Abstract
The genome-wide transcriptional response of the model organism Arabidopsis thaliana to cytokinin has been investigated by different research groups as soon as large-scale transcriptomic techniques became affordable. Over the last 10 years many transcriptomic datasets related to cytokinin have been generated using different technological platforms, some of which are published only in databases, culminating in an RNA sequencing experiment. Two approaches have been made to establish a core set of cytokinin-regulated transcripts by meta-analysis of these datasets using different preferences regarding their selection. Here we add another meta-analysis derived from an independent microarray platform (CATMA), combine all the meta-analyses available with RNAseq data in order to establish an advanced core set of cytokinin-regulated transcripts, and compare the results with the regulation of orthologous rice genes by cytokinin. We discuss the functions of some of the less known cytokinin-regulated genes indicating areas deserving further research to explore cytokinin function. Finally, we investigate the promoters of the core set of cytokinin-induced genes for the abundance and distribution of known cytokinin-responsive cis elements and identify a set of novel candidate motifs.
Highlights
Cytokinins are a class of plant hormones with a broad range of functions in regulating plant growth and development as well as physiologicial processes (Werner and Schmülling, 2009; Kieber and Schaller, 2014)
The genome-wide transcriptional response of Arabidopsis thaliana to cytokinins was investigated by different research groups as soon as large-scale transcriptomics became affordable
The flood of data started in 2002 with a publication addressing shoot induction in calli by cytokinin (Che et al, 2002), followed by two studies dedicated to cytokinin induction in seedlings (Rashotte et al, 2003; Brenner et al, 2005), the latter using the full genome ATH1 GeneChip®, and a study focusing on the response regulator ARR22 (Kiba et al, 2004)
Summary
Cytokinins are a class of plant hormones with a broad range of functions in regulating plant growth and development as well as physiologicial processes (Werner and Schmülling, 2009; Kieber and Schaller, 2014). An attempt to identify a core set of cytokinin-regulated genes has been made using a single microarray dataset and applying elaborate statistical methods in order to narrow down the number of genes (Nemhauser et al, 2006) This attempt, relying on only one single microarray experiment, was tained with the inevitable insecurities inherent to the technology and prone to contain false positive genes. Two approaches to establish a core set of cytokinin-regulated transcripts by meta-analysis of transcriptomic data using different preferences regarding the datasets used have been published (Brenner et al, 2012; Bhargava et al, 2013)
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