Dissecting the temporal genetic networks programming soybean embryo development from embryonic morphogenesis to post-germination
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1043054 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To understand the molecular events underlying seed desiccation and germination, we performed transcriptome analysis of soybean (Glycine max) embryos at three seed developmental stages (early, mid and late desiccation), mature dry seeds, and three germination stages (3, 16 and 27 hour-after-imbibition).
2024-10-16 | GSE248224 | GEO
Project description:Leigh syndrome (LS) is a severe manifestation of mitochondrial disease in children and is currently incurable. The lack of effective models hampers our understanding of the mechanisms underlying the neuronal pathology of LS. Using patient-derived induced pluripotent stem cells and CRISPR/Cas9 engineering, we developed a human model of LS due to mutations in the complex IV assembly gene SURF1. Single-cell RNA-sequencing and multi-omics analysis revealed compromised neuronal morphogenesis in mutant neural cultures and brain organoids. The defects emerged at the level of neural progenitor cells (NPCs), which retained a glycolytic proliferative state that failed to instruct neuronal morphogenesis. LS NPCs carrying mutations in the complex I gene NDUFS4 recapitulated morphogenesis defects. Interventions supporting the metabolic programming of NPCs restored neuronal morphogenesis, including SURF1 gene augmentation and PGC1A induction via bezafibrate treatment. Our findings provide mechanistic insights and suggest interventional strategies for a rare mitochondrial disease with major unmet medical needs.
2021-01-29 | PXD019112 | Pride
Project description:To understand the molecular events underlying seed maturation, quiescence and germination, we performed transcriptome analysis of soybean (Glycine max) embryos at four seed developmental stages (cotyledon, early, mid and late maturation), mature dry seeds, and seedlings, eight days after seed sowing.
2017-07-12 | GSE99571 | GEO
Project description:To invistage the transcsriptome re-programming from oat grain development to germination
2024-01-03 | GSE224726 | GEO
Project description:How epigenetics is involved in the transition from seed maturation to seed germination largely remains elusive. To uncover the possible role of epigenetics in gene expression during the transition from seed maturation to seed germination in soybean, the transcriptome of cotyledons from four stages of soybean seed maturation and germination, including mid-late maturation, late maturation, seed dormancy and seed germination, were profiled by Illumina sequencing. For the genes that are quantitatively regulated at the four stages, two antagonistic epigenetic marks, H3K4me3 and H3K27me3, together with the binding of RNA polymerase II, were investigated at the four stages by chromatin immunoprecipitation (ChIP). For 10 out of 16 genes examined, the relative enrichment of histone modification marks (H3K4me3 and H3K27me3) and RNA polymerase II binding on their promoter regions correlates well with their relative expression levels at four stages, suggesting the involvement of epigenetics in transcriptional regulation. A striking finding is that seed germination-specific genes start to show open chromatin (H3K4me3) during late seed maturation although their transcripts do not accumulate, which is further supported by RNA polymerase II binding. Together, our results provide the first evidence that seed germination genes can be primed for transcription (open chromatin and RNA polymerase II binding) during seed maturation, highlighting that the transition from seed maturation to seed germination starts at late seed maturation stages at both the genetic and epigenetic levels.
2011-05-10 | GSE29134 | GEO
Project description:How epigenetics is involved in the transition from seed maturation to seed germination largely remains elusive. To uncover the possible role of epigenetics in gene expression during the transition from seed maturation to seed germination in soybean, the transcriptome of cotyledons from four stages of soybean seed maturation and germination, including mid-late maturation, late maturation, seed dormancy and seed germination, were profiled by Illumina sequencing. For the genes that are quantitatively regulated at the four stages, two antagonistic epigenetic marks, H3K4me3 and H3K27me3, together with the binding of RNA polymerase II, were investigated at the four stages by chromatin immunoprecipitation (ChIP). For 10 out of 16 genes examined, the relative enrichment of histone modification marks (H3K4me3 and H3K27me3) and RNA polymerase II binding on their promoter regions correlates well with their relative expression levels at four stages, suggesting the involvement of epigenetics in transcriptional regulation. A striking finding is that seed germination-specific genes start to show open chromatin (H3K4me3) during late seed maturation although their transcripts do not accumulate, which is further supported by RNA polymerase II binding. Together, our results provide the first evidence that seed germination genes can be primed for transcription (open chromatin and RNA polymerase II binding) during seed maturation, highlighting that the transition from seed maturation to seed germination starts at late seed maturation stages at both the genetic and epigenetic levels. Illumina sequencing of transcripts from cotyledons of mid-maturation (B1 stage) and late maturation (AA1 stage) seeds, whole dry seeds, and cotyledons of seedlings six days after imbibition.
2011-05-10 | E-GEOD-29134 | biostudies-arrayexpress
Project description:Wheat seed germination directly affects wheat yield and quality. The wheat grains mainly include embryo and endosperm, and both play important roles in seed germination, seedling survival and subsequent vegetative growth. ABA can positively regulate dormancy induction and then negatively regulates seed germination at low concentrations. H2O2 treatment with low concentration can promote seed germination of cereal plants. Although various transcriptomics and proteomics approaches have been used to investigate the seed germination mechanisms and response to various abiotic stresses in different plant species, an integrative transcriptome analysis of wheat embryo and endosperm response to ABA and H2O2 stresses has not reported so far. We used the elite Chinese bread wheat cultivar Zhenmai 9023 as material and performed the first comparative transcriptome microarray analysis between embryo and endosperm response to ABA and H2O2 treatments during seed germination using the GeneChip® Wheat Genome Array Wheat seed germination includes a great amount of regulated genes which belong to many functional groups. ABA/H2O2 can repress/promote seed germination through coordinated regulating related genes expression. Our results provide new insights into the transcriptional regulation mechanisms of embryo and endosperm response to ABA and H2O2 treatments during seed germination
2014-12-11 | GSE64030 | GEO
Project description:Elucidating direct roles of natural variation in biological processes has been challenging due to the difficulty in dissecting the causal role of a gene in traits displaying continuous variation. The decision of a seed to germinate is an easily quantifiable binary choice, which makes it an ideal phenotype to assess the contribution of natural variation in adaptation of plants to begin their lifecycle under optimal conditions. seeds must integrate a complex array of environmental signals to begin their lifecycle under optimal conditions. Light availability is a crucial environmental stimulus that promotes germination in many small seed plant species including Arabidopsis thaliana. Upon perception of light by photoreceptors, phytohormones act as internal signals to coordinate germination but the karrikin (KAR) signalling pathway through the HTL/KAI2 receptor is thought to play a rudimentary role in Arabidopsis germination (REF). Here we show that the AtHTL/KAI2 pathway is required and sufficient to promote germination under low light conditions. Activation of the AtHTL/KAI2 receptor by nanomolar Karrikin2 (KAR2) concentrations or inactivation of SMAX1 bypass the light requirement for germination. By performing a screen of A. thaliana accessions that can germinate under low light conditions, we identified an accession from Afghanistan (Ara-1) which misexpressed AtKAI2/HTL and had a nearly identical transcriptional signature to the activation of AtKAI2 upon addition of KAR2 in the reference accession. Our data suggest that AtKAI2 is a central regulator of germination in natural Arabidopsis populations in response to light availability, to optimize germination timing in their ecological niche.
2021-09-01 | GSE161704 | GEO
Project description:Wheat seed germination directly affects wheat yield and quality. The wheat grains mainly include embryo and endosperm, and both play important roles in seed germination, seedling survival and subsequent vegetative growth. ABA can positively regulate dormancy induction and then negatively regulates seed germination at low concentrations. H2O2 treatment with low concentration can promote seed germination of cereal plants. Although various transcriptomics and proteomics approaches have been used to investigate the seed germination mechanisms and response to various abiotic stresses in different plant species, an integrative transcriptome analysis of wheat embryo and endosperm response to ABA and H2O2 stresses has not reported so far. We used the elite Chinese bread wheat cultivar Zhenmai 9023 as material and performed the first comparative transcriptome microarray analysis between embryo and endosperm response to ABA and H2O2 treatments during seed germination using the GeneChip® Wheat Genome Array Wheat seed germination includes a great amount of regulated genes which belong to many functional groups. ABA/H2O2 can repress/promote seed germination through coordinated regulating related genes expression. Our results provide new insights into the transcriptional regulation mechanisms of embryo and endosperm response to ABA and H2O2 treatments during seed germination The six groups including embryo and endosperm response to pure water (CK), ABA and H2O2 were havested respectively, which were CK_embryo (CKem), CK_endosperm (CKe), ABA_embryo (ABAem), ABA_endosperm (ABAe), H2O2_embryo (H2O2em), H2O2_endosperm (H2O2e). Three independent experiments were performed for each group.
2014-12-11 | E-GEOD-64030 | biostudies-arrayexpress
Project description:Salinity is one of the main environmental stresses worldwide limiting soybean growth and yield. Seed imbibition and radical emergence are generally less affected by salinity in soybean. Towards unraveling the mechanisms underlying salt tolerance in soybean at germination stage, a comprehensive quantitative proteomic analysis of proteins from soybean embryonic axis during germination sensu stricto (GSS) under saline conditions was performed. Application of 100 and 200 mmol L-1 NaCl at GSS was significantly accompanied by the change in abundance (>2-fold) of 97 and 75 proteins, respectively. Most of these proteins were involved in three major functions, namely stress response and defense, protein turnover and protection and primary metabolism. Our results pave the way towards the identification of suitable biomarkers useful for improving salt tolerance in soybean.
2016-08-15 | MSV000080044 | MassIVE