Auxin regulates functional gene groups in a fold-change-specific manner in Arabidopsis thaliana roots.
Auxin regulates functional gene groups in a fold-change-specific manner in Arabidopsis thaliana roots.
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DOI：
10.1038/s41598-017-02476-8
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发表时间：
2017-05-30
影响因子：
4.6
通讯作者：
Mironova VV
中科院分区：
文献类型：
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作者：
Omelyanchuk NA;Wiebe DS;Novikova DD;Levitsky VG;Klimova N;Gorelova V;Weinholdt C;Vasiliev GV;Zemlyanskaya EV;Kolchanov NA;Kochetov AV;Grosse I;Mironova VV
生长素在植物形态建成的各个方面都起着关键作用。它同时协调各种各样的过程，如细胞壁生物发生，通过细胞周期的过渡，或各种化学物质的代谢。在系统级别，对于这样一个复杂的编排的协调原则理解得很差。在这里，我们进行了RNA-seq实验，以定量的倍数变化特异性方式研究不同生物过程，分子功能或细胞组分的基因组内对生长素处理的转录反应。我们发现拟南芥根用生长素处理6小时，（i）有功能组内的基因响应生长素与一个令人惊讶的相似的倍的变化，（ii）这些倍的变化从一个组到另一个不同。这些发现使人们很容易推测存在一些转录逻辑，以特定的折叠变化方式协调功能组内基因的表达。为了获得一些初步了解这种协调的表达，我们进行了基序富集分析，并发现顺式调控元件TBX 1 -3，SBX，REG和TCP/site 2作为候选人赋予倍数变化的特定响应生长素在拟南芥。
Auxin plays a pivotal role in virtually every aspect of plant morphogenesis. It simultaneously orchestrates a diverse variety of processes such as cell wall biogenesis, transition through the cell cycle, or metabolism of a wide range of chemical substances. The coordination principles for such a complex orchestration are poorly understood at the systems level. Here, we perform an RNA-seq experiment to study the transcriptional response to auxin treatment within gene groups of different biological processes, molecular functions, or cell components in a quantitative fold-change-specific manner. We find for Arabidopsis thaliana roots treated with auxin for 6 h that (i) there are functional groups within which genes respond to auxin with a surprisingly similar fold changes and that (ii) these fold changes vary from one group to another. These findings make it tempting to conjecture the existence of some transcriptional logic orchestrating the coordinated expression of genes within functional groups in a fold-change-specific manner. To obtain some initial insight about this coordinated expression, we performed a motif enrichment analysis and found cis-regulatory elements TBX1-3, SBX, REG, and TCP/site2 as the candidates conferring fold-change-specific responses to auxin in Arabidopsis thaliana.