Potassium (K+) is a critical nutrient required for plant growth and development. To advance our understanding of the architecture and dynamic regulation of the K+ responsive gene regulatory network, we have performed transcriptomic analysis of K+ deprived WT (col-0) and cipk9 mutant in Arabidopsis thaliana. Computational analysis showed that K+ deprivation induces a burst of transcriptional activity, generating diverse expression patterns into distinct sectors targeting specific biological processes. We found that the modules of co-expressed genes can define the differences between WT and cipk9 mutant. We have also generated transcriptional regulatory networks and identified key factors determining seedling development and K+ deprivation -induced transcriptional reprogramming. Several TFs and targets were uncovered as network components with a role in diverse pathways. Analysis of subnetworks surrounding the TFs acting as hub using transcriptome profiling provided insights into their regulatory role in defined modules of the K+ deprivation network. The results suggested that expression of several stress responsive TFs and specific K+ transporters determine nutrient response in the cipk9 mutant. Further, we identified temporal TF-target binding relationship on CIPK9 promoter using available (DNA affinity purification sequencing, DAP-Seq) data. Collectively, our work illuminates the complexity of the K+ deprivation gene regulatory network, identifies novel unknown regulators of CIPK9, and provides a valuable resource for functional studies on K+ signaling components in plant development and stress conditions.
rachel-kt/Transcriptome-analysis-Arabidopsis
Transcriptomic analysis of K+ deprived WT (col-0) and cipk9 mutant in Arabidopsis thaliana to advance our understanding of the architecture and dynamic regulation of the K+ responsive gene regulatory network.
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