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| Status |
Public on Mar 16, 2021 |
| Title |
Comparison of transcriptomic adjustments to availability of sugar, cellular energy, and oxygen in germinating rice embryos |
| Organism |
Oryza sativa |
| Experiment type |
Expression profiling by array
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| Summary |
During germination, the availability of sugars, oxygen, or cellular energy fluctuates under dynamic environmental conditions, and the global RNA profile of rice genes can be affected by their availabilities. In the aerobically germinating rice embryos, most sugar-regulated genes are responsive to low energy and anaerobic conditions, indicating that sugar-regulation is closely associated with energy and anaerobic signaling. The interference pattern of sugar-regulation by either anaerobic or low energy conditions indicates that induction is likely the more prevalent regulatory mechanism than repression for the alteration in the expression of sugar-regulated genes in aerobically germinating rice embryos. Among the aerobically sugar-regulated genes, limited genes exhibit sugar regulation under anaerobic conditions, indicating that anaerobic conditions strongly influence sugar-regulated gene expression. Anaerobically responsive genes are highly overlapped with low-energy responsive genes. In particular, the expression levels of anaerobically downregulated genes are consistent with those induced by low energy-conditions, suggesting that anaerobic downregulation results from the prevention of aerobic respiration due to the absence of the final electron acceptor, i.e., molecular oxygen. It was noted that abscisic acid (ABA)-responsive genes were over-representative of the genes upregulated under low energy conditions, in contrast to the downregulated genes. This suggests that either ABA itself or upstream signaling components of the ABA signaling pathway are likely to be involved in the signaling pathways activated by low energy conditions.
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| Overall design |
To test sugar-responsive gene expression in germinating rice embryos under either aerobic or anaerobic conditions, we analyzed saliva from 6 rice samples the Affymetrix RJpGene-1_1-st-v1. Data was processed by Affymetrix Gene Expression Array Computational Tool. Two techinical replicates were performed.
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| Contributor(s) |
Lim M, Hwang Y |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Mar 15, 2021 |
| Last update date |
Mar 19, 2021 |
| Contact name |
Yeon-Ki Kim |
| E-mail(s) |
kim750a11@gmail.com
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| Phone |
82-31-321-6351
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| Organization name |
GreenGene Biotech Inc.
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| Department |
GreenGene Biotech Inc.
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| Lab |
Genomics & Genetics Ins.
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| Street address |
38-2 Namdong
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| City |
Yongin |
| State/province |
Kyonggido |
| ZIP/Postal code |
449-728 |
| Country |
South Korea |
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| Platforms (1) |
| GPL25932 |
[RJPGene-1_1-st] Affymetrix Rice (US) Gene 1.0 ST Array [transcript (gene) version] |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA714560 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE168915_RAW.tar |
69.3 Mb |
(http)(custom) |
TAR (of CEL, CHP) |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
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