Arabidopsis thaliana
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ABSTRACT:
PROVIDER: PRJNA93225 | ENA |
REPOSITORIES: ENA
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Project description:To understand the gene network that controls plant tolerance to cold stress, we carried out a near full genome transcript expression profiling in Arabidopsis using Affymetrix GeneChips that contain approximately 24,000 genes. For microarray analysis, Arabidopsis seedlings were cold treated at 0 C for 0 h, 3 h, 6 h, and 24 h. A total of 939 genes were statistically determined to be cold-regulated with 655 being up-regulated and 284 down-regulated. A large number of the early cold-responsive genes encode transcription factors that likely control late-responsive genes, which implies a multitude of transcriptional cascades. In addition, many genes involved in post-transcriptional and chromatin level regulation were also cold regulated suggesting their involvement in cold responsive gene regulation. A number of genes important for the biosynthesis or signaling of plant hormones, such as abscisic acid, gibberellic acid and auxin, are regulated by cold stress, which is of potential importance in coordinating cold tolerance with growth and development. We compared the cold-responsive transcriptomes of wild type and ice1, a mutant defective in an upstream transcription factor required for chilling and freezing tolerance. The transcript levels of many cold-responsive genes were altered in the ice1 mutant not only during cold stress conditions, but also before cold treatments. Our study provides a global picture of the Arabidopsis cold-responsive transcriptome and its control by ICE1, and thus will be valuable for understanding gene regulation under cold stress and the molecular mechanisms of cold tolerance. Keywords: Cold Stress response
2005-10-01 | GSE3326 | GEO
Project description:To understand the gene network that controls plant tolerance to cold stress, we carried out a near full genome transcript expression profiling in Arabidopsis using Affymetrix GeneChips that contain approximately 24,000 genes. For microarray analysis, Arabidopsis seedlings were cold treated at 0 C for 0 h, 3 h, 6 h, and 24 h. A total of 939 genes were statistically determined to be cold-regulated with 655 being up-regulated and 284 down-regulated. A large number of the early cold-responsive genes encode transcription factors that likely control late-responsive genes, which implies a multitude of transcriptional cascades. In addition, many genes involved in post-transcriptional and chromatin level regulation were also cold regulated suggesting their involvement in cold responsive gene regulation. A number of genes important for the biosynthesis or signaling of plant hormones, such as abscisic acid, gibberellic acid and auxin, are regulated by cold stress, which is of potential importance in coordinating cold tolerance with growth and development. We compared the cold-responsive transcriptomes of wild type and ice1, a mutant defective in an upstream transcription factor required for chilling and freezing tolerance. The transcript levels of many cold-responsive genes were altered in the ice1 mutant not only during cold stress conditions, but also before cold treatments. Our study provides a global picture of the Arabidopsis cold-responsive transcriptome and its control by ICE1, and thus will be valuable for understanding gene regulation under cold stress and the molecular mechanisms of cold tolerance. Experiment Overall Design: Two replicates for each time point of 0 hours, 3 hours, 6 hours and 24 hours of cold treatment for the wildtype (control) and ice1 (mutant).
2007-07-13 | E-GEOD-3326 | biostudies-arrayexpress
Project description:Plants must properly integrate noisy temperature signals to monitor seasonal progression. However, the global regulatory landscape underlying cold acclimation and adaption of plants to noisy and fluctuating natural cold conditions remain poorly investigated. Here, we perform a deep-coverage RNA-seq to investigate the transcriptome dynamics of Arabidopsis thaliana plants grown over weeks of a fluctuating temperature regime, mimicking natural cold conditions of autumn and early winter, or grown using an average daily temperature profile without any temperature fluctuations. We show that progressive cold induces three main patterns of transcriptional response: dynamic-, cooling- and chilling-responsive gene activation. Progressive cold induces a complex network of regulators that could be responsible for the regulation of distinct transcriptional programs. Surprisingly, we find only small differences in cold-responsive gene expression between average and fluctuating conditions. We also highlight that temperature before time is the principal driver of cold transcriptional reprogramming. By combining RNA-seq and ATAC-seq data, we observe that the induction of cold-responsive genes is associated with an increase of promoter accessibility whereas down-regulated genes do not lose accessibility, allowing plants to rapidly reactivate transcription after the return of favourable conditions.
2026-09-10 | GSE283017 | GEO
Project description:Plants must properly integrate noisy temperature signals to monitor seasonal progression. However, the global regulatory landscape underlying cold acclimation and adaption of plants to noisy and fluctuating natural cold conditions remain poorly investigated. Here, we perform a deep-coverage RNA-seq to investigate the transcriptome dynamics of Arabidopsis thaliana plants grown over weeks of a fluctuating temperature regime, mimicking natural cold conditions of autumn and early winter, or grown using an average daily temperature profile without any temperature fluctuations. We show that progressive cold induces three main patterns of transcriptional response: dynamic-, cooling- and chilling-responsive gene activation. Progressive cold induces a complex network of regulators that could be responsible for the regulation of distinct transcriptional programs. Surprisingly, we find only small differences in cold-responsive gene expression between average and fluctuating conditions. We also highlight that temperature before time is the principal driver of cold transcriptional reprogramming. By combining RNA-seq and ATAC-seq data, we observe that the induction of cold-responsive genes is associated with an increase of promoter accessibility whereas down-regulated genes do not lose accessibility, allowing plants to rapidly reactivate transcription after the return of favourable conditions.
2026-09-10 | GSE283016 | GEO
Project description:The effect of PLC inhibitor on cold responsive transcriptome.
| PRJNA109505 | ENA
Project description:Our results show that ICE1 controls plant male fertility via impacting anther dehydration. The loss-of-function mutation in ICE1 gene in Arabidopsis caused anther indehiscence and decreased pollen viability as well as germination rate. Further analysis revealed that the anthers in the mutant of ICE1 (ice1-2) had the structure of stomium, though the epidermis did not shrink to dehisce. The anther indehiscence and influenced pollen viability as well as germination in ice1-2 were due to abnormal anther dehydration, for most of anthers dehisced with drought treatment and pollen grains from those dehydrated anthers had similar viability and germination rates compared with wild type. Accordingly, the sterility of ice1-2 could be rescued by ambient dehydration treatments. Likewise, the stomatal differentiation of ice1-2 anther epidermis was disrupted in a different manner compared with that in leaves. ICE1 specifically bound to MYC-recognition elements in the promoter of FAMA, a key regulator of guard cell differentiation, to activate FAMA expression. Transcriptome profiling in the anther tissues further exhibited ICE1-modulated genes associated with water transport and ion exchange in the anther. Together, this work reveals the key role of ICE1 in male fertility control and establishes a regulatory network mediated by ICE1 for stomata development and water movement in the anther.
2018-09-13 | GSE107260 | GEO
Project description:We analysed the effect of cold priming on cold and high light regulation of gene expression. 5 days after the first cold treatment the primary stress response was widely reset. Then, a second (triggering) cold stimulus (24 h 4 °C) and a triggering high-light stimulus (2 h 800 µmol quanta m-2 s-1), which regulate many stress responsive genes in the same direction in naïve plants, caused widely specific and even inverse regulation of priming-responsive genes.
2020-06-08 | GSE151749 | GEO
Project description:We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome under drought, cold, high-salinity and ABA treatment conditions and idenfied many stress- or ABA- responsive putative functional RNAs and fully-overlapping sense-antisense transcripts in Arabidopsis genome. Keywords: stress response
2008-11-19 | GSE9646 | GEO
Project description:Arabidopsis cold regulated transcriptome, translatome and CSP1 RNA regulon
| PRJNA167103 | ENA
Project description:Alternative splicing plays a major role in expanding the potential informational content of eukaryotic genomes. It is an important post-transcriptional regulatory mechanism that can increase protein diversity and affect mRNA stability. Cold stress, which adversely affects plants growth and development, regulates the transcription and splicing of plants splicing factors. This affects the pre-mRNA processing of many genes. To identify cold regulated alternative splicing we applied Affymetrix Arabidopsis tiling arrays to survey the transcriptome under cold treatment conditions.
2013-05-12 | GSE35996 | GEO