Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
LCT&EB, Novosibirsk State University, Novosibirsk, Russia.
Sci Rep. 2017 May 30;7(1):2489. doi: 10.1038/s41598-017-02476-8.
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.
生长素在植物形态发生的几乎各个方面都起着关键作用。它同时协调着多种过程，如细胞壁生物发生、细胞周期的转变，或广泛的化学物质的代谢。这种复杂的协调的协调原则在系统水平上理解得很差。在这里，我们进行了一个 RNA-seq 实验，以研究在不同生物学过程、分子功能或细胞成分的基因组中，生长素处理对转录反应的影响，以特定的倍数变化特异性方式进行。我们发现，在拟南芥根中用生长素处理 6 小时后，（i）在功能组内存在基因对生长素反应具有惊人相似的倍数变化的功能组，并且（ii）这些倍数变化在不同组之间变化。这些发现使得人们不禁猜测存在一些转录逻辑，以特定的倍数变化特异性方式协调功能组内基因的协调表达。为了获得关于这种协调表达的一些初步见解，我们进行了 motif 富集分析，发现 TBX1-3、SBX、REG 和 TCP/site2 顺式调控元件是赋予拟南芥生长素特异性倍数变化反应的候选者。
