NV;Dmitriev AA;Belenikin MS;Koroban NV;Speranskaya AS;Krinitsina AA;Krasnov GS;Lakunina VA;Snezhkina AV;Sadritdinova AF;Kishlyan NV;Rozhmina TA;Klimina KM;Amosova AV;Zelenin AV;Muravenko OV;Bolsheva NL;Kudryavtseva AV
栽培亚麻（Linum usitatissimum L.）是一种重要的工业价值植物。一些亚麻品系可以经历可遗传的表型和基因型变化（LIS-1插入是最常见的），以响应营养胁迫，被称为塑料线。塑性品系的后代，稳定地继承了这些变化，被称为遗传营养型。microRNAs（miRNAs）参与基因表达的重要调控机制。他们以前被假定参加营养胁迫反应，因此，可以参与遗传营养型的形成。在本研究中，我们进行了高通量测序的小RNA（sRNAs）提取亚麻植物生长在正常，磷酸盐缺乏和营养过剩的条件下，以确定miRNA和评估其表达。我们的分析揭示了来自21个家族的96个保守的miRNAs在亚麻中的表达。此外，首次鉴定出475个新的潜在miRNAs，并预测了它们的靶点。然而，没有一个鉴定的miRNA是从LIS-1转录的。使用qPCR对在营养胁迫下上调或下调的七种miRNA（miR168、miR169、miR395、miR398、miR399、miR408和lus-miR-N1）的表达进行了评估（基于高通量测序数据）。参考基因检索鉴定ETIF3H和ETIF3E基因最适合用于该目的。在磷酸盐缺乏的条件下，新的潜在的lus-miR-N1的下调和保守的miR 399的上调被揭示。此外，观察到lus-miR-N1与其预测靶点泛素激活酶E1基因以及miR399与其预测靶点泛素结合酶E2基因的表达呈负相关。因此，在我们的研究中，鉴定了在亚麻塑料系和基因营养型中表达的miRNAs，并首次使用高通量测序和qPCR评估了它们的表达和它们的靶标的表达。这些数据提供了新的见解，营养胁迫反应调控塑料亚麻品种。
Cultivated flax (Linum usitatissimum L.) is an important plant valuable for industry. Some flax lines can undergo heritable phenotypic and genotypic changes (LIS-1 insertion being the most common) in response to nutrient stress and are called plastic lines. Offspring of plastic lines, which stably inherit the changes, are called genotrophs. MicroRNAs (miRNAs) are involved in a crucial regulatory mechanism of gene expression. They have previously been assumed to take part in nutrient stress response and can, therefore, participate in genotroph formation. In the present study, we performed high-throughput sequencing of small RNAs (sRNAs) extracted from flax plants grown under normal, phosphate deficient and nutrient excess conditions to identify miRNAs and evaluate their expression. Our analysis revealed expression of 96 conserved miRNAs from 21 families in flax. Moreover, 475 novel potential miRNAs were identified for the first time, and their targets were predicted. However, none of the identified miRNAs were transcribed from LIS-1. Expression of seven miRNAs (miR168, miR169, miR395, miR398, miR399, miR408, and lus-miR-N1) with up- or down-regulation under nutrient stress (on the basis of high-throughput sequencing data) was evaluated on extended sampling using qPCR. Reference gene search identified ETIF3H and ETIF3E genes as most suitable for this purpose. Down-regulation of novel potential lus-miR-N1 and up-regulation of conserved miR399 were revealed under the phosphate deficient conditions. In addition, the negative correlation of expression of lus-miR-N1 and its predicted target, ubiquitin-activating enzyme E1 gene, as well as, miR399 and its predicted target, ubiquitin-conjugating enzyme E2 gene, was observed. Thus, in our study, miRNAs expressed in flax plastic lines and genotrophs were identified and their expression and expression of their targets was evaluated using high-throughput sequencing and qPCR for the first time. These data provide new insights into nutrient stress response regulation in plastic flax cultivars.