Transcript profiles of developing Arabidopsis dgat1-1 mutant seed
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA508214 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8275170_1.fastq.gz | Fastqsanger.gz | |||
| SRR8275170_2.fastq.gz | Fastqsanger.gz | |||
| SRR8275180_1.fastq.gz | Fastqsanger.gz | |||
| SRR8275180_2.fastq.gz | Fastqsanger.gz | |||
| SRR8275190_1.fastq.gz | Fastqsanger.gz |
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Project description:Global transcript profiling of Arabidopsis dgat1-1 seed at different stages of embryo development was used to identify differentially expressed genes in the mutant compared to wild-type (Col-0) seed. These genes provided information about the remodeling of lipid metabolism and TAG synthesis in response to the lack of DGAT1 activity.
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Project description:Inhibition of Diacylglycerol O-acyltransferase 1 (DGAT1) has been a mechanism of interest for metabolic disorders. DGAT1 inhibition has been shown to be a key regulator in an array of metabolic pathways; however, based on the DGAT1 KO mouse phenotype the anticipation is that pharmacological inhibition of DGAT1 could potentially lead to skin related adverse effects. One of the aims in developing small molecule DGAT1 inhibitors that target key metabolic tissues is to avoid activity on skin-localized DGAT1 enzyme. In this report we describe a modeling-based approach to identify molecules with physical properties leading to differential exposure distribution. In addition, we demonstrate histological and RNA based biomarker approaches that can detect sebaceous gland atrophy pre-clinically that could be used as potential biomarkers in a clinical setting.
2014-02-20 | GSE49375 | GEO
Project description:Inhibition of Diacylglycerol O-acyltransferase 1 (DGAT1) has been a mechanism of interest for metabolic disorders. DGAT1 inhibition has been shown to be a key regulator in an array of metabolic pathways; however, based on the DGAT1 KO mouse phenotype the anticipation is that pharmacological inhibition of DGAT1 could potentially lead to skin related adverse effects. One of the aims in developing small molecule DGAT1 inhibitors that target key metabolic tissues is to avoid activity on skin-localized DGAT1 enzyme. In this report we describe a modeling-based approach to identify molecules with physical properties leading to differential exposure distribution. In addition, we demonstrate histological and RNA based biomarker approaches that can detect sebaceous gland atrophy pre-clinically that could be used as potential biomarkers in a clinical setting. Mice were treated with DGAT1 inhibitors for 14 days and dorsal skin biopsies (3-5 mm^2) were taken. RNA was profiled on custom Affymetrix microarrays. The primary goal was to identify robust and consistent biomarkers of DGAT1 inibition in skin.
2014-02-20 | E-GEOD-49375 | biostudies-arrayexpress
Project description:Enhanced fatty acid (FA) synthesis and uptake underpin the sustained membrane biogenesis and ATP production required for melanoma cell growth and division1-4. However, to thrive, melanoma cells must avoid a potential reduction in cell growth signalling, rampant reactive oxygen species (ROS) generation, and the build-up of toxic lipid species that can accompany excess free FA5. Here, we uncover and address the significance of frequent amplification and up-regulation of the Diacylglycerol O-acyltransferase 1 (DGAT1) gene in melanoma, whose encoded product catalyses the final step of Triacyglyceride (TAG) synthesis. Consistent with the classification of DGAT1 as an oncogene, we found that forced DGAT1 expression in p53 mutant zebrafish melanocytes was sufficient to induce melanoma, and accelerated melanoma progression initiated by co-expression of oncogenic BRAF or NRAS. Regarding DGAT1 function in human melanoma cells, its depletion, or alternatively pharmacological inhibition, suppressed mTOR-S6K signalling and increased levels of acyl carnitine species— FA derivatives that are the limiting substrate for FA oxidation (FAO). In turn, increased FAO induced mitochondrial malfunction, ROS generation, and lipid peroxidation. However, the resultant oxidative stress induced NRF2 and SESTRIN2 (SESN2) expression, which limited the extent of cell death. Conversely, DGAT1 over-expression enhanced mTOR-S6K signalling and cell growth, and protected against ROS, particularly in hypoxic conditions. Together, our data establish DGAT1 as a bona fide oncogene essential in melanoma cells for enabling FA accumulation.
2023-03-10 | PXD017487 | Pride
Project description:Clear cell renal cell carcinoma (ccRCC) represents a lethal disease and classically resistant to cytotoxic chemotherapy, highlighting the importance of identifying new therapeutic vulnerabilities. We performed a functional siRNA screening for all 2-oxoglutarate (2-OG)-dependent enzymes in ccRCC using 3-D soft agar colony formation assay, and combined with TCGA data, we identified Jumonji domain-containing 6 (JMJD6) as an essential gene for ccRCC tumorigenesis. Downregulation of JMJD6 abolished ccRCC colony formation in vitro and inhibited orthotopic tumor growth in vivo. Integrated analyses of ChIP-seq and RNA-seq identified that JMJD6 can transcriptionally regulate the expression of diacylglycerol O-acyltransferase 1 (DGAT1) by co-occupying the target gene promoter with H3K4me3. Downregulation of JMJD6 caused decreased expression of DGAT1 at both mRNA and protein level. Inhibition or depletion of DGAT1 induced decreased cell growth in vitro or inhibited tumor growth in vivo. Mechanistically, decreased DGAT1 caused decreased LD formation in ccRCC, while restoration of JMJD6 expression can restore DGAT1 level, and LD formation as well as cell growth. In summary, JMJD6 is essential for ccRCC lipid storage and tumorigenesis through a DGAT1-dependent signaling. Therefore, the JMJD6-DGAT1 axis serves as a potential therapeutic avenue for ccRCC.
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2009-09-25 | E-GEOD-16754 | biostudies-arrayexpress
Project description:This file contains gene microarray data from FACS purified mouse memory phenotype CD4+ T cells (CD44hiCD45RBloCD25-), which were isolated from lymph node and spinal cord tissues of mice with experimental autoimmune encephalomyelitis (EAE), a widely studied model of human multiple sclerosis (MS). Memory phenotype CD4+ T cells infiltrating the CNS during EAE expressed high levels of mRNA for Dgat1 encoding diacylglycerol-O-acyltransferase-1 (DGAT1). We studied the biology of DGAT1 in EAE models and in assays of T cell differentiation and function.
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Project description:Transfected siRNAs and miRNAs regulate numerous transcripts that have only limited complementarity to the active strand of the RNA duplex. This process reflects natural target regulation by miRNAs, but is an unintended (“off-target”) consequence of siRNA-mediated silencing. Here we demonstrate that this unintended off-target silencing is widespread, and occurs in a manner reminiscent of target silencing by miRNAs. A high proportion of unintended transcripts silenced by siRNAs showed 3’ UTR sequence complementarity to the seed region of the siRNA. Base mismatches within the siRNA seed region reduced the set of original off-target transcripts but generated new sets of silenced transcripts with sequence complementarity to the mismatched seed sequence. An inducible shRNA silenced a subset of transcripts that were silenced by an siRNA of the same sequence, demonstrating that unintended silencing is sequence-mediated and is independent of delivery method. In all cases, off-target transcript silencing was accompanied by loss of the corresponding protein and occurred with similar dependence on siRNA concentration as silencing of the target transcript. These results demonstrate that short stretches of sequence complementarity to the seed region of the siRNA are key to the silencing of unintended transcripts, and that this limits the specificity of siRNA-mediated transcript silencing. Because these off-target events are sequence-dependent, inclusion of multiple independent siRNAs to the target of interest can help to distinguish true positives from false positives in functional genetic analyses. Keywords: siRNA, RNAi, sequence alignment, off-target, seed region
2006-09-12 | GSE5814 | GEO
Project description:Purpose: To elucidate the physiological and molecular mechanisms underlying seed development, we conducted a genome-wide transcriptional profiling of developing seeds of ‘Sarsyun’ at four different time points (21, 28, 35, and 42 DAF). 34,423 contigs from four different developing seeds (21, 28, 35, and 42 DAF) were analyzed for transcript abundance and changes to the timing of transcript abundance in relation to the accumulation of seed storage products. Most genes involved in seed photosynthesis and carbohydrate metabolism were highly expressed at 21 or 28 DAF and were subsequently downregulated. Expression of genes coding for oleosins and fatty acid synthesis and elongation markedly increased at 28 DAF through 35 DAF, respectively, remaining high thereafter. Expression of major storage protein genes increased at 28 or 35 DAF. Overall, our results showed that dynamic changes to transcript abundance of most genes in relation to seed storage products occurred between 28 and 35 DAF.
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Project description:Common bean (Phaseolus vulgaris L.) is the most consumed grain legume in developing countries in Latin America and Sub-Saharan Africa1. Like other legumes, common bean seeds are rich in protein, carbohydrates, fibers and other health-promoting phenolic compounds thus being vital for food security and income source for local small farmers2. Seed quality traits depend on accumulation of various storage molecules during the seed development (SD) process and influenced by the genotype and adaptive changes to environment3. Concerning common bean, there is still a lack of a deeper molecular knowledge of SD that is hampering the development of new biotech approaches for seed trait modulation and could timely address challenges of agriculture or industry. Our present work aims to unravel the molecular mechanisms underlying SD using a proteomic approach. To achieve this goal, we characterized SD in terms biomass, seed length and weight in the genotype SER16, one of the most promissory drought-resistant release of the CIAT-CGIAR. Seed samples were collected at the 4 main SD stages: Late-Embryogenesis (10 days after anthesis, d.a.a.), Early (20 d.a.a.) and Late Maturation (30 d.a.a.) and Desiccation (40 d.a.a.). The analysis of bean proteome was conducted using a gel-free proteomic analysis (LC-MS/MS) under the scope of EU-FP7-PRIME-XS project. A total of 410 unique proteins were differentially expressed throughout the 4 major seed development stages, in which most of the identified proteins belong in the ‘protein metabolism’ (31,98%) functional category, that includes synthesis, regulation, folding. Other functional categories are represented such as carbohydrate and lipid metabolism (11,26%) and stress/defense and redox metabolism (11,04%). We identified 93 proteins were unique to the first (10-20 d.a.a.), 22 to the second (20-30 d.a.a.) and 40 to the last (30-40 d.a.a.) phase transition, reflecting the major biological processes occurring at this specific seed developmental stage. This study will contribute to reveal key metabolic pathways and mechanisms with potential role in modulating common bean seed development and quality traits.
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