Auxin regulates functional gene groups in a fold-change-specific manner in Arabidopsis thaliana roots

N. A. Omelyanchuk, D. S. Wiebe, D. D. Novikova, V. G. Levitsky, N. Klimova, V. Gorelova, C. Weinholdt, G. V. Vasiliev, E. V. Zemlyanskaya, N. A. Kolchanov, A. V. Kochetov, I. Grosse, V. V. Mironova

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14 Citations (Scopus)


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 treatmentwithin 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.

Original languageEnglish
Article number2489
Pages (from-to)2489
Number of pages11
JournalScientific Reports
Issue number1
Publication statusPublished - 30 May 2017


  • Arabidopsis Proteins/chemistry
  • Arabidopsis/drug effects
  • Gene Expression Regulation, Plant/genetics
  • Indoleacetic Acids/metabolism
  • Plant Roots/genetics
  • Protein Folding/drug effects
  • Signal Transduction/drug effects

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