Metabolomics and Transcriptomics Reveal Key Metabolism Pathways of Giant Embryo Development in Rice
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ABSTRACT:
PROVIDER: PRJNA725152 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14324663_1.fastq.gz | Fastqsanger.gz | |||
| SRR14324663_2.fastq.gz | Fastqsanger.gz | |||
| SRR14324664_1.fastq.gz | Fastqsanger.gz | |||
| SRR14324664_2.fastq.gz | Fastqsanger.gz | |||
| SRR14324665_1.fastq.gz | Fastqsanger.gz |
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Project description:Rice embryos are rich in high-quality protein, fat, vitamins and minerals, representing the most important nutritional part of brown rice. However, the molecular mechanism of rice embryo development is poorly understood. In this study, map-based cloning, metabolomics, and transcriptomics were applied to explore the giant embryo rice cultivar Dapeimi grown under natural conditions. The map-based cloning results demonstrated that Dapeimi is a novel allelic mutant of GE, and the functional mutation site is a single cytosine deletion in the exon1, which differed from the findings of previous reports. The identification and analysis of differential metabolites indicated that plants lacking the GE mainly promoted amino acid metabolism, energy metabolism, and lipid metabolism pathways in the rice embryo. Changes of gene expression in related metabolic regulatory networks were analyzed, and substantial changes in the transcriptome supported the metabolomics results. By analyzing rice embryo development through a combination of strategies, this research contributes to a greater understanding of the molecular mechanism of rice embryo development, and provides a theoretical foundation for improving rice nutrition and breeding high-nutrition varieties.
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Project description:Rice embryos are rich in high-quality protein, lipid, vitamins and minerals, representing the most important nutritional part of brown rice. However, the molecular mechanism of rice embryo development is poorly understood. In this study, two rice cultivars with contrasting embryo size (the giant embryo cultivar Dapeimi and the normal embryo cultivar 187R) were used to explore excellent genes controlling embryo size, and the developed near-isogenic lines (NILs) (NIL-D, which has the giant embryo phenotype, and its matching line, NIL-X) were used to explore transcript and metabolic properties in the earlier maturation stage of giant embryo development under natural conditions. The map-based cloning results demonstrated that Dapeimi is a novel allelic mutant of the rice GIANT EMBRYO (GE) gene, and the functional mutation site is a single cytosine deletion in the exon1. A total of 285 differentially accumulated metabolites (DAMs) and 677 differentially expressed genes (DEGs) were identified between NIL-D and NIL-X. The analysis of DAMs indicated that plants lacking GE mainly promoted energy metabolism, amino acid metabolism, and lipid metabolism pathways in the rice embryo. Pearson correlation coefficient showed that 300 pairs of gene-metabolites were highly correlated. Among them, OsZS_02G0528500 and OsZS_12G0013700 were considered to be key genes regulating L-Aspartic acid and L-Tryptophan content during rice giant embryo development, which are promising to be good candidate genes to improve rice nutrition. By analyzing rice embryo development through a combination of strategies, this research contributes to a greater understanding of the molecular mechanism of rice embryo development, and provides a theoretical foundation for breeding high-nutrition varieties.
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Project description:"Shangshida NO.5" is a giant embryo mutant resulting from giant embryo gene (GE) dysfunction in "Chao2-10" rice. Here, we compared the antihypertensive effects of "Chao2-10" brown rice (C2-10), "Shangshida NO.5" brown rice (GER), and pre-germinated "Shangshida NO.5" brown rice (PGER) in spontaneously hypertensive rats (SHR). Male SHR at 6 weeks of age were divided into four groups and were fed with (a) a control diet (control), (b) a 40% C2-10-supplemented diet (C2-10), (c) a 40% GER-supplemented diet (GER), or (d) a 40% PGER-supplemented diet (PGER) for 8 weeks, and their physiological and biochemical parameters were measured. The results showed that the C2-10-, GER-, and PGER-supplemented diets significantly decreased systolic blood pressure (SBP) and diastolic blood pressure (DBP) during the experiment. At the end of the experimental period, the SBP and DBP of the C2-10, GER, and PGER groups were 7.6, 23.3, and 31.1 mmHg and 9.8, 21.1, and 29 mmHg lower than those in the control group, respectively, suggesting the GER and PGER diets were better able to inhibit blood pressure elevation than the C2-10 diet. The serum creatinine levels in the C2-10, GER, and PGER groups and the blood urea nitrogen content in the PGER group were significantly lower than those of the control group, indicating that C2-10-, GER-, and especially PGER-supplemented diets improved renal function. In addition, the antioxidant activity of the C2-10 group and especially of the GER and PGER groups also improved. The above results suggest that "Shangshida NO.5" rice, particularly pre-germinated rice, is a good dietary supplement for preventing the development of hypertension.
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Project description:We characterized the mouse trophoblast giant cell epigenome and gene expression profiles. We then compared these data to our data on underrepresentation in the polyploid trophoblast giant cells. We profiled 5 histone modifications (+ chromatin input) using ChIP-Seq, and digital expression profiles (3' RNA-Seq) for trophoblast giant cells derived from mouse. Furthermore, we profiled digital expression profiles (3' RNA-Seq) for in vivo trophoblast giant cells samples from e9.5 wildtype mouse trophoblast giant cells. We found that underrepresented domains in trophoblast giant cells are enriched for repressive marks and anti-correlate with active marks and transcription.
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Project description:We characterized the mouse trophoblast giant cell epigenome and gene expression profiles. We then compared these data to our data on underrepresentation in the polyploid trophoblast giant cells.
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Project description:Giant cell granulomas of the jaws often occur sporadically as single central or peripheral lesions. They are characterized by KRAS, FGFR1, or TRPV4 somatic mutations, the latter occurring exclusively in the central form. Less commonly, multiple giant cell lesions can develop in the context of syndromes such as cherubism, which is an autosomal dominant bone disease. Morphologically, giant cell granulomas can closely resemble other giant cell-rich lesions such as non-ossifying fibroma and aneurysmal bone cyst, and to a minor extent giant cell tumour of bone and chondroblastoma. The epigenetic basis of these giant cell-rich tumours is unclear and, recently, DNA methylation profile has been shown to be clinically useful for the diagnosis of other tumour types, including brain tumours as well as bone and soft tissue sarcomas. Therefore, we aimed to assess the DNA methylation profile of central and peripheral sporadic giant cell granulomas of the jaws and cherubism to test whether DNA methylation patterns can help to distinguish these entities. Additionally, we further compared the DNA methylation profile of these lesions with those of other giant cell-rich mimics to investigate if the microscopic similarities extend to the epigenetic level. Our results showed that central and peripheral sporadic giant cell granulomas of the jaws and cherubism share a related DNA methylation pattern with that of peripheral sporadic giant cell granulomas and cherubism appearing slightly distinct, while central sporadic giant cell granulomas show overlap with both of the former. Non-ossifying fibroma, aneurysmal bone cyst, giant cell tumour of bone, and chondroblastoma, on the other hand, have distinct methylation patterns. Therefore, DNA methylation profiling is currently not capable of clearly distinguishing sporadic and cherubism-associated giant cell lesions of the jaws. Conversely, it could discriminate sporadic giant cell granulomas from their giant cell-rich mimics.
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