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Article

Transcriptomic Data Meta-Analysis Sheds Light on High Light Response in Arabidopsis thaliana L.

1
Institute of Cytology and Genetics Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
2
Institute of Computational Mathematics and Mathematical Geophysics Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
3
Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036 Krasnoyarsk, Russia
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Academic Editors: Yuriy L. Orlov, Ming Chen and Oxana B. Dobrovolskaya
Int. J. Mol. Sci. 2022, 23(8), 4455; https://doi.org/10.3390/ijms23084455
Received: 23 March 2022 / Revised: 13 April 2022 / Accepted: 15 April 2022 / Published: 18 April 2022
(This article belongs to the Special Issue Plant Biology and Biotechnology: Focus on Genomics and Bioinformatics)
The availability and intensity of sunlight are among the major factors of growth, development and metabolism in plants. However, excessive illumination disrupts the electronic balance of photosystems and leads to the accumulation of reactive oxygen species in chloroplasts, further mediating several regulatory mechanisms at the subcellular, genetic, and molecular levels. We carried out a comprehensive bioinformatic analysis that aimed to identify genetic systems and candidate transcription factors involved in the response to high light stress in Arabidopsis thaliana L. using resources GEO NCBI, string-db, ShinyGO, STREME, and Tomtom, as well as programs metaRE, CisCross, and Cytoscape. Through the meta-analysis of five transcriptomic experiments, we selected a set of 1151 differentially expressed genes, including 453 genes that compose the gene network. Ten significantly enriched regulatory motifs for TFs families ZF-HD, HB, C2H2, NAC, BZR, and ARID were found in the promoter regions of differentially expressed genes. In addition, we predicted families of transcription factors associated with the duration of exposure (RAV, HSF), intensity of high light treatment (MYB, REM), and the direction of gene expression change (HSF, S1Fa-like). We predicted genetic components systems involved in a high light response and their expression changes, potential transcriptional regulators, and associated processes. View Full-Text
Keywords: high light stress; transcriptomic data; Arabidopsis thaliana L.; gene network; transcription factors; transcription factors binding sites; systems biology; meta-analysis high light stress; transcriptomic data; Arabidopsis thaliana L.; gene network; transcription factors; transcription factors binding sites; systems biology; meta-analysis
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MDPI and ACS Style

Bobrovskikh, A.V.; Zubairova, U.S.; Bondar, E.I.; Lavrekha, V.V.; Doroshkov, A.V. Transcriptomic Data Meta-Analysis Sheds Light on High Light Response in Arabidopsis thaliana L. Int. J. Mol. Sci. 2022, 23, 4455. https://doi.org/10.3390/ijms23084455

AMA Style

Bobrovskikh AV, Zubairova US, Bondar EI, Lavrekha VV, Doroshkov AV. Transcriptomic Data Meta-Analysis Sheds Light on High Light Response in Arabidopsis thaliana L. International Journal of Molecular Sciences. 2022; 23(8):4455. https://doi.org/10.3390/ijms23084455

Chicago/Turabian Style

Bobrovskikh, Aleksandr V., Ulyana S. Zubairova, Eugeniya I. Bondar, Viktoriya V. Lavrekha, and Alexey V. Doroshkov. 2022. "Transcriptomic Data Meta-Analysis Sheds Light on High Light Response in Arabidopsis thaliana L." International Journal of Molecular Sciences 23, no. 8: 4455. https://doi.org/10.3390/ijms23084455

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