RNA-seq analysis of the transcriptional response to blue and red light in the extremophilic red alga, Cyanidioschyzon merolae.
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 lights were found to regulate 35 % of the total genes in C. merolae. Blue light affected the transcription of genes involved in 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.
Computational Science and Engineering, Koc University, Rumeli Feneri Yolu, Sariyer, Istanbul, Turkey.
Mehmet
M
Tardu
Molecular Biology and Genetics, Koc University, Rumeli Feneri Yolu, Sariyer, Istanbul, Turkey.
Ugur Meric
UM
Dikbas
Molecular Biology and Genetics, Koc University, Rumeli Feneri Yolu, Sariyer, Istanbul, Turkey.
Ibrahim
I
Baris
Computational Science and Engineering, Koc University, Rumeli Feneri Yolu, Sariyer, Istanbul, Turkey. hkavakli@ku.edu.tr.|Molecular Biology and Genetics, Koc University, Rumeli Feneri Yolu, Sariyer, Istanbul, Turkey. hkavakli@ku.edu.tr.|Chemical and Biological Engineering, Koc University, Rumeli Feneri Yolu, Sariyer, Istanbul, Turkey. hkavakli@ku.edu.tr.
Ibrahim Halil
IH
Kavakli
D002244:Carbon / Q000378:metabolism; D002736:Chloroplasts / Q000235:genetics / Q000528:radiation effects; D000071825:Extremophiles / Q000235:genetics / Q000528:radiation effects; D018745:Genome, Plant / Q000528:radiation effects; D059014:High-Throughput Nucleotide Sequencing; D008027:Light; D008928:Mitochondria / Q000235:genetics; D010788:Photosynthesis / Q000235:genetics* / Q000528:radiation effects; D010802:Phylogeny; D010860:Pigments, Biological / Q000096:biosynthesis; D000461:Rhodophyta / Q000235:genetics* / Q000528:radiation effects; D059467:Transcriptome / Q000235:genetics* / Q000528:radiation effects
D010860:Pigments, Biological; D002244:Carbon
Blue light; Cyanidioschyzon merolae; Gene regulation; RNA-seq; Red algae; Red light; Transcriptomics