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| Status |
Public on Sep 10, 2016 |
| Title |
RNA-seq analysis of the transcriptional response to blue and red light in the extremophilic red alga, Cyanidioschyzon merolae |
| Organism |
Cyanidioschyzon merolae |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Light is one of the main environmental cues that affects the physiology and behavior of many organisms. The effect of light on genome-wide transcriptional regulation has been well-studied in green algae and plants, but not in red algae. Cyanidioschyzon merolae is used as a model red algae, and is suitable for studies on transcriptomics because of its compact genome with a relatively small number of genes. In addition, complete genome sequences of the nucleus, mitochondrion, and chloroplast of this organism have been determined. Together, these attributes make C. merolae an ideal model organism to study the response to light stimuli at the transcriptional and the systems biology levels. Previous studies have shown that light significantly affects cell signaling in this organism, but there are no reports on its blue light- and red light-mediated transcriptional responses. We investigated the direct effects of blue and red light at the transcriptional level using RNA-seq. Blue and red light were found to regulate 35% of the total genes in C. merolae. Blue light affected the transcription of genes involved protein synthesis while red light specifically regulated the transcription of genes involved in photosynthesis and DNA repair. Blue or red light regulated genes involved in carbon metabolism and pigment biosynthesis. Overall, our data showed that red and blue light regulate the majority of the cellular, cell division, and repair processes in C. merolae.
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| Overall design |
mRNA profiles of wild type C. merolae 10D cells were generated under blue light, red light and complete darkness conditions by deep sequencing, in two biological replicates, using Illumina MiSeq platform.
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| Contributor(s) |
Tardu M, Dikbas UM, Baris I, Kavakli IH |
| Citation(s) |
27614431 |
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| Submission date |
Jun 28, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
mehmet tardu |
| E-mail(s) |
mtardu@umich.edu
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| Organization name |
University of Michigan
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| Department |
Chemistry
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| Lab |
Koutmou Lab
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| Street address |
930 N University Ave
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| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
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| Platforms (1) |
| GPL22093 |
Illumina MiSeq (Cyanidioschyzon merolae) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA327116 |
| SRA |
SRP077524 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE83828_Gene_expression_data.xlsx |
1.0 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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