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Series GSE176161 Query DataSets for GSE176161
Status Public on Feb 15, 2022
Title Gene expression during hormone-induced shoot regeneration in Arabidopsis thaliana explants exposed to different temperatures
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary Many plants are able to regenerate upon cutting, and this process can be enhanced in vitro by incubating explants on hormone-supplemented media. While such protocols have been used for decades, little is known about the molecular details of how incubation conditions influence their efficiency. In this study, we show that warm temperature promotes both callus formation and shoot regeneration efficiency in Arabidopsis thaliana. Our RNA sequencing analysis unveil that this accompanied by the enhanced expression of several regeneration-associated genes, such as CUP-SHAPED COTYLEDON 1 (CUC1), encoding a transcription factor involved in shoot meristem formation, and ISOPENTENYLTRANSFERASE (IPT1) and YUCCA1/4 (YUC1/4), encoding key enzymes for cytokinin and auxin biosynthesis, respectively. Consistently, mutations in CUC1 and IPT1 or chemical inhibition of YUCs reduce the enhancement of shoot regeneration at warm temperature. When combined with ChIP sequencing analyses, our RNA sequencing data further reveal that histone variant H2A.Z is enriched on these differentially expressed loci at 17°C and that its occupancy level decreases when the ambient temperature increases to 27°C. This study thus unveil a new epigenetic mechanism that influences hormone-induced regeneration and brings further insights on how incubation temperature is a crucial parameter in optimizing protocols for in vitro tissue culture.
Overall design RNA sequencing in Arabidopsis thaliana hypocotyl explants exposed to CIM for 4 days then SIM for 4 days, at either 17°C or 27°C
Contributor(s) Lambolez A, Kawamura A, Sugimoto K
Citation(s) 35157760
Submission date Jun 04, 2021
Last update date Feb 16, 2022
Contact name Alice Lambolez
Organization name The University of Tokyo
Department Faculty of Science, Department of Biological Sciences
Lab Kakutani Lab
Street address 7 Chome-3-1 Hongo
City Bunkyo
State/province Tokyo
ZIP/Postal code 113-8654
Country Japan
Platforms (1)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (15)
GSM5359137 Col_22C_0h_rep1
GSM5359138 Col_22C_0h_rep2
GSM5359139 Col_22C_0h_rep3
BioProject PRJNA735204
SRA SRP322735

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Supplementary file Size Download File type/resource
GSE176161_Coverage_all_17C_VS_27C_CIM_SIM_RNA-seq.bed.gz 939.5 Kb (ftp)(http) BED
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