Analysis in C. merolae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA362821 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5194840_1.fastq.gz | Fastqsanger.gz | |||
| SRR5194840_2.fastq.gz | Fastqsanger.gz | |||
| SRR5194834_1.fastq.gz | Fastqsanger.gz | |||
| SRR5194834_2.fastq.gz | Fastqsanger.gz | |||
| SRR5194835_1.fastq.gz | Fastqsanger.gz |
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Project description:RNA-seq experiment in wildtype Cyanidioschyzon merolae cultures. The aim of the experiment was the comparison of the transcriptomic activity with H3K27me3 profile. The results revealed a negative correlation between expression and H3K27me3 occupancy. The experiment contains 3 biological replicates.
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Project description:Transcriptomic analysis in C. merolae
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Project description:Chromatin immunopreciptation coupled with Illumina sequencing to H3K27me3 occupancy in model red alga, C. merolae. The results revealed preferential abundance over repetitive elements, instead of the genes. This histone mark enriches also over subtelomeric and telomeric regions of the chromosomes. C. merolae H3K27me3 has a canonical repressive function as in the higher eukaryotes and forms differential clusters over the gene bodies with different levels of repression. Overall, our study provides important insights toward the function of chromatin-mediated repression in the evolutionary aspect.
2017-04-01 | GSE93913 | GEO
Project description:Cyanidioschyzon merolae (C. merolae) is an acidophilic red alga growing in a naturally low carbon dioxide (CO2) environment. Although it uses a ribulose 1,5-bisphosphate carboxylase/oxygenase with high affinity for CO2, the survival of C. merolae relies on functional photorespiratory metabolism. In this study, we quantified the transcriptomic response of C. merolae to changes in CO2 conditions. We found distinct changes upon shifts between CO2 conditions, such as a concerted up-regulation of photorespiratory genes and responses to carbon starvation. We used the transcriptome data set to explore a hypothetical CO2 concentrating mechanism in C. merolae, based on the assumption that photorespiratory genes and possible candidate genes involved in a CO2 concentrating mechanism are co-expressed. A putative bicarbonate transport protein and two α-carbonic anhydrases were identified, which showed enhanced transcript levels under reduced CO2 conditions. Genes encoding enzymes of a PEP-CK-type C4 pathway were co-regulated with the photorespiratory gene cluster. We propose a model of a hypothetical low CO2 compensation mechanism in C. merolae integrating these low CO2-inducible components.
2017-07-31 | GSE100372 | GEO
Project description: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. Identification of blue light and red light regulated genes by deep sequencing in biological duplicates. qRT-PCR was performed to verify the RNA-seq results.
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Project description:To evaluate role of PRC2 on transcriptional regulation in Cyanidioschyzon merolae, we generated loss of function mutants of a Ez homolog in Cyanidioschyzon merolae by homologous recombination based mutagenesis. Then we performed comparative transcriptome analyses using data obtained from Cme(z) and WT.
2023-09-21 | GSE221632 | GEO
Project description: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.
2016-09-10 | GSE83828 | GEO
Project description: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.
2016-09-01 | GSE67303 | GEO
Project description:RNA-seq analysis of the transcriptional response to blue and red light in the extremophilic red alga, Cyanidioschyzon merolae
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Project description:Cyanidioschyzon merolae sequenced by whole genome shotgun method
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