Expression data of WT and Attim17-1 Arabidopsis seeds during stratification and germination
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE48488 | GEO | 2014/07/31
SECONDARY ACCESSION(S): PRJNA210318
REPOSITORIES: GEO
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Project description:We analysed the translatome and transcriptome of Arabidopsis thaliana Col-0 WT at five distinct physiological states during seed germination. The aim was to obtain a global overview of genes under translational control during seed-seedling transition.
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Project description:We identified a regulator of Arabidopsis thaliana seed germination: FLOE1 (AT4G28300). We used RNA-seq to uncover genes that are diffenrentially regulated in dry seeds, imbibed seeds and seeds imbibed in 220mM NaCl.
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Project description:Pectins localize in the primary cell wall and consist of multiblock co?polymers among which homogalacturonan (HG) is the simplest and most abundant form. Methylesterification pattern of HG is tuned by pectin methylesterases (PMEs), which activity is itself controlled by specific inhibitors or PMEIs. PME?mediated regulation of HG methylesterification plays a major role in controlling several developmental processes, including seed germination and dark grown hypocotyl elongation. Arabidopsis PME36 is preferentially expressed during the late stages of silique development and, using the knock?out mutant pme36-1, we showed that PME36 is required to implement the characteristic pattern of demethylesterified pectins in mature seed. However, although this pattern was strongly impaired in pme36-1 mature seed, no phenotypical change was observed in the mutant during seed germination and seedling dark growth, suggesting the existence of a compensatory mechanism overcoming the defect in pectin demethylesterification. To get insight into this mechanism, a transcriptomic analysis by microarrays was performed on pme36-1 and Col0 wild-type, in seed at two early stages of germination, preceding tegument rupture: 16 hours and 24 hours after transfer from cold room (stratification) to dark growth condition.
2020-07-31 | GSE155433 | GEO
Project description:Histone acetylation is involved in the regulation of gene expression in plants and eukaryotes. Histone deacetylases (HDACs) are enzymes that catalyze the removal of acetyl groups from histones, which is associated with the repression of gene expression. To study the role of histone acetylation in the regulation of gene expression during seed germination, trichostatin A (TSA), a specific inhibitor of histone deacetylase, was used to treat imbibing Arabidopsis thaliana seeds. GeneChip arrays were used to show that TSA induces up-regulation of 45 genes and down-regulation of 27 genes during seed germination. Eight TSA-up-regulated genes were selected for further analysis - RAB18, RD29B, ATEM1, HSP70 and four late embryogenesis abundant protein genes (LEA). A gene expression time course shows that these eight genes are expressed at high levels in the dry seed and repressed upon seed imbibition at an exponential rate. In the presence of TSA, the onset of repression of the eight genes is not affected but the final level of repressed expression is elevated. Chromatin immunoprecipitation and HDAC assays show that there is a transient histone deacetylation event during seed germination at one day after imbibition, which serves as a key developmental signal that affects the repression of the eight genes. This SuperSeries is composed of the SubSeries listed below.
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Project description:RNAseq profiling of 10 time points during germination in Arabidopsis, from freshly harvested seed, through mature seed, stratification, germination and to post-germination.
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Project description:sRNA-seq profiling of 10 time points during germination in Arabidopsis, from freshly harvested seed, through mature seed, stratification, germination and to post-germination.
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Project description:NUCLEOPORIN 1 (NUP1), a member of the Nuclear Pore Complex (NPC), is located on the inner side of the nuclear membrane. It is highly expressed in seeds; however, its role in seeds including germination has not been explored yet. Here, we identified an ABA hypersensitive phenotype of nup1 during germination. ABA treatment drastically changes the expression pattern of thousands of genes in nup1, including the major transcription factors (TFs) involved in germination, ABI3, ABI4, and ABI5. Double mutant analysis of NUP1 and these ABA-related genes showed that mutations in ABI5 can rescue the phenotype of nup1, suggesting that NUP1 acts upstream of ABI5 to regulate seed germination. ABI5, a negative regulator of germination was previously reported to be predominantly expressed in nucleus. Our subnuclear localization study indicates ABI5 is mostly localized in nucleoplasm. It is abundant in dry seeds and rapidly degraded during germination, but the details of its degradation site is unclear. Here, we found that NUP1 is physically associated with ABI5 and the 19S regulatory particle (RP) of the 26S proteasome near NPC. Mutation in NUP1 delayed the ABI5 degradation through its post-translation retention in nucleolus after abiotic stress treatment. Taken together, we propose, NUP1 anchors the proteasome to NPC and modulates Arabidopsis seed germination through proteasome-mediated degradation of ABI5 in the vicinity of NPC in nucleoplasm.
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Project description:Seed germination is characterized by a constant change of gene expression across different time points. These changes are related to specific processes, which eventually determine the onset of seed germination. To get a better understanding on the regulation of gene expression during seed germination, we measured gene expression levels of Arabidopsis thaliana Bay x Sha recombinant inbred lines (RILs) at four important seed germination stages (primary dormant, after-ripened, six-hour after imbibition, and radicle protrusion stage) using. We mapped the eQTL of the gene expression and the result displayed the distinctness of the eQTL landscape for each stage. We found several eQTL hotspots across stages associated with the regulation of expression of a large number of genes. Together, we have revealed that the genetic regulation of gene expression is dynamic along the course of seed germination.
2020-06-24 | E-MTAB-9080 | biostudies-arrayexpress
Project description:Purpose: The goals of this study are to compare the transcriptome profiling between wild type and sweet1 under the treatments of either the glucose, ABA or both during germination. Methods: After 3-day imbibition, sweet1 seeds were sown on ½ MS medium and grown under constant light, 22 °C for 24 hours. Seeds were transferred to ½ MS liquid medium supplemented with either 60 mM Glc, 5 µM ABA or both for 6 hours. Four biological replicates were collected for each treatment. Total RNA was extracted by RNeasy PowerPlant Kit (13500-50, Qiagen), The libraries were prepared from 1 µg total RNA using KAPA mRNA Hyper Prep kit (KK8581, Roche) with KAPA Dual-indexed Adapter kit (KK8722, Roche). The libraries were sequenced by Hiseq 2500 (Illumina) with paired-end reads. Results: Gene expression level was quantified using Kallisto v 0.44.0 by mapping to Arabidopsis thaliana (version 11) primary transcript sequences. Samples were evaluated based on pair-wise comparison between different conditions and outliers within each treatment were removed for the further analysis based on PCA results. Candidates with more than 10 counts per million reads in at least 50% samples, |b| ≥ 0.2 and q-value < 0.05 were identified as differentially expressed genes (DEGs) using Sleuth program. Hierarchical clustering of DEGs uncovered several pathways that may contribute to glucose antagonizing ABA function. Conclusions: This study represents the detailed analysis of transcriptome in germinating seeds under ABA+Glc treatment. Our study provides a new perspective on the interaction between ABA and Glc in response to external stimuli to control the seed germination.
2023-01-01 | GSE193111 | GEO
Project description:Seeds are highly resilient to the external environment, which allow plants to persist in unpredictable and unfavorable conditions. Some plant species have adopted a bet-hedging strategy to germinate a variable fraction of seeds in any given condition, and this could be explained by population-based threshold models. Here, in the model plant Arabidopsis (Arabidopsis thaliana) we induced secondary dormancy to address the transcriptional heterogeneity among seeds that leads to binary germination/non-germination outcomes. We developed a single seed RNA-seq strategy that allowed us to observe a reduction in seed transcriptional heterogeneity as seeds enter stress conditions, followed by an increase during recovery. We identified groups of genes whose expression showed a specific pattern through a time course and used these groups to position the individual seeds along the transcriptional gradient of germination competence. In agreement, transcriptomes of dormancy-deficient seeds (mutant of DELAY OF GERMINATION 1 gene) showed a shift towards higher values of the germination competence index. Interestingly, a significant fraction of genes with variable expression encoded translation-related factors. In summary, interrogating hundreds of single seed transcriptomes during secondary dormancy-inducing treatment revealed variability among the transcriptomes that could result from the distribution of population-based sensitivity thresholds. Our results also showed that single seed RNA-seq is the method of choice for analyzing seed bet-hedging-related phenomena.
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