Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA330620 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3932360_1.fastq.gz | Fastqsanger.gz | |||
| SRR3932360_2.fastq.gz | Fastqsanger.gz | |||
| SRR3932355_1.fastq.gz | Fastqsanger.gz | |||
| SRR3932355_2.fastq.gz | Fastqsanger.gz | |||
| SRR3932356_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project 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.
2016-07-21 | E-GEOD-84606 | biostudies-arrayexpress
Project description:Sequencing of mRNA extracted from 14 day old Columbia and hos1-3 seedlings grown at 22°C 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]
2016-07-21 | GSE84606 | GEO
Project description:EV39+40 mRNA levels in Wild-type versus ddm1 Arabidopsis thaliana seedlings
| PRJNA91031 | ENA
Project description:EV33+34 mRNA levels in Wild-type versus ddm1 Arabidopsis thaliana seedlings
| PRJNA91027 | ENA
Project description:VC109+111 mRNA levels in Wild-type versus ddm1 Arabidopsis thaliana seedlings
| PRJNA91029 | ENA
Project description:VC110+112 mRNA levels in Wild-type versus ddm1 bolting Arabidopsis thaliana plants
| PRJNA91033 | ENA
Project description:EV23+24 mRNA levels in Wild-type versus ddm1/+ backcross bolting Arabidopsis thaliana plants
| PRJNA91025 | ENA
Project description:Lines of evidence indicate that nuclear pore complex profoundly affects the timing of plant flowering, but the underlying mechanisms remain poorly elucidated. Here, we report that Nucleoporin 96 (Nup96) acts as a negative regulator of long-day photoperiodic flowering in Arabidopsis. Through multiple approaches, we identified and verified an E3 ubiquitin ligase HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE 1 (HOS1) interacting in vivo with Nup96. Nup96 and HOS1 proteins mainly localize and interact on nuclear membrane. Loss-of-function of Nup96 leads to destruction of HOS1 proteins without changing its mRNA abundance, which results in over-accumulation of the key activator of long-dayphotoperiodic flowering, CONSTANS (CO) proteins, as that in hos1 mutants. Unexpectedly, we observed that mutation of HOS1 gene strikingly diminishes Nup96 protein level, suggesting that Nup96 and HOS1 are mutually stabilized and thus they form a novel repressive module to regulate CO protein turnover. Therefore, the nup96 and hos1 single mutants and nup96 hos1 double mutant have very much similar early-flowering phenotypes and overlapping transcriptome changes. Together, this study reveals a new repression mechanism, where the Nup96-HOS1 repressive module gates the level of CO proteins, to prevent precocious flowering of Arabidopsis under long day conditions.
2019-10-31 | GSE138706 | GEO
Project description:mRNA levels in Wild-type versus ddm1 Arabidopsis thaliana seedlings and bolting plants. Features found to be significantly enriched for DNA methylation were determined. This SuperSeries is composed of the SubSeries listed below.
2004-06-12 | GSE1354 | GEO
Project description:mRNA levels in Wild-type versus ddm1 Arabidopsis thaliana seedlings and bolting plants. Features found to be significantly enriched for DNA methylation were determined. This SuperSeries is composed of the following subset Series: GSE1324: EV23+24 mRNA levels in Wild-type versus ddm1/+ backcross bolting Arabidopsis thaliana plants GSE1325: EV33+34 mRNA levels in Wild-type versus ddm1 Arabidopsis thaliana seedlings GSE1326: VC109+111 mRNA levels in Wild-type versus ddm1 Arabidopsis thaliana seedlings GSE1327: EV39+40 mRNA levels in Wild-type versus ddm1 Arabidopsis thaliana seedlings GSE1328: VC110+112 mRNA levels in Wild-type versus ddm1 bolting Arabidopsis thaliana plants Refer to individual Series
2010-06-09 | E-GEOD-1354 | biostudies-arrayexpress