Computational identification and analysis of novel sugarcane microRNAs.
Computational identification and analysis of novel sugarcane microRNAs.
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DOI：
10.1186/1471-2164-13-290
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发表时间：
2012-07-02
期刊：
影响因子：
4.4
通讯作者：
Ferreira PC
中科院分区：
文献类型：
--
作者：
Thiebaut F;Grativol C;Carnavale-Bottino M;Rojas CA;Tanurdzic M;Farinelli L;Martienssen RA;Hemerly AS;Ferreira PC
microRNA调控基因表达在植物发育和对生物和非生物胁迫的响应中起着关键作用。深度测序分析加速了许多植物中小RNA的发现过程，并扩大了我们对miRNA调控过程的理解。因此，我们对甘蔗miRNAs进行了小RNA测序，以了解它们的复杂性并探索它们在甘蔗生物学中的作用。进行了生物信息学搜索，以发现在遭受干旱和盐胁迫以及病原体感染的甘蔗植物中可以调节的新的miRNAs。通过在相关高粱基因组中存在miRNA前体，我们在甘蔗中鉴定了623个新的成熟miRNA候选者。其中，44种被归类为高置信度miRNA。通过分析其推定的靶标来评估新的miRNAs候选物的生物学功能。这组真正的甘蔗miRNA包括那些可能靶向丝氨酸/苏氨酸激酶、Myb和锌指蛋白的miRNA。此外，MADS盒转录因子和RPP 2B蛋白，在发育和抗病过程中发挥作用，可以分别通过切割（21-nt-物种）和DNA甲基化（24-nt-物种）进行调节。一个大规模的调查sRNA在甘蔗中使用的计算方法已经确定了大量的新的miRNA，并提供了详细的基因型组织培养的miRNA表达谱。单子叶植物之间的比较分析是有价值的，以澄清有关的保护方面的miRNA和他们的目标，在植物的基因组尚未测序。我们的研究结果有助于了解miRNA在复杂的多倍体甘蔗基因组调控途径中的作用。
MicroRNA-regulation of gene expression plays a key role in the development and response to biotic and abiotic stresses. Deep sequencing analyses accelerate the process of small RNA discovery in many plants and expand our understanding of miRNA-regulated processes. We therefore undertook small RNA sequencing of sugarcane miRNAs in order to understand their complexity and to explore their role in sugarcane biology. A bioinformatics search was carried out to discover novel miRNAs that can be regulated in sugarcane plants submitted to drought and salt stresses, and under pathogen infection. By means of the presence of miRNA precursors in the related sorghum genome, we identified 623 candidates of new mature miRNAs in sugarcane. Of these, 44 were classified as high confidence miRNAs. The biological function of the new miRNAs candidates was assessed by analyzing their putative targets. The set of bona fide sugarcane miRNA includes those likely targeting serine/threonine kinases, Myb and zinc finger proteins. Additionally, a MADS-box transcription factor and an RPP2B protein, which act in development and disease resistant processes, could be regulated by cleavage (21-nt-species) and DNA methylation (24-nt-species), respectively. A large scale investigation of sRNA in sugarcane using a computational approach has identified a substantial number of new miRNAs and provides detailed genotype-tissue-culture miRNA expression profiles. Comparative analysis between monocots was valuable to clarify aspects about conservation of miRNA and their targets in a plant whose genome has not yet been sequenced. Our findings contribute to knowledge of miRNA roles in regulatory pathways in the complex, polyploidy sugarcane genome.
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