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 s...

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Autores principales:	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
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/3eeb01be48734394a8ad79bc0f630b1b
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spelling	oai:doaj.org-article:3eeb01be48734394a8ad79bc0f630b1b2021-12-02T16:07:45ZAuxin regulates functional gene groups in a fold-change-specific manner in Arabidopsis thaliana roots10.1038/s41598-017-02476-82045-2322https://doaj.org/article/3eeb01be48734394a8ad79bc0f630b1b2017-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-02476-8https://doaj.org/toc/2045-2322Abstract 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.N. A. OmelyanchukD. S. WiebeD. D. NovikovaV. G. LevitskyN. KlimovaV. GorelovaC. WeinholdtG. V. VasilievE. V. ZemlyanskayaN. A. KolchanovA. V. KochetovI. GrosseV. V. MironovaNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-11 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q 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 Auxin regulates functional gene groups in a fold-change-specific manner in Arabidopsis thaliana roots
description	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 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.
format	article
author	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
author_facet	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
author_sort	N. A. Omelyanchuk
title	Auxin regulates functional gene groups in a fold-change-specific manner in Arabidopsis thaliana roots
title_short	Auxin regulates functional gene groups in a fold-change-specific manner in Arabidopsis thaliana roots
title_full	Auxin regulates functional gene groups in a fold-change-specific manner in Arabidopsis thaliana roots
title_fullStr	Auxin regulates functional gene groups in a fold-change-specific manner in Arabidopsis thaliana roots
title_full_unstemmed	Auxin regulates functional gene groups in a fold-change-specific manner in Arabidopsis thaliana roots
title_sort	auxin regulates functional gene groups in a fold-change-specific manner in arabidopsis thaliana roots
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/3eeb01be48734394a8ad79bc0f630b1b
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Auxin regulates functional gene groups in a fold-change-specific manner in Arabidopsis thaliana roots

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