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Chlamydomonas reinhardtii

ABSTRACT: Prevalence, evolution and cis-regulation of diel transcription in Chlamydomonas reinhardtii

PROVIDER: PRJNA264777 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1622080.fastq.gz	Fastqsanger.gz
	SRR1622090.fastq.gz	Fastqsanger.gz
	SRR1622081.fastq.gz	Fastqsanger.gz
	SRR1622091.fastq.gz	Fastqsanger.gz
	SRR1622082.fastq.gz	Fastqsanger.gz

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Prevalence, evolution and cis-regulation of diel transcription in Chlamydomonas reinhardtii

Project description:Biological rhythms in response to both endogenous (circadian) and exogenous (e.g. diel) cycles, with a period of ~24 hours, are a prominent feature of many living systems. In green algal species, knowledge on the extent of diel rhythmicity of genome wide gene expression, its evolution, and its cis-regulatory mechanism is limited. In this study, we identified cyclically expressed genes under diel conditions in Chlamydomonas reinhardtii and found that ~50% of the 17,114 annotated genes exhibited cyclic expression. The cyclic expression patterns indicate a clear succession of biological processes during the course of a day. Among 237 functional categories enriched in cyclically expressed genes, >90% were phase-specific, including photosynthesis, cell division and motility processes. By contrasting cyclic expression between C. reinhardtii and Arabidopsis thaliana putative orthologs, we found significant but weak conservation in cyclic gene expression patterns. On the other hand, within C. reinhardtii cyclic expression was preferentially maintained, particularly amongst older duplicates, and the evolution of phase between paralogs is limited to relatively minor shifts in time. Finally, to better understand the cis regulatory basis of diel expression, putative cis-regulatory elements were identified that could predict the expression phase of a subset of the cyclic transcriptome. Our findings demonstrate both the prevalence of as well as the complex regulatory circuitry required to control cyclic expression in a green algal model, highlighting the need to consider diel expression in studying algal molecular networks and in future biotechnological applications.

2014-10-25 | GSE62671 | GEO

RNA-seq of Chlamydomonas reinhardtii under diel conditions to identify cycling genes

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Expression analysis of Chlamydomonas reinhardtii exposed to silver

Project description:Chlamydomonas reinhardtii exposed to various concentrations of silver

2013-10-01 | GSE48677 | GEO

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Project description:RNA populations in Chlamydomonas reinhardtii Keywords: Highly parallel pyrosequencing Small RNAs were prepared from Chlamydomonas reinhardtii total extracts,ligated to a 3' adaptor and a 5' acceptor sequentially, and then RT-PCR amplified. PCR products were reamplified using a pair of 454 cloning primers and provided to 454 Life Sciences (Branford, CT) for sequencing. For technical details, see Tao Zhao, Guanglin Li, Shijun Mi, Shan Li, Gregory J. Hannon, Xiu-Jie Wang, and Yijun Qi. 2007. A Complex System of Small RNAs in the Unicellular Green Alga Chlamydomonas reinhardtii. Genes & Development

2007-05-15 | E-GEOD-7308 | biostudies-arrayexpress

Endogenous small RNAs from Chlamydomonas reinhardtii strain J3(mt-) vegetative cells

Project description:endogenous small RNAs from Chlamydomonas reinhardtii strain J3(mt-) vegetative cells Keywords: High throughput 454 small RNA sequencing

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Expression analysis of Chlamydomonas reinhardtii exposed to silver

Project description:Chlamydomonas reinhardtii exposed to various concentrations of silver For this experiment,C. reinhardtii were exposed to (4) different concentrations of silver, as biological triplicates

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Chlamydomonas reinhardtii transcriptional responses to cerium dioxide nanoparticles

Project description:Agilent gene expression microarrays (Bham Chlamydomonas reinhardtii Agilent-029192 15k v1) were used to profile transcriptional changes afeter exposure of Chlamydomonas reinardtii algae to cerium dioxide nanoparticles.

2014-09-01 | E-MTAB-2454 | biostudies-arrayexpress

UV-B-induced gene expression changes in Chlamydomonas reinhardtii

Project description:We analysed global gene expression changes in Chlamydomonas reinhardtii in response to 1h UV-B, applied at the same low level that was seen to promote subsequent UV-B stress tolerance, in order to elucidate the transcriptional reprogramming that leads to UV-B acclimation. mRNA profiles generated by deep sequencing from triplicate replicate Chlamydomonas reinhardtii samples sourced from independent cultures either protected from UV-B or exposed to 1h acclimation-level UV-B.

2015-11-11 | E-GEOD-68739 | biostudies-arrayexpress

Transcriptomics analysis of the Chlamydomonas reinhardtii diurnal cycle.

Project description:Here, we report a transcriptomics analysis on a day in the life of Chlamydomonas reinhardtii. Cultures of this unicellular alga were grown in photobioreactors on a 12 h light / 12 h dark cycle. Samples were collected at regular intervals and subjected to a transcriptomics analysis by RNA-Seq.

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