Summarizing and exploring data of a decade of cytokinin-related transcriptomics

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.

Keywords: cis element; cytokinin; gene regulation; hormone action; meta-analysis; regulatory network; signal transduction; transcriptomics.

Figure 1

Data sources and Venn diagram summarizing large-scale transcriptomic studies related to cytokinin. (A) Source and type of data reporting cytokinin-regulated gene expression used in this study. Overlap analysis of cytokinin-induced (B) and cytokinin-repressed (C) genes identified in the different studies. The color code of the circles in (B,C) corresponds to the code in the table shown in (A). The core sets of regulated genes are encircled with a black line.

Figure 2

Annotated subcellular localizations, molecular functions and biological processes of the core set of cytokinin-induced genes. The genes listed in Table 2A were evaluated with regard to their GO categorization using the GO categorization tool provided by TAIR (http://www.arabidopsis.org/tools/bulk/go/index.jsp), which matches a given set of genes with a reduced set of basic GO terms (GOslim). The resulting table was imported into Microsoft Excel for generating the cake diagrams. The Excel diagrams were reformatted using CorelDRAW to fit them into the frame of a figure.

Figure 3

Sequences and frequencies of novel potential type-B response regulator binding sites that were enriched in promoters of cytokinin-responsive genes in comparison to a control set of promoters. (A) Enriched motifs derived from the consensus sequence (ACT)(AG)(GT)AT(ACT)(CT)(ACGT), characterized as binding motif for the type-B ARRs ARR11 and ARR14 (Franco-Zorrilla et al., 2014). (B) Enriched motifs derived from all possible DNA octamers containing a central AT.

Figure 4

Sequence logo of a novel model of a potential type-B response regulator binding site. The motif combines all single motifs found in the analyses pictured in Figures 3A,B and shows the frequencies of the bases at the respective position in all promoters of the 65 cytokinin-regulated genes shown in Table 2A.