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

Frontiers in Plant Science
Wolfram G Brenner, Thomas Schmülling

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 ...Continue Reading

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Citations

Apr 16, 2015·Journal of Experimental Botany·Anne Cortleven, Thomas Schmülling
Apr 26, 2015·Journal of Experimental Botany·Paul J Zwack, Aaron M Rashotte
Apr 20, 2016·Plant, Cell & Environment·Ángela María Sánchez-LópezJavier Pozueta-Romero
Jan 23, 2018·The New Phytologist·Georgy A RomanovThomas Schmülling
Apr 26, 2020·The Plant Journal : for Cell and Molecular Biology·Jan de VriesJohn M Archibald
Aug 22, 2018·International Journal of Molecular Sciences·Jaroslav PavlůMartin Černý
Mar 1, 2018·Development·Joseph J Kieber, G Eric Schaller
Dec 19, 2018·International Journal of Molecular Sciences·Martin HönigKarel Doležal
Jan 8, 2021·Frontiers in Plant Science·Sergey N LominGeorgy A Romanov
Mar 7, 2021·Genes·Katarzyna Hnatuszko-KonkaIzabela Grzegorczyk-Karolak
Mar 9, 2021·Frontiers in Plant Science·Jan SkalakJan Hejatko
Jun 25, 2021·The Plant Journal : for Cell and Molecular Biology·Joanna K PolkoJoseph J Kieber

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Datasets Mentioned

BETA
GSE55902

Methods Mentioned

BETA
chip
PCR

Software Mentioned

Bioconductor affy package
Microsoft Visual Basic for
Excel
BLAST
AmiGO
R
Toucan2
CATMA
CorelDRAW

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