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Series GSE79353 Query DataSets for GSE79353
Status Public on Sep 29, 2017
Title Genome-wide analysis of transcription, H2A.Z, nucleosomes and HSF1 dynamics in response to temperature increase in Arabidopsis thaliana [RNA-seq I]
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary Plants are sessile organisms and therefore must sense and respond to changes of their surrounding conditions such as ambient temperature, which vary diurnally and seasonally. It is not yet clear how plants sense temperature and integrate this information into their development. We have previously shown that H2A.Z-nucleosomes are evicted in response to warmer temperatures. It is not clear however, whether the link between transcriptional responsiveness and changes in H2A.Z binding in context of temperature shifts is a global trend that can be seen throughout the genome, or the phenomenon is specific to a specialised set of temperature-responsive genes. In addition to the role of H2A.Z-nucleosome dynamics in the transcriptional response to temperature, it was shown that genes strongly misregulated in the h2a.z mutant are enriched for gene categories involved in response to multiple environmental cues. This suggests that H2A.Z could be implicated in the transcriptional response to various environmental inputs, raising the question: What brings the specificity of H2A.Z dynamics in response to temperature? To address this question we have profiled H2A.Z-nucleosome occupancy genome wide (using ChIP-seq) during a time course after temperature variation and compared its dynamics to transcriptional changes. We identified a fast, targeted and transient eviction of H2A.Z associated with transcriptional activation in response to temperature for a few hundreds genes. This eviction is associated with a reduction of the stability of the nucleosome. Moreover the genes with a fast H2A.Z eviction were strongly enriched in heat shock elements in their promoter and we observed a strong association between HSF1 binding and H2AZ eviction at warm temperature. These results highlight the importance of the interplay between transcription factors and chromatin to allow a controlled and dynamics response to temperature.
Overall design RNA-seq were generated in duplicate for seedlings shifted to warm temperature
Contributor(s) Wigge P, Cortijo S, Charoensawan V
Citation(s) 28893714
Submission date Mar 17, 2016
Last update date May 15, 2019
Contact name Sandra Cortijo
Organization name Sainsbury Laboratory, Cambridge University
Street address Bateman Street
City Cambridge
ZIP/Postal code CB2 1LR
Country United Kingdom
Platforms (2)
GPL13222 Illumina HiSeq 2000 (Arabidopsis thaliana)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (27)
GSM2092742 RNA-seq_17c_0min_rep1
GSM2092743 RNA-seq_17c_15min_rep1
GSM2092744 RNA-seq_17c_15min_rep2
This SubSeries is part of SuperSeries:
GSE79355 Genome-wide analysis of transcription, H2A.Z, nucleosomes and HSF1 dynamics in response to temperature increase in Arabidopsis thaliana
BioProject PRJNA315570
SRA SRP071947

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE79353_RAW.tar 21.3 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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