Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA264464 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Functionally complemented dog1-1 mutant with a YFP-DOG1 fusion protein under the control of its native promoter were used as starting material for in vivo pull-down of YFP: DOG1 and its interacting proteins from seed tissues in native conditions. DOG1 interacting proteins were identified by mass spectrometry. Pull-downs were performed in biological triplicates using dry or 24 h water imbibed seeds, directly after harvest (dormant condition) and after 7 months of dry storage (non-dormant condition).
2017-07-07 | PXD006347 | Pride
Project description:We analysed the transcriptome of dry seeds (the end product of seed maturation) of three genotypes with different DOG1 expression levels. These included the WT Ler (low DOG1 expression), the near isogenic line NILDOG1-Cvi (strong DOG1 expression) and the non-dormant dog1-1 mutant (absence of DOG1 expression). NILDOG1-Cvi is the Ler WT containing an introgression of the Cvi accession on chromosome 5, which includes the DOG1 gene (Bentsink et al., 2006). The dog1-1 mutant is in the NILDOG1-Cvi genetic background. The aim was to obtain a global overview of the effect of different levels of DOG1 expression during seed maturation on the dry seed transcriptome.
2016-01-14 | GSE65471 | GEO
Project description:We have identified RDO5 as a phosphatase that promotes seed dormancy, most likely independent from ABA and DOG1. To obtain an indication about the genetic and molecular pathways by which RDO5 functions, we performed a transcriptomic comparison between rdo5-1 and its wild-type NIL-DOG1 at different seed stages, using the Arabidopsis Affymetrix AGRONOMICS1 tiling microarrays
2014-11-01 | GSE62578 | GEO
Project description:Production of morphologically and physiologically variable seeds is an important strategy that helps plants to survive in unpredictable natural conditions. However, the model plant Arabidopsis thaliana and most agronomically essential crops yield visually homogenous seeds. Using automated phenotype analysis, we observed that in Arabidopsis small seeds tend to have higher primary and secondary dormancy levels when compared to large ones. Transcriptomic analysis revealed distinct gene expression profiles between large and small seeds. Large seeds had higher expression of translation-related genes implicated in germination competence. In contrast, small seeds showed elevated expression of many positive regulators of dormancy, including a key regulator of this process – the DOG1 gene. Differences in DOG1 expression were associated with differential production of its alternative cleavage and polyadenylation isoforms where in small seeds proximal poly(A) site is selected resulting in a short mRNA isoform. Furthermore, single-seed RNA-seq analysis demonstrated that large seeds resemble DOG1 knockout mutant seeds. Finally, on the single seed level, the expression of genes affected by seed size was correlated with the expression of genes positioning seeds on the path towards germination. Our results demonstrate an unexpected link between seed size and dormancy phenotypes in a species producing highly homogenous seed pools, suggesting that the correlation between seed morphology and physiology is more widespread than initially assumed.
2023-10-16 | GSE203310 | GEO
Project description:We analysed the transcriptome of dry seeds (the end product of seed maturation) of three genotypes with different DOG1 expression levels. These included the WT Ler (low DOG1 expression), the near isogenic line NILDOG1-Cvi (strong DOG1 expression) and the non-dormant dog1-1 mutant (absence of DOG1 expression). NILDOG1-Cvi is the Ler WT containing an introgression of the Cvi accession on chromosome 5, which includes the DOG1 gene (Bentsink et al., 2006). The dog1-1 mutant is in the NILDOG1-Cvi genetic background. The aim was to obtain a global overview of the effect of different levels of DOG1 expression during seed maturation on the dry seed transcriptome. Gene expression in dry seeds of three genotypes was compared: Ler, NILDOG1 and the dog1-1 mutant. For each genotype, three replicates were used.
2016-01-14 | E-GEOD-65471 | biostudies-arrayexpress
Project description:Eukaryotic genomes are pervasively transcribed by RNA polymerase II. Yet, the molecular and biological implications of such a phenomenon are still largely puzzling. Here, we describe noncoding RNA transcription upstream of the Arabidopsis thaliana DOG1 gene, which governs salt stress responses and is a key regulator of seed dormancy. We find that expression of the DOG1 gene is induced by salt stress, thereby causing a delay in seed germination. We uncover extensive transcriptional activity on the promoter of the DOG1 gene, which produces a variety of lncRNAs. These lncRNAs, named PUPPIES, are co-directionally transcribed and extend into the DOG1 coding region. We show that PUPPIES RNAs respond to salt stress and boost DOG1 expression, resulting in delayed germination. This positive role of pervasive PUPPIES transcription on DOG1 gene expression is associated with augmented pausing of RNA polymerase II, slower transcription and higher transcriptional burst size. These findings highlight the positive role of upstream co-directional transcription in controlling transcriptional dynamics of downstream genes.
2023-02-01 | GSE208755 | GEO
Project description:Combined transcriptome and translatome analyses reveal a role for tryptophan dependent auxin biosynthesis in the control of DOG1 dependent seed dormancy
| PRJNA304010 | ENA
Project description:A Synthetic Gene-Metabolic Oscillator
Reference:
Fung et al; Nature (2005) 435:118-122
Name of kinetic law
Reaction
Glycolytic flux, V_gly:
nil -> AcCoA;
Flux to TCA cycle/ETOH, V_TCA:
AcCoA -> TCA/EtOH;
HOAc ex/import,reversible, V_out:
HOAc -> HOAc_E
V_Pta:
AcCoA + Pi -> AcP + CoA
reversible, V_Ack:
AcP + ADP -> OAc + ATP
V_Acs:
OAC + ATP -> AcCoA +PPi
Acetic acid-base equillibrium, reversible, V_Ace:
OAC + H -> HOAc
Expression of LacI, R_LacI:
nil -> LacI
Expression of Acs, R_Acs:
nil -> Acs
Expression of Pta, R_Pta:
nil -> Pta
LacI degradation, R_dLacI:
LacI -> nil
Acs degradation, R_dAcs:
Acs -> nil
Pta degradation, R_dPta:
Pta -> nil
For this model the differential equation for V_Ace was changed from:
C*(AcP*H-K_eq*OAC) with C = 100 in the supplemental material
to C*(OAc*H-K_eq*HOAc) with C = 100, as in
Bulter et. al; PNAS(2004),101,2299-2304
, and a value for K_eq of 5*10^-4 after communication with the authors.
translated to SBML by:
Lukas Endler(luen at tbi.univie.ac.at), Christoph Flamm (xtof at tbi.univie.ac.at)
Biomodels Curation
The model reproduces 3a of the paper for glycolytic flux Vgly = 0.5. The authors have agreed that the values on Y-axis are marked wrong and hence there is a discrepancy between model simulation results and the figure. Also, note that the values of concentration and time are in dimensionless units. The model was successfully tested on MathSBML and Jarnac.
2024-09-02 | BIOMD0000000067 | BioModels
Project description:Stable transgenic seeds expressing SnRK2.6 as an N-terminally tagged YFP fusion in two genetic backgrounds, NIL-DOG1 and dog1-1, were used as the starting biological material. The target protein was purified through immunoprecipitation from native dry seed crude extracts of both genotypes in three independent biological replicates. Samples were split and measured using both DDA and PRM-based methods. This assay aimed to investigate the influence of the dog1-1 mutation on the phosphorylation status of SnRK2.6 activation loops.
2024-06-27 | PXD053457 | JPOST Repository