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Auxin regulates functional gene groups in a fold-change-specific manner in Arabidopsis thaliana roots. / Omelyanchuk, N. A.; Wiebe, D. S.; Novikova, D. D. et al.

In: Scientific Reports, Vol. 7, No. 1, 2489, 30.05.2017, p. 2489.

Research output: Contribution to journal › Article › peer-review

Harvard

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 2017, 'Auxin regulates functional gene groups in a fold-change-specific manner in Arabidopsis thaliana roots', Scientific Reports, vol. 7, no. 1, 2489, pp. 2489. https://doi.org/10.1038/s41598-017-02476-8

APA

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. (2017). Auxin regulates functional gene groups in a fold-change-specific manner in Arabidopsis thaliana roots. Scientific Reports, 7(1), 2489. [2489]. https://doi.org/10.1038/s41598-017-02476-8

Vancouver

Omelyanchuk NA, Wiebe DS, Novikova DD, Levitsky VG, Klimova N, Gorelova V et al. Auxin regulates functional gene groups in a fold-change-specific manner in Arabidopsis thaliana roots. Scientific Reports. 2017 May 30;7(1):2489. 2489. doi: 10.1038/s41598-017-02476-8

Author

Omelyanchuk, N. A. ; Wiebe, D. S. ; Novikova, D. D. et al. / Auxin regulates functional gene groups in a fold-change-specific manner in Arabidopsis thaliana roots. In: Scientific Reports. 2017 ; Vol. 7, No. 1. pp. 2489.

BibTeX

@article{4658ce26f93847a9974949022769150c,
title = "Auxin regulates functional gene groups in a fold-change-specific manner in Arabidopsis thaliana roots",
abstract = "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.",
keywords = "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, MICROARRAY, TRANSCRIPTION, MATURATION, ELEMENTS, RESPONSES, PROMOTERS, RNA-SEQ, BINDING, EMBRYOGENESIS, EXPRESSION",
author = "Omelyanchuk, {N. A.} and Wiebe, {D. S.} and Novikova, {D. D.} and Levitsky, {V. G.} and N. Klimova and V. Gorelova and C. Weinholdt and Vasiliev, {G. V.} and Zemlyanskaya, {E. V.} and Kolchanov, {N. A.} and Kochetov, {A. V.} and I. Grosse and Mironova, {V. V.}",
year = "2017",
month = may,
day = "30",
doi = "10.1038/s41598-017-02476-8",
language = "English",
volume = "7",
pages = "2489",
journal = "Scientific Reports",
issn = "2045-2322",
publisher = "Nature Publishing Group",
number = "1",

}

RIS

TY - JOUR

T1 - Auxin regulates functional gene groups in a fold-change-specific manner in Arabidopsis thaliana roots

AU - Omelyanchuk, N. A.

AU - Wiebe, D. S.

AU - Novikova, D. D.

AU - Levitsky, V. G.

AU - Klimova, N.

AU - Gorelova, V.

AU - Weinholdt, C.

AU - Vasiliev, G. V.

AU - Zemlyanskaya, E. V.

AU - Kolchanov, N. A.

AU - Kochetov, A. V.

AU - Grosse, I.

AU - Mironova, V. V.

PY - 2017/5/30

Y1 - 2017/5/30

N2 - 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.

AB - 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.

KW - Arabidopsis Proteins/chemistry

KW - Arabidopsis/drug effects

KW - Gene Expression Regulation, Plant/genetics

KW - Indoleacetic Acids/metabolism

KW - Plant Roots/genetics

KW - Protein Folding/drug effects

KW - Signal Transduction/drug effects

KW - MICROARRAY

KW - TRANSCRIPTION

KW - MATURATION

KW - ELEMENTS

KW - RESPONSES

KW - PROMOTERS

KW - RNA-SEQ

KW - BINDING

KW - EMBRYOGENESIS

KW - EXPRESSION

UR - http://www.scopus.com/inward/record.url?scp=85019975159&partnerID=8YFLogxK

U2 - 10.1038/s41598-017-02476-8

DO - 10.1038/s41598-017-02476-8

M3 - Article

C2 - 28559568

AN - SCOPUS:85019975159

VL - 7

SP - 2489

JO - Scientific Reports

JF - Scientific Reports

SN - 2045-2322

IS - 1

M1 - 2489

ER -

ID: 9866109