Computational Reconstruction of the Transcription Factor Regulatory Network Induced by Auxin in Arabidopsis thaliana L

In plant hormone signaling, transcription factor regulatory networks (TFRNs), which link the master transcription factors to the biological processes under their control, remain insufficiently characterized despite their crucial function. Here, we identify a TFRN involved in the response to the key...

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Bibliographic Details
Published in:Plants (Basel) 2024-07, Vol.13 (14), p.1905
Main Authors: Omelyanchuk, Nadya A, Lavrekha, Viktoriya V, Bogomolov, Anton G, Dolgikh, Vladislav A, Sidorenko, Aleksandra D, Zemlyanskaya, Elena V
Format: Article
Language:English
Subjects:
Abscisic acid
Arabidopsis thaliana
Auxin
Auxins
Biological activity
Biosynthesis
Chlorophyll
DNA binding proteins
DNA methylation
Genes
Genomes
Lignin
microarray
Physiological aspects
Phytohormones
regulatory network
transcription factor
Transcription factors
transcriptome
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Summary:In plant hormone signaling, transcription factor regulatory networks (TFRNs), which link the master transcription factors to the biological processes under their control, remain insufficiently characterized despite their crucial function. Here, we identify a TFRN involved in the response to the key plant hormone auxin and define its impact on auxin-driven biological processes. To reconstruct the TFRN, we developed a three-step procedure, which is based on the integrated analysis of differentially expressed gene lists and a representative collection of transcription factor binding profiles. Its implementation is available as a part of the CisCross web server. With the new method, we distinguished two transcription factor subnetworks. The first operates before auxin treatment and is switched off upon hormone application, the second is switched on by the hormone. Moreover, we characterized the functioning of the auxin-regulated TFRN in control of chlorophyll and lignin biosynthesis, abscisic acid signaling, and ribosome biogenesis.
ISSN:2223-7747
2223-7747
DOI:10.3390/plants13141905