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Differentially expressed genes between WT and AtC3H17-overexpressing transgenic plants

ABSTRACT: We characterized the biological and molecular functions of AtC3H17, a unique Arabidopsis gene encoding a non-tandem CCCH zinc finger protein, in plant development. To investigate the downstream regulatory mechanisms of AtC3H17, whole genome microarray expression profiling was carried out. The experiment was designed to identify differentially expressed genes between WT and AtC3H17-overexpressing transgenic plants (AtC3H17 OXs) grown for 14 days under SD growth conditions. Interestingly, the most up-regulated genes were 12S seed storage globulin genes, CRUCIFERIN A (CRA1) and CRUCIFERIN 3 (CRU3), and seed oil-body protein genes such as OLEOSIN 1 (OLEO1) and OLEO2 in AtC3H17 OXs compared with WT. We performed quantitative RT-PCR and confirmed that transcription levels of CRU3, OLEO1, OLEO2, and 2S seed storage albumin 1 (At2S1) were higher in AtC3H17 OX seedlings than in WT seedlings.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE75702 | GEO | 2015/12/05

SECONDARY ACCESSION(S): PRJNA305103

REPOSITORIES: GEO

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Differentially expressed genes between WT and AtC3H17-overexpressing transgenic plants

Project description:We characterized the biological and molecular functions of AtC3H17, a unique Arabidopsis gene encoding a non-tandem CCCH zinc finger protein, in plant development. To investigate the downstream regulatory mechanisms of AtC3H17, whole genome microarray expression profiling was carried out. The experiment was designed to identify differentially expressed genes between WT and AtC3H17-overexpressing transgenic plants (AtC3H17 OXs) grown for 14 days under SD growth conditions. Interestingly, the most up-regulated genes were 12S seed storage globulin genes, CRUCIFERIN A (CRA1) and CRUCIFERIN 3 (CRU3), and seed oil-body protein genes such as OLEOSIN 1 (OLEO1) and OLEO2 in AtC3H17 OXs compared with WT. We performed quantitative RT-PCR and confirmed that transcription levels of CRU3, OLEO1, OLEO2, and 2S seed storage albumin 1 (At2S1) were higher in AtC3H17 OX seedlings than in WT seedlings. Differentially expressed genes between WT and AtC3H17 OX at 14 days after germination under SD conditions (8-h-light and 16-h-dark cycle) were explored in whole genome level. Two AtC3H17 OX samples were compared to WT sample as a control.

2015-12-05 | E-GEOD-75702 | biostudies-arrayexpress

Arabidopsis thaliana: wild type vs. scl15 mutant

Project description:Epigenetic regulation of gene expression is critical for controlling embryonic properties during the embryo-to-seedling phase transition. Here we report that a HISTONE DEACETYLASE19 (HDA19)-associated regulator, SCARECROW LIKE15 (SCL15), is essential for repressing the seed maturation program in vegetative tissues. SCL15 is expressed and GFP-tagged SCL15 predominantly localizes to the vascular bundles, particularly in the phloem companion cells and neighbouring specialized cells. Mutation of SCL15 leads to a global shift in gene expression in seedlings to a profile resembling late embryogenesis in seeds. In scl15 seedlings, many genes involved in seed maturation are markedly derepressed and 12S globulin accumulates; this is correlated with elevated levels of histone acetylation at a subset of seed-specific loci. SCL15 physically interacts with HDA19 and direct targets of HDA19-SCL15 association are identified. These studies revealed that SCL15 acts as an HDA19-associated regulator to repress embryonic traits in seedlings.

2015-03-30 | GSE67395 | GEO

Arabidopsis thaliana: wild type vs. scl15 mutant

2015-03-30 | E-GEOD-67395 | biostudies-arrayexpress

Ribosome profiling reveals changes in translational status of soybean transcripts during immature cotyledon development

Project description:To understand translational capacity on a genome-wide scale across three developmental stages of immature soybean seed cotyledons, ribosome profiling was performed in combination with RNA sequencing and cluster analysis. Transcripts representing 216 unique genes demonstrated a higher level of translational activity in at least one stage by exhibiting higher translational efficiencies (TEs) in which there were relatively more ribosome footprint sequence reads mapping to the transcript than were present in the control total RNA sample. The majority of these transcripts were more translationally active at the early stage of seed development and included 12 unique serine or cysteine proteases and 16 2S albumin and low molecular weight cysteine-rich proteins that may serve as substrates for turnover and mobilization early in seed development. It would appear that the serine proteases and 2S albumins play a vital role in the early stages. In contrast, our investigation of profiles of 19 genes encoding high abundance seed storage proteins, such as glycinins, beta-conglycinins, lectin, and Kunitz trypsin inhibitors, showed that they all had similar patterns in which the TE values started at low levels and increased approximately 2 to 6-fold during development. The highest levels of these seed protein transcripts were found at the mid-developmental stage, whereas the highest ribosome footprint levels of only up to 1.6 TE were found at the late developmental stage. These experimental findings suggest that the major seed storage protein coding genes are primarily regulated at the transcriptional level during normal soybean cotyledon development. Finally, our analyses also identified a total of 370 unique gene models that showed very low TE values including over 48 genes encoding ribosomal family proteins and 95 gene models that are related to energy and photosynthetic functions, many of which have homology to the chloroplast genome.

2018-03-23 | GSE66580 | GEO

Differentially expressed genes between WT and HRE1α OX, WT and HRE1β OX, and WT and AtRH17 OX

Project description:Differentially expressed genes between WT and HRE1α OX, WT and HRE1β OX, and WT and AtRH17 OX

| PRJNA638540 | ENA

Transcription profiling of developing pea cotyledons over-expressing VfAAP1

Project description:Nitrogen application to legume seeds regulates seed metabolism and composition. In order to improve nitrogen flux into the embryo, the Vicia faba amino acid permease VfAAP1 (Miranda et al. Amino acid permeases in developing seeds of Vicia faba L.: expression precedes storage protein synthesis and is regulated by amino acid supply. Plant J 2001 28: 61-72) was expressed in pea under control of the seed-specific LeB4 promotor (Bäumlein et al. Cis-analysis of a seed protein gene promoter: the conservative RY repeat CATGCATG within legumin box is essential for tissue-specific expression of a legumin gene. Plant J 1992 2: 233-239). Several transgenic lines have been generated. Mature seeds of the homozygous marker gene-free line AAP14/10 showed an increase in amino acid supply, seed nitrogen and protein content due to higher globulin fraction. The effect of VfAAP1 was tested under field conditions in two growing periods, 2005 and 2006, and the data could be confirmed. Over-expression of VfAAP1 interferes with storage protein metabolism and alters fluxes of nitrogen during seed growth. The influence of VfAAP1 on altered gene expression in developing cotyledons was analysed using a 6k-Oligo-microarray. Four developmental stages (18, 22, 26 and 30 DAP) from seeds, grown 2006, of the transgenic line AAP14/10 were hybridized against wildtype control.

2008-05-01 | E-MEXP-1557 | biostudies-arrayexpress

Transcript abundance data from seedlings of wild-type Ws and ged1 (greening after extended darkness 1) mutant

Project description:An Arabidopsis mutant showing an altered ability to green on illumination after extended periods of darkness has been isolated in a screen for genomes uncoupled (gun) mutants. Following illumination for 24 h, 10-day-old dark-grown mutant seedlings accumulated 5 times more chlorophyll than wild-type seedlings and this was correlated with differences in plastid morphology observed by transmission electron microscopy. The mutant has been named greening after extended darkness 1 (ged1). We used microarrays to detail the global profiles of transcript abundances in the mutant in comparison to the wild type. Microarray analysis showed much lower amounts of transcripts of genes encoding seed storage proteins, oleosins and late embryogenesis abundant (LEA) proteins in 7-day-old seedlings of ged1 compared to wild type. RNA-gel-blot analyses confirmed very low levels of transcripts of seed protein genes in ged1 seedlings grown for 2-10 days in the dark, and showed higher amounts of transcripts of photosynthesis-related genes in illuminated 10-day-old dark-grown ged1 seedlings compared to wild type. Keywords: Genotype

2008-08-12 | GSE12401 | GEO

Quantitative proteomic analyses reveal the dynamics of protein and amino acid accumulation in soybean seed from early to late stages of seed filling

Project description:Global analyses of protein profiling during seed development in soybean is paramount to understand the metabolic processes that correspond to the differential protein accumulation and hence seed quality in soybean. Using high throughput tandem mass tag (TMT) based tagging techniques, we identified 4,172 proteins in three stages namely early, mid, and late seed filling. We mapped the identified metabolic pathways associated with seed filling. An elevated level of several kinases was observed from the early to mid-stages of seed filling, indicating that protein phosphorylation was a major event that occurred during this period. The early to late stages of seed filling was characterized by an increased level of proteins associated with the cell wall, oil, and vacuolar-related processes. Twenty-five seed storage protein genes located on 12 different chromosomes were identified. Among the seed storage proteins, 7S (B-subunit) and 11S (Gy3, Gy4, Gy5) exhibited steadily increased abundance from early to late-stage seed development, whereas, 2S albumin exhibited decreased abundance during the same period. An increased abundance of proteases, senescence-associated proteins and, oil synthesis proteins was observed from the mid to late stages of seed filling. The mid to late stages of seed filling were also characterized by a lower abundance of transferases, transporters, Kunitz family trypsin, and protease inhibitors. Two enzymes associated with methionine synthesis exhibited lower abundance from early to late stages. This study unveiled the expression of several key enzymes/proteins associated with amino acid and protein syntheses and their accumulation during seed development which will assist scientists and breeders to develop new value-added soybeans with improved protein quality.

2021-06-06 | MSV000087577 | MassIVE

Fate specific mRNA storage in seeds

Project description:We analyzed the monsome and polysome associated transcripts of seeds and seedlings and identify transcripts specifically associated with monosome and polysome in both tissues The aim was to generate a global view about the state of mRNA storage in the seeds and the their fate during seed germination.

2019-09-18 | GSE76905 | GEO

Project description:Targeted sequencing of sorghum seed storage protein genes

| PRJEB38186 | ENA

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