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

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 com...

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Bibliographic Details
Published in:	Scientific reports Vol. 7; no. 1; pp. 2489 - 11
Main Authors:	Omelyanchuk, N. A., Wiebe, D. S., Novikova, D. D., Levitsky, V. G., Klimova, N., Gorelova, V., Weinholdt, C., Vasiliev, G. V., Zemlyanskaya, E. V., Kolchanov, N. A., Kochetov, A. V., Grosse, I., Mironova, V. V.
Format:	Journal Article
Language:	English
Published:	London Nature Publishing Group UK 30-05-2017 Nature Publishing Group Nature Portfolio
Subjects:	38/39 38/77 38/91 631/114/2404 631/1647/48 631/208/191/2018 631/449/1741/1576 Arabidopsis - drug effects Arabidopsis - genetics Arabidopsis - metabolism Arabidopsis Proteins - chemistry Arabidopsis Proteins - genetics Arabidopsis thaliana Cell cycle Cell walls Gene Expression Regulation, Plant - genetics Genes Humanities and Social Sciences Indoleacetic Acids - metabolism Indoleacetic Acids - pharmacology Morphogenesis multidisciplinary Plant Roots - genetics Plant Roots - growth & development Plant Roots - metabolism Protein Folding - drug effects Regulatory sequences Ribonucleic acid RNA Roots Science Science (multidisciplinary) Signal Transduction - drug effects Signal Transduction - genetics Tbx1 protein Transcription
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Summary:	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 .
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	2045-2322 2045-2322
DOI:	10.1038/s41598-017-02476-8