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Title: Transcription profiling by high throughput sequencing of Arabidopsis hos1-3 seedlings      
dateReleased:
07-21-2016
description:
Sequencing of mRNA extracted from 14 day old Columbia and hos1-3 seedlings grown at 22C 12:12 light dark Cold acclimation has been shown to be attenuated by the degradation of the INDUCER OF CBF EXPRESSION1 protein by the E3 ubiquitin ligase HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES1 (HOS1). However, recent work has suggested that HOS1 may have a wider range of roles in plants than previously appreciated. Here, we show that hos1 mutants are affected in circadian clock function, exhibiting a long-period phenotype in a wide range of temperature and light environments. We demonstrate that hos1 mutants accumulate polyadenylated mRNA in the nucleus and that the circadian defect in hos1 is shared by multiple mutants with aberrant mRNA export, but not in a mutant attenuated in nucleo-cytoplasmic transport of microRNAs. As revealed by RNA sequencing, hos1 exhibits gross changes to the transcriptome with genes in multiple functional categories being affected. In addition, we show that hos1 and other previously described mutants with altered mRNA export affect cold signaling in a similar manner. Our data support a model in which altered mRNA export is important for the manifestation of hos1 circadian clock defects and suggest that HOS1 may indirectly affect cold signaling through disruption of the circadian clock [PMID: 24254125] Col and hos1-3 seeds were surface sterilized and stratified at 4C for 2 to 4 d on Murashige and Skoog (MS) agar (Melford) and 0.9% agar (Sigma-Aldrich) with no Suc added to the media, grown for 14 days at 22C in 12:12 light dark, and harvested at dawn into liquid nitrogen. Total RNA was extracted using standard protocols. Five micrograms of total RNA was submitted to sequencing using standard protocols for Illumina TruSeq (version 3) technologies.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-84606
refinement:
raw
alternateIdentifiers:
84606
keywords:
functional genomics
dateModified:
01-31-2017
availability:
available
types:
gene expression
name:
Arabidopsis thaliana
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-84606/E-GEOD-84606.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-84606/E-GEOD-84606.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE84606
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

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