Transcript profiling reveals complex auxin signalling pathway and transcription regulation involved in dedifferentiation and redifferentiation during somatic embryogenesis in cotton.
Transcript profiling reveals complex auxin signalling pathway and transcription regulation involved in dedifferentiation and redifferentiation during somatic embryogenesis in cotton.
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转录谱分析揭示了棉花体细胞胚胎发生过程中去分化和再分化过程中复杂的生长素信号通路和转录调控
DOI：
10.1186/1471-2229-12-110
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发表时间：
2012-07-20
影响因子：
5.3
通讯作者：
Xu J
中科院分区：
文献类型：
--
作者：
Yang X;Zhang X;Yuan D;Jin F;Zhang Y;Xu J
体细胞胚胎发生（somatic embryogenesis， SE）是高等植物体细胞去分化并重组为新植物的过程，是细胞全能性的一个重要例证。然而，调控SE的确切分子机制尚不清楚。为了描述这一独特过程的分子事件，我们结合生化和组织学方法，对棉花这一典型植物物种进行了转录组分析。基因表达的全基因组谱分析允许鉴定这种发育过程特征的新分子标记。结果利用rna - seq技术鉴定了5076个棉花SE差异表达基因。这些基因的表达谱和功能分配表明，在这一过程中存在显著的转录复杂性，与形态学、组织学变化和内源性吲哚-3-乙酸（IAA）改变有关。生物信息学分析表明，这些基因在代谢途径和次生代谢物生物合成等基本过程中富集。具有丰富的蛋白质结合功能和水解酶活性的单基因。转录因子编码基因在SE期间被差异调控。生长素丰度、转运和应答与差异调控基因的复杂通路表明，生长素相关转录物属于IAA生物合成、吲哚-3-丁酸（IBA）代谢、IAA偶联代谢、生长素转运、生长素应答蛋白/吲哚乙酸诱导蛋白（Aux/IAA）、生长素应答因子（ARF）、生长素小RNA （SAUR）、Aux/IAA降解等生长素相关蛋白。这使得一个复杂的生长素利用系统在SE中实现多种目的。采用实时荧光定量PCR （qRT-PCR）对不同表达模式的基因进行了分析，并进行了功能定位，以验证RNA-Seq对棉花SE基因表达谱的实用性。结论本研究首次全面分析了棉花SE基因的转录组动力学，为棉花SE基因表达谱提供了蓝图。我们的主要目标是使RNA-Seq技术适应这一显著的发展过程，并分析基因表达谱。重点介绍了复杂的生长素信号通路和转录调控。结合生物化学和组织学方法，本研究提供了棉花SE基因的完整表达数据集，为进一步研究植物胚胎发生的功能提供了重要的平台资源。
BackgroundSomatic embryogenesis (SE), by which somatic cells of higher plants can dedifferentiate and reorganize into new plants, is a notable illustration of cell totipotency. However, the precise molecular mechanisms regulating SE remain unclear. To characterize the molecular events of this unique process, transcriptome analysis, in combination with biochemical and histological approaches, were conducted in cotton, a typical plant species in SE. Genome-wide profiling of gene expression allowed the identification of novel molecular markers characteristic of this developmental process.ResultsRNA-Seq was used to identify 5,076 differentially expressed genes during cotton SE. Expression profile and functional assignments of these genes indicated significant transcriptional complexity during this process, associated with morphological, histological changes and endogenous indole-3-acetic acid (IAA) alteration. Bioinformatics analysis showed that the genes were enriched for basic processes such as metabolic pathways and biosynthesis of secondary metabolites. Unigenes were abundant for the functions of protein binding and hydrolase activity. Transcription factor–encoding genes were found to be differentially regulated during SE. The complex pathways of auxin abundance, transport and response with differentially regulated genes revealed that the auxin-related transcripts belonged to IAA biosynthesis, indole-3-butyric acid (IBA) metabolism, IAA conjugate metabolism, auxin transport, auxin-responsive protein/indoleacetic acid-induced protein (Aux/IAA), auxin response factor (ARF), small auxin-up RNA (SAUR), Aux/IAA degradation, and other auxin-related proteins, which allow an intricate system of auxin utilization to achieve multiple purposes in SE. Quantitative real-time PCR (qRT-PCR) was performed on selected genes with different expression patterns and functional assignments were made to demonstrate the utility of RNA-Seq for gene expression profiles during cotton SE.ConclusionWe report here the first comprehensive analysis of transcriptome dynamics that may serve as a gene expression profile blueprint in cotton SE. Our main goal was to adapt the RNA-Seq technology to this notable development process and to analyse the gene expression profile. Complex auxin signalling pathway and transcription regulation were highlighted. Together with biochemical and histological approaches, this study provides comprehensive gene expression data sets for cotton SE that serve as an important platform resource for further functional studies in plant embryogenesis.
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影响因子：
3.7
作者：
Huang, Chuanxin;Jia, Yichang;Wang, Yizheng
通讯作者：
Wang, Yizheng
影响因子：
4.3
作者：
Grabowska, Agnieszka;Wisniewska, Anita;Filipecki, Marcin
通讯作者：
Filipecki, Marcin
影响因子：
11.6
作者：
Boutilier, K;Offringa, R;Campagne, MMV
通讯作者：
Campagne, MMV
影响因子：
64.8
作者：
Kepinski, S;Leyser, O
通讯作者：
Leyser, O
影响因子：
3
作者：
Jiménez, VM;Bangerth, F
通讯作者：
Bangerth, F