Collection of various small RNA sequencing libraries of C. Reinhardtii.
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2000
ORGANISM(S): Chlamydomonas reinhardtii
SUBMITTER: Sebastian Mueller
PROVIDER: E-MTAB-8526 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Alga-derived lipids represent an attractive potential source of biofuels. However, lipid accumulation in algae is a stress response tightly coupled to growth arrest, thereby imposing a major limitation on productivity. To identify master regulators of lipid accumulation and decipher the regulation of lipid biosynthetic pathway, we performed an integrative chromatin signature and transcriptomic analysis in the alga Chlamydomonas reinhardtii. Genome-wide histone modification profiling revealed remarkable differences in functional chromatin states between algae and higher eukaryotes and uncovered regulatory components at the core of lipid accumulation pathways. We identified the transcription factor PSR1 as a pivotal master switch that triggers cytosolic lipid hyper-accumulation an order of magnitude higher than stress regimens have achieved. Dissection of the PSR1 target network corroborates its central role in coordinating multiple stress responses. The comprehensive maps of functional chromatin signatures in a major clade of eukaryotic life and the discovery of a central regulator of algal lipid metabolism will facilitate targeted engineering strategies in microalgae. 1. Genome-wide H3K4me3 time series profiling (at 0 hr, 10 min, 30 min, 1 hr, 2hr, 6 hr, 8 hr, 24 hr and 48 hr after nitrogen starvation) was performed to determine time point to capture maximal chromatin changes. 2. Genome-wide H3K4me3, H3K27ac, H3K9me3, H3K27me3, H3K36me3 and Pol II profiling were performed at 0 hr, 1 hr after nitrogen starvation and 1 hr after sulfur starvation to determine chromatin signatures. Genome-wide H3K4me2 profiling was performed at 0 hr before starvation. 3. Transcriptome time series profiling (at 0 hr, 10 min, 30 min, 1 hr, 2hr, 6 hr, 8 hr, 24 hr and 48 hr after nitrogen and sulfur starvation separately) for chromatin signature characterization and integrative analysis. 4. Genome-wide PSR1 binding profiling was performed with polyclonal antibody against PSR1 peptide A region and PSR1 peptide B region individually. (At 30 min and 1 hr after nitrogen starvation, and 1 hr, 2 hr and 6 hr after sulfur starvation.) Please note that the following reference genome and gene models used in these experiments are linked below; C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz reference_gene_model.gtf.gz These are based off Phytozome (http://www.phytozome.net/) which does not provide access to earlier version data.
2015-07-28 | E-GEOD-59629 | biostudies-arrayexpress
Project description:Light is the driving force of photosynthesis. However, excessive light can be harmful. Photoinhibition, or lightinduced photodamage, is one of the key processes limiting photosynthesis. When the absorbed light exceeds the amount that can be dissipated by photosynthetic electron flow and other processes, damaging radicals are formed that mostly inactivate photosystem II (PSII). A well defined mechanism that protects the photosynthetic apparatus from photoinhibition has been described in the model green alga Chlamydomonas reinhardtii and plants. Chlorella ohadii is a green microalga, isolated from biological desert soil crusts, that thrives under extreme high light (HL) in which other organisms do not survive. Here, we show that this alga evolved unique protection mechanisms distinct from those of C. reinhardtii and plants. When grown under extreme HL, significant structural changes were noted in the C. ohadii thylakoids, including a drastic reduction in the antennae and the formation of stripped core PSII, lacking its outer and inner antennae. This is accompanied by a massive accumulation of protective carotenoids and proteins that scavenge harmful radicals. At the same time, several elements central to photoinhibition protection in C. reinhardtii, such as psbS, the stress related light harvesting complex (LHCSR), PSII protein phosphorylation and state transitions are entirely absent or were barely detected in C. ohadii.
2023-05-08 | PXD038706 | Pride
Project description:Like many microalgae unicellular green alga, Chlamydomonas reinhardtii also accumulates energy rich storage lipid and starch under nutrient-limited conditions, such as phosphorus (P) and nitrogen (N) limitation. To dissect the transcriptional regulation of lipid and starch biosynthesis in response to nutrient limitation, we have characterized the biological role of a candidate regulator: the MYB family transcription factor, PSR1 (phosphorus starvation response 1). Genetically modified (psr1 compromised) and wild-type lines were grown under P limiting and sufficient conditions and assayed at two time points by SOLiD RNA-seq.
2016-01-08 | E-MTAB-2556 | biostudies-arrayexpress
Project description:Ribosome profiling is a technique that permits genome-wide, quantitative analysis of translation and has found broad application in recent years. Here, we describe a modified profiling protocol and software package designed to benefit more broadly the translation community in terms of simplicity and utility. The protocol, applicable to diverse organisms, including organelles, is based largely on previously published profiling methodologies, but employs duplex-specific nuclease as a convenient, bias-free, species-independent way to reduce rRNA contamination. Our protocol typically produces high levels of triplet periodicity, facilitating the detection of coding sequences, including upstream, downstream and overlapping open reading frames (ORFs). This feature also allows the identification of an alternative ribosome conformation evident during termination of protein synthesis. To test the effectiveness of DSN in ribosome profiling, we generated Ribo-Seq libraries from mouse tissue culture cells and from the green alga Chlamydomonas reinhardtii.
2015-10-16 | E-MTAB-2934 | biostudies-arrayexpress
Project description:Here we generated protein abundance data, covering between 2337 and 3708 proteins, from Chlamydomonas reinhardtii cells grown in various experiments and employed them with constraint-based metabolic models to estimate in vivo maximum apparent turnover numbers for this model organism.
2023-08-01 | PXD037599 | Pride
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
Project description:Chlamydomonas reinhardtii forms lipid droplets rich in triacylglycerols when nutrient-deprived. To begin studying the mechanisms underlying this process, N-deprivation was used to induce triacylglycerol accumulation and changes in developmental programs such as gametogenesis. Comparative global analysis of transcripts under induced and non-induced conditions was applied as a first approach to study molecular changes that promote or accompany triacylglycerol accumulation in cells encountering a new nutrient environment. Towards this goal, high-throughput sequencing technology was employed to generate large numbers of expressed sequence tags of 8 biologically independent libraries (2 454 libraries, 6 Illumina libraries), four for each condition, N-replete and N-deprived, that allowed a statistically sound comparison of expression levels under the two tested conditions. Inferences on metabolism based on transcriptional analysis can only be indirect but were supported in parts by biochemical experiments. N-deprivation led to a marked redirection of metabolism as the carbon source acetate was no longer converted to cell building blocks by the glyoxylate cycle and gluconeogensis, but funneled directly into fatty acid biosynthesis. Protein biosynthesis and photosynthesis were down-regulated and genes of gametogenesis activated. A notable finding was that the genes encoding photosynthetic accessory PSBS proteins of currently unclear function in C. reinhardtii were strongly expressed following N-deprivation, providing a clue to their physiological role. Lipase-encoding genes were found to be some of the most regulated following N-deprivation, suggesting a remodeling of membranes under these conditions. The data provided here represent a rich source for the exploration of the mechanism of oil accumulation in microalgae. Examing N-replete and N-deprived conditions. One biological replicate each condition.
2010-09-24 | E-GEOD-24366 | biostudies-arrayexpress
Project description:Chlamydomonas reinhardtii forms lipid droplets rich in triacylglycerols when nutrient-deprived. To begin studying the mechanisms underlying this process, N-deprivation was used to induce triacylglycerol accumulation and changes in developmental programs such as gametogenesis. Comparative global analysis of transcripts under induced and non-induced conditions was applied as a first approach to study molecular changes that promote or accompany triacylglycerol accumulation in cells encountering a new nutrient environment. Towards this goal, high-throughput sequencing technology was employed to generate large numbers of expressed sequence tags of 8 biologically independent libraries (6 Illumina libraries, 2 454 libraries), four for each condition, N-replete and N-deprived, that allowed a statistically sound comparison of expression levels under the two tested conditions. Inferences on metabolism based on transcriptional analysis can only be indirect but were supported in parts by biochemical experiments. N-deprivation led to a marked redirection of metabolism as the carbon source acetate was no longer converted to cell building blocks by the glyoxylate cycle and gluconeogensis, but funneled directly into fatty acid biosynthesis. Protein biosynthesis and photosynthesis were down-regulated and genes of gametogenesis activated. A notable finding was that the genes encoding photosynthetic accessory PSBS proteins of currently unclear function in C. reinhardtii were strongly expressed following N-deprivation, providing a clue to their physiological role. Lipase-encoding genes were found to be some of the most regulated following N-deprivation, suggesting a remodeling of membranes under these conditions. The data provided here represent a rich source for the exploration of the mechanism of oil accumulation in microalgae. Examining N-replete and N-deprived conditions. Three biological replicates each condition.
2010-09-24 | E-GEOD-24365 | biostudies-arrayexpress
Project description:Phosphorus (P) is an essential nutrient that is limiting in many environments. When P is scarce organisms employ strategies for conservation of internal stores, and to efficiently scavenge P from their external surroundings. In this study we investigated the acclimation response of Chlamydomonas reinhardtii to P deficiency, comparing the transcriptional profiles of P starved wild-type cells to the P replete condition. RNA was prepared from P-containing or P-deprived logarithmic growth phase cells and subjected to RNA-Seq analysis. During the 24 hours after the imposition of P starvation we observed that from the 407 significantly changing genes (> 2 fold change, corrected p-value < 0.05) in the wild-type 317 genes were up-regulated, in average 8.36-fold, and 90 genes were down-regulated by 3.43-fold, in average. Many of the upregulated genes encoded enzymes involved in specific responses to P starvation, including PHOX, encoding the major secreted alkaline phosphatase, and multiple putative, high-efficiency phosphate transporter genes. More general responses included the up-regulation of genes involved in photoprotective processes (LHCSR3, LHCSR1, LHCBM9, PTOX1) and genes involved in protein modification and degradation. Down-regulated mRNAs indicated an early stage of the reduction of chloroplast ribosomal proteins, which are considered to be a reservoir for P in the cell. Chlamydomonas reinhardtii strain 21 gr (CC1690, wild-type) grown in TAP medium (Harris 1989) in a rotary incubator (200 rpm) at 25 M-BM-0C in continuous light (70 M-BM-5mol m-2 s-1). For 24 hours, either 1.1 mM phosphate or 0 mM were provided with the growth media. P deprivation was achieved by washing cells twice in midlogarithmic growth phase with liquid TAP medium without P (TAP-P) and cells were resuspended at a density of 2.5 mg/ml Chlorophyll in TAP or TAP-P. Cell aliquots were collected for mRNA isolation 24 h after being transferred either to TAP or TAP-P medium.
2014-04-05 | E-GEOD-56505 | biostudies-arrayexpress
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