Ontology highlight
ABSTRACT:
PROVIDER: PRJNA369422 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5240833_1.fastq.gz | Fastqsanger.gz | |||
| SRR5240833_2.fastq.gz | Fastqsanger.gz | |||
| SRR5240884_1.fastq.gz | Fastqsanger.gz | |||
| SRR5240884_2.fastq.gz | Fastqsanger.gz | |||
| SRR5240885_1.fastq.gz | Fastqsanger.gz |
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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:Through transcriptome profiling using RNA-seq, we investigated the mechanisms behind bacterial endosymbiont (Burkholderia rhizoxinica) control over host (Rhizopus microsporus) reproductive biology. By analyzing differential expression across six different conditions, including fungal opposite mates growing independently with or without endosymbionts, as well as opposite mates growing together with endosymbionts (mating) or without endosymbionts (no mating), we were able to identify that endosymbionts control expression of a Ras signaling protein critical for sexual reproduction in many fungi (Ras2). As little is known regarding sexual reproduction in Mucoromycotina, we also used these data to investigate conservation of sex-related genes across all fungi, as well as predict potential genes involved in sensing of trisporic acid, the mating pheromone used by these fungi. 6 different conditions were analyzed, each consisting of two biological replicates. These included Rhizopus microsporus ATCC52813 (sex +) growing alone with endosymbionts, R. microsporus ATCC52814 (sex -) growing alone with endosymbionts, ATCC 52813 growing alone without endosymbionts, ATCC52814 growing alone without endosymbionts, ATCC52813 and ATCC52814 growing together with endosymbionts (successfully mating), and ATCC52813 and ATCC52814 growing together without endosymbionts (failure to mate). In each condition, fungi were cultivated on half-strength PDA and plugs of mycelium were placed at the edge of the plate. After 6 days, approximately 2.5 cm of tissue were harvested from the center of the plate. Each biological replicate consists of 5 plates which were pooled prior to RNA extraction to ensure sufficient tissue was collected.
2017-05-13 | E-GEOD-57644 | biostudies-arrayexpress
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: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: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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2017-05-13 | GSE57644 | GEO