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Volume 26
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10.3390/ijms262211152
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This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Article

Promoter Motif Profiling and Binding Site Distribution Analysis of Transcription Factors Predict Auto- and Cross-Regulatory Mechanisms in Arabidopsis Flowering Genes

by
Eszter Virág
1,2,*,
Beáta B. Tóth
3,
Barbara Kutasy
2,4,
Ágnes Nagy
2,
Klaudia Pákozdi
2,
József Péter Pallos
2,
Gábor Kardos
1 and
Géza Hegedűs
5
1
Department of Planetary Health, One Health Institute, Faculty of Health Science, University of Debrecen, Egyetem Sq. 1, 4032 Debrecen, Hungary
2
Research Institute for Medicinal Plants and Herbs Ltd., Lupaszigeti Str. 4, 2011 Budakalász, Hungary
3
Department of Infection Control and Hospital Epidemiology, One Health Institute, Faculty of Health Science, University of Debrecen, Egyetem Sq. 1, 4032 Debrecen, Hungary
4
Department of Plant Physiology and Plant Ecology, Institute of Agronomy, Georgikon Campus, Hungarian University of Agriculture and Life Sciences, Festetics Str. 7, 8360 Keszthely, Hungary
5
Department of Information Technology and Its Applications, Faculty of Information Technology, University of Pannonia, Gasparich Márk Str. 18/A, 8900 Zalaegerszeg, Hungary
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2025, 26(22), 11152; https://doi.org/10.3390/ijms262211152
Submission received: 12 October 2025 / Revised: 13 November 2025 / Accepted: 17 November 2025 / Published: 18 November 2025
(This article belongs to the Special Issue Transcription Factors in Plant Gene Expression Regulation, 2nd Edition)
Versions Notes

Abstract

The transition to flowering in Arabidopsis thaliana is governed by complex transcriptional regulatory networks, in which promoter-associated cis-regulatory elements integrate both developmental and environmental cues. To investigate these regulatory interactions, we analyzed promoter motifs of 18 flowering-related genes using curated motif resources, including the Eukaryotic Promoter Database (EPD) and JASPAR, applying stringent statistical thresholds. Transcription factors (TFs), which were predicted to bind across all examined promoters, were designated as putative master regulators, resulting in the identification of 36 candidates, predominantly belonging to the MADS-box, DOF, and IDD families. Positional analyses revealed both proximal and distal binding sites, including a notable motif at −1024 in PISTILLATA and at +466 in SEPALLATA3, potentially indicative of autoregulatory control. Comparative analysis further identified 96 gene-specific associations, reflecting a balance between shared and specialized regulatory mechanisms. Treatment with β-aminobutyric acid (BABA), which has a flowering delaying effect, repressed SQUAMOSA and increased DOF-type TFs, indicating a chromatin-associated reprogramming process, which may coordinate the transcriptional suppression of flowering activators. These findings refine current models of floral regulatory networks and provide testable hypotheses regarding autoregulatory and cross-regulatory circuits in the control of flower development.
Keywords: Arabidopsis thaliana; transcription factor binding; gene promoter; flowering Arabidopsis thaliana; transcription factor binding; gene promoter; flowering

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MDPI and ACS Style

Virág, E.; Tóth, B.B.; Kutasy, B.; Nagy, Á.; Pákozdi, K.; Pallos, J.P.; Kardos, G.; Hegedűs, G. Promoter Motif Profiling and Binding Site Distribution Analysis of Transcription Factors Predict Auto- and Cross-Regulatory Mechanisms in Arabidopsis Flowering Genes. Int. J. Mol. Sci. 2025, 26, 11152. https://doi.org/10.3390/ijms262211152

AMA Style

Virág E, Tóth BB, Kutasy B, Nagy Á, Pákozdi K, Pallos JP, Kardos G, Hegedűs G. Promoter Motif Profiling and Binding Site Distribution Analysis of Transcription Factors Predict Auto- and Cross-Regulatory Mechanisms in Arabidopsis Flowering Genes. International Journal of Molecular Sciences. 2025; 26(22):11152. https://doi.org/10.3390/ijms262211152

Chicago/Turabian Style

Virág, Eszter, Beáta B. Tóth, Barbara Kutasy, Ágnes Nagy, Klaudia Pákozdi, József Péter Pallos, Gábor Kardos, and Géza Hegedűs. 2025. "Promoter Motif Profiling and Binding Site Distribution Analysis of Transcription Factors Predict Auto- and Cross-Regulatory Mechanisms in Arabidopsis Flowering Genes" International Journal of Molecular Sciences 26, no. 22: 11152. https://doi.org/10.3390/ijms262211152

APA Style

Virág, E., Tóth, B. B., Kutasy, B., Nagy, Á., Pákozdi, K., Pallos, J. P., Kardos, G., & Hegedűs, G. (2025). Promoter Motif Profiling and Binding Site Distribution Analysis of Transcription Factors Predict Auto- and Cross-Regulatory Mechanisms in Arabidopsis Flowering Genes. International Journal of Molecular Sciences, 26(22), 11152. https://doi.org/10.3390/ijms262211152

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