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| Status |
Public on Mar 01, 2023 |
| Title |
RRC1 is required for epidermal phyB siganling by maintaining the circadian rhythm by suppressing the alternative splicing of core clock genes. |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose : The goal of this study is to identify transcriptome changes induced by rrc1 mutation under red light. We compared the transcriptome of MLB (ML1pro::phyB-GFP/phyB-9) with EMS27 grown either in darkness or continuous red light to investigate the genes that the expression and the splicing patterns are regulated by epidermal phyB and/or RRC1. The transcriptome of Col-0 and rrc1-689 was further compared to enlarge the list of putative splicing targets of RRC1.
Methods : Seedlings grown under either monochromatic red light (19 μmol/m2s) or darkness for 60 hours on 1/2 MS agar plates were sampled. Total RNAs were extracted using the Spectrum Plant Total RNA Extraction Kit (Sigma-Aldrich). RNA libraries were generated and sequenced on the Illumina NextSeq 500 platform. The analysis was performed with three biological replicates. Roughly 90% of the sequencing reads were mapped to specific loci on the Arabidopsis TAIR10 reference genome using the TopHat pipeline. Mapped sequencing files were further processed with Aspli1.9 R package for Differentially Expressed Gene (DEG) analysis and Differentially Spliced Gene (DSG) analysis.
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| Overall design |
Epidermal phyB-induced gene expression change was identified by comparing Dark-grown MLB with Red-grown MLB, while RRC1-induced gene expression or splicing change was identified by comparing Red-grown control line (Col-0 or MLB) with Red-grown rrc1 mutant (rrc1-689 or EMS27). All samples in triplicates.
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| Contributor(s) |
Kim H, Kim J, Choi G |
| Citation(s) |
36651061 |
| BioProject |
PRJNA817881 |
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| Submission date |
Mar 21, 2022 |
| Last update date |
May 31, 2023 |
| Contact name |
hanim kim |
| E-mail(s) |
qkfkvkvk93@gmail.com
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| Phone |
82-010-4311-0332
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| Organization name |
KAIST
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| Department |
biological science
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| Street address |
Daehak-ro 291
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| City |
Daejeon |
| ZIP/Postal code |
34141 |
| Country |
South Korea |
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| Platforms (1) |
| GPL19580 |
Illumina NextSeq 500 (Arabidopsis thaliana) |
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| Samples (24)
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