Comparative genome-wide identification of transcriptional start sites in two environmentally relevant cyanobacteria reveals unexpected diversity in the transcriptome architecture
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PROVIDER: PRJNA230785 | ENA |
REPOSITORIES: ENA
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Project description:Prochlorococcus is a genus of abundant and ecologically important marine cyanobacteria. Here, we present the comprehensive comparison of the structure and composition of the transcriptomes of two closely related Prochlorococcus strains, which, despite their similarities, have adapted their gene pool to specific environmental constraints. We used large-scale strand-specific cDNA sequencing, microarray RNA profiling and computational analyses to characterize the transcriptomes of Prochlorococcus sp. MED4 and Prochlorococcus sp. MIT9313, representatives of the two major ecotypes adapted to high and low light conditions, respectively. We present genome-wide maps of transcriptional start sites (TSS) for both organisms. Our data suggest antisense transcription for three quarters of all genes. A direct comparison revealed very little conservation in the use of TSS and the nature of non-coding transcripts between both strains. We conclude that the major transcriptional output from these highly streamlined genomes consists of antisense RNA and that a hitherto unrecognized high degree of variability exists in the transcriptional architecture of these rapidly evolving prokaryotes. Furthermore, we detected extremely short 5’ untranslated regions with a median length of only 27 nt and 29 nt for MED4 and MIT9313, respectively, and noticed the absence of the Shine-Dalgarno motif, which is suggestive of alternative mechanisms for the initiation of translation. For 8 % of all protein-coding genes, the median length to the initiator codon is 10 nt or shorter, suggesting that leaderless translation and ribosomal protein S1-dependent translation constitute the primary avenues for protein synthesis in Prochlorococcus.
2013-12-07 | GSE53065 | GEO
Project description:Prochlorococcus is a genus of abundant and ecologically important marine cyanobacteria. Here, we present the comprehensive comparison of the structure and composition of the transcriptomes of two closely related Prochlorococcus strains, which, despite their similarities, have adapted their gene pool to specific environmental constraints. We used large-scale strand-specific cDNA sequencing, microarray RNA profiling and computational analyses to characterize the transcriptomes of Prochlorococcus sp. MED4 and Prochlorococcus sp. MIT9313, representatives of the two major ecotypes adapted to high and low light conditions, respectively. We present genome-wide maps of transcriptional start sites (TSS) for both organisms. Our data suggest antisense transcription for three quarters of all genes. A direct comparison revealed very little conservation in the use of TSS and the nature of non-coding transcripts between both strains. We conclude that the major transcriptional output from these highly streamlined genomes consists of antisense RNA and that a hitherto unrecognized high degree of variability exists in the transcriptional architecture of these rapidly evolving prokaryotes. Furthermore, we detected extremely short 5M-bM-^@M-^Y untranslated regions with a median length of only 27 nt and 29 nt for MED4 and MIT9313, respectively, and noticed the absence of the Shine-Dalgarno motif, which is suggestive of alternative mechanisms for the initiation of translation. For 8 % of all protein-coding genes, the median length to the initiator codon is 10 nt or shorter, suggesting that leaderless translation and ribosomal protein S1-dependent translation constitute the primary avenues for protein synthesis in Prochlorococcus. Prochlorococcus cells were either grown under standard growth conditions or various stress conditions (darkness, high light, iron or nitrogen depletion, cold or heat stress). Stress conditions were subsequently pooled and hybridized on one microarray.
2013-12-07 | E-GEOD-53065 | biostudies-arrayexpress
Project description:Prochlorococcus is a genus of abundant and ecologically important marine cyanobacteria. Here, we present a comprehensive comparison of the structure and composition of the transcriptomes of two Prochlorococcus strains, which, despite their similarities, have adapted their gene pool to specific environmental constraints. We present genome-wide maps of transcriptional start sites (TSS) for both organisms, which are representatives of the two most diverse clades within the two major ecotypes adapted to high- and low-light conditions, respectively. Our data suggest antisense transcription for three-quarters of all genes, which is substantially more than that observed in other bacteria. We discovered hundreds of TSS within genes, most notably within 16 of the 29 prochlorosin genes, in strain MIT9313. A direct comparison revealed very little conservation in the location of TSS and the nature of non-coding transcripts between both strains. We detected extremely short 5' untranslated regions with a median length of only 27 and 29 nt for MED4 and MIT9313, respectively, and for 8% of all protein-coding genes the median distance to the start codon is only 10 nt or even shorter. These findings and the absence of an obvious Shine-Dalgarno motif suggest that leaderless translation and ribosomal protein S1-dependent translation constitute alternative mechanisms for translation initiation in Prochlorococcus. We conclude that genome-wide antisense transcription is a major component of the transcriptional output from these relatively small genomes and that a hitherto unrecognized high degree of complexity and variability of gene expression exists in their transcriptional architecture.
| S-EPMC4184020 | biostudies-literature
Project description:The effects of environmentally relevant concentrations of aqueous atorvastatin on Xenopus laevis
| PRJNA989614 | ENA
Project description:Numerous studies report active pharmaceutical compounds detected in both wastewater effluent and surface waters. Exposure to statin drugs in general, and atorvastatin in particular, is likely to be a concern. We hypothesized that chronic exposure to low concentrations of atorvastatin in water would result in an adverse effect on production of steroids regulating growth and development of the model amphibian Xenopus laevis. To assess the potential for impacts we used three experimental assays. The FETAX assay was used to evaluate the effects of a range of doses of atorvastatin on developing embryos. A 60 day metamorphosis assay assessed the effects of aqueous atorvastatin exposure at environmentally concentrations on metamorphosing tadpoles. A 60 day chronic flow-through exposure evaluated the effects of chronic low concentrations of atorvastatin on adults. The data from the FETAX assay confirmed uptake, activity, and effect of atorvastatin in X. laevis tadpoles. The results of the 60-day flow-through exposure on metamorphosing tadpoles showed significant evidence of altered cholesterol biosynthesis. The dose-dependent increase in cyp19a1 expression also indicated that the steroidogenesis pathway was affected. The RNAseq analysis confirmed that exposure to environmentally relevant concentrations of atorvastatin does cause significant alterations to global transcriptional profiles in a manner consistent with dysregulation of the cholesterol biosynthesis pathway, both through the downregulation of many genes involved in that pathway, but also in the impacts to other, related pathways. The qPCR data for both adult males and adult females indicated only slight changes in expression with the exception that hmgcr was significantly downregulated in males, and cyp3a4 expression was significantly downregulated in females. The data we present here indicated that chronic exposure to environmentally relevant concentrations of atorvastatin does have the potential to impact early life stage frogs, particularly by altering expression of genes involved in critical molecular pathways.
2023-07-07 | GSE236279 | GEO
Project description:Hornyhead turbot (Pleuronichthys verticalis), a sentinel flatfish species, were intraperitoneally injected with environmentally relevant mixtures of polybrominated diphenyl ethers (PBDEs) or polychlorinated biphenyls (PCBs). After 96 h, fish were sacrificed and liver tissue was collected for gene expression analysis using a custom-designed microarray.
2020-10-01 | GSE151532 | GEO
Project description:To investigate the effects of glucocorticoids on the gene expression profiles in zebrafish, we performed a microarray-based transcriptomic study using larvae exposed to three representative glucocoriticoids at environmentally relevant high and low concentrations. Transcriptiomic profiel of developing zebrafish larvae exposed to dexamethasone, prednisolone or triamcinolone at 50 pM to 50 nM from 3 hours post-fertilisation to 5 days post-fertilisation were analyzed using G2519F Agilent Zebrafish Whole Genome Oligo Microarray Ver3.0, 4x44K.
2017-07-01 | GSE93227 | GEO
Project description:As an essential primary producer, cyanobacteria play an important role in the global cycle for both carbon and nitrogen in the ecosystems. Though the influence of nanoplastics on the carbon metabolism of cyanobacteria, especial Microcystis aeruginosa, a dominant species causing cyanobacterial blooms, is well studied, little is known about nanoplastics affecting the nitrogen metabolism.
2023-09-01 | GSE214536 | GEO
Project description:N,N-Diethyl-meta-toluamide (DEET) is a synthetic insect repellent invented in 1946 by the US Department of Agriculture for use by military personnel and now used worldwide as evidenced by its detection at various levels in human urine, serum, semen, and cord serum (1–5). While the neurological effects of DEET have been widely investigated (6–8), its effects on the germline and reproductive health are less understood. Here we used the nematode Caenorhabditis elegans, a genetically and cytologically tractable model system that shares a high degree of conservation of its genes and biochemical pathways with humans and is highly predictive of mammalian reprotoxicity, to study how DEET affects the germline (9–12). We found that exposure to environmentally relevant levels of DEET causes activation of p53/CEP-1-dependent germ cell apoptosis and alters recombination by inducing elevated levels of meiotic DNA double-strand breaks (DSBs) and crossovers (COs) resulting in chromosome abnormalities and missegregation. RNA sequencing (RNA-seq) analysis links DEET induced alterations in the expression of genes related to oxidation and reduction (redox) processes and chromatin structure to reduced mitochondrial function, altered DSB repair progression, and impaired early embryonic cell division. Our work shows that exposure to environmentally relevant levels of DEET interferes with gene expression, leading to increased oxidative stress and altered chromatin structure resulting in detectable germline effects that can pose a risk to reproductive health.
2024-02-07 | GSE242682 | GEO
Project description:Polychlorinated diphenyl ethers are lipophilic, persistent, and bioaccumulable compounds widely used as flame-retardants. These are chemicals of increasing environmental concern due to their lipophilic, persistent, and bioaccumulable characteristics. The objective of this study was to analyze the potential bioavailability and bioaccumulation of BDE-209 as a source of toxicity. Zebrafish embryos were exposed for 8 days to sediments spiked with an environmentally relevant concentration of BDE-209. We analyzed gene expression changes, thyroid function, and several markers for neurotoxicity. Results of this research highlight the need to consider the capability of BDE-209 to be bioavailable and bioaccumulate, indicating the potential hazardous effects.
2013-01-01 | GSE39169 | GEO