RNA-Seq of zebrafish ovary treated with artificial light at night (ALAN) against a normal light dark sample
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2500, SENSE mRNA-Seq Library Prep Kit V2 (Lexogen, Austria), Trizol method
ORGANISM(S): Danio rerio
SUBMITTER: Rajendra Labala
PROVIDER: E-MTAB-13218 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Artificial light at night (ALAN) disrupts natural light cycles and interferes with light-dependent biological processes, yet its cellular-level impacts on marine wildlife remain poorly understood. Here, we examined diel brain transcriptomic alterations in the diurnal damselfish Dascyllus aruanus sampled at both day and night after three nights of ALAN exposure. ALAN partially disrupted circadian rhythmicity, altering diel expression of the core clock regulator bmal1 and glucocorticoid-regulated genes. At night, ALAN triggered activation of immediate-early genes, indicative of heightened neuronal arousal, acute neural stress, and suppression of restorative nocturnal processes. The following day, transcriptomic divergence between ALAN-exposed and control fish deepened, with widespread downregulation of genes governing vascular homeostasis, coagulation, and immune function. Together, these findings demonstrate that ALAN reshapes brain transcriptomic programs across the entire diel cycle, identifying molecular signatures of physiological disruption in light-polluted marine environments.
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Project description:Artificial light at night (ALAN) disrupts natural light-dark cycles, posing ecological challenges for wildli in urban areas. Here we investigated the efcts of ALAN on gene expression in the brain, liver, skin, and gonads of green anole lizards (Anolis carolinensis) whose urban populations are increasingly exposed to light pollution. To identify genetic pathways impacted by ALAN exposure we analysed expression of genes associated with circadian and metabolic regulation at midday, midnight and at midnight with artificial light. Difrential expression analysis revealed that clock-related genes (PER1, NR1D1, CRY2) were significantly altered in the brain, liver, and skin following ALAN treatment and genes involved in glucagon regulation (GCG) and lipid metabolism (NOCT) were difrentially expressed in the liver, indicating metabolic disruptions. Skin exhibited unique responses to ALAN suggesting that repair responses may be altered as genes related to cellular processes, such as wound healing, were upregulated under normal light and dark conditions. Our findings also show that ALAN disrupts core circadian genes, impacting physiological processes including hormone regulation, glucose homeostasis, and potentially reproductive cycles. This study provides the first transcriptomic evidence of the efcts of light pollution on green anoles, highlighting the need to preserve natural light cycles in urban habitats. An interactive online database developed for this study allows further exploration of gene expression changes, to promote research on artificial light-polluted environments.
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Project description:RNA-Seq of zebrafish ovary treated with artificial light at night (ALAN) against a normal light dark sample
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Project description:Sunlight influences various physiological processes, including circadian clock regulation and DNA repair via D-box enhancer elements. However, the broader transcriptional effects of visible light remain unclear. To investigate this, we compared light-mediated gene expression in zebrafish (Danio rerio) and the blind Somalian cavefish (Phreatichthys andruzzii), a species that evolved in perpetual darkness and lacks light-dependent circadian and DNA repair responses. We performed RNA sequencing of zebrafish and cavefish embryonic cell lines exposed to blue light (468 nm, for up to 6 hours), followed by gene ontology analysis and functional validation via bioinformatic, in vitro, and in vivo approaches. We revealed a light-dependent activation of a set of mitochondrial and heme metabolism genes via D-box enhancer elements. This transcriptional response was absent in cavefish cells. Further analysis revealed that while all zebrafish and cavefish PAR-bZip factors can activate the D-box, cavefish homologs exhibit diminished activity, suggesting an evolutionary reduction in light responsiveness. The D-box emerges as a key regulator of light-driven transcription in zebrafish, extending its role beyond circadian and DNA repair pathways to metabolic and mitochondrial processes. These findings provide insights into the evolution of light-sensing transcriptional mechanisms and lay the groundwork for future studies on their physiological implications.
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Project description:The metabolic bases of the interaction between the coral Acropora millepora and its dinoflagellate symbiont were investigated by comparing gene expression levels under light and dark conditions at the whole transcriptome level. Among the differentially expressed genes identified, a suite of genes involved in cholesterol transport was found to be up-regulated under light conditions, confirming the significance of this compound in the coral symbiosis. Although ion transporters likely to have roles in calcification were not differentially expressed in this study, expression levels of many genes associated with skeletal organic matrix composition and organization were higher in light conditions. This implies that the rate of organic matrix synthesis is one factor limiting calcification at night. Thus, LEC during the day is likely to be a consequence of increases in both matrix synthesis and the supply of precursor molecules as a result of photosynthetic activity.
2015-07-22 | GSE70488 | GEO
Project description:Transcriptional profiling of light response in the zebrafish at several organizational levels: the whole animal, the organ and the cell. Exposure of larvae, heart organ cultures and cell culture cells to light pulses of 1 and 3 hours duration and measurement of changes in gene expression compared to controls kept in the dark.
2011-03-01 | E-MTAB-381 | biostudies-arrayexpress
Project description:Microarray data allowed detection of genes that are induced by light in the zebrafish pineal gland Adult (0.5-1.5 years old) transgenic zebrafish, Tg(aanat2:EGFP)Y8, which express enhanced green fluorescent protein (EGFP) in the pineal gland under the control of the aanat2 regulatory regions, were used. Fish were raised under 12-hr light:12-hr dark (LD) cycles, in a temperature controlled room. Fish were transferred to constant darkness (DD) at the end of the day prior to the experiment. Fish were exposed to a 1-hr light pulse (light intensity of 12 W/m2) prior to sampling (light treatment) or kept under constant darkness for control (dark treatment). The tissues were collected from light- and dark-treated fish at 6 time points with 4-hr intervals throughout one daily cycle, corresponding to CT2, 6, 10, 14, 18 and 22. Fish were anesthetized in 1.5 mM Tricane (Sigma), sacrificed by decapitation, and pineal glands were removed under a fluorescent dissecting microscope. Pools of 12 pineal glands were prepared at each condition and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit (QIAGEN), according to the manufacturer's instructions.
2013-12-14 | E-GEOD-53288 | biostudies-arrayexpress
Project description:We were awarded a BBSRC grant about a year ago to undertake some affymetrix gene chip profiling of light and CO2 systemic signalling in Arabidopsis. The design of the proposed experiment is given below and the appropriate funding has been provided by the BBSRC. The aim of the project is to identify the temporal profile of those genes that respond to light and CO2 systemic signals in developing leaves. Moreover, as thes two signals have opposing effects on leaf development to ascertain whether they involve similar or parallel signalling pathways. The experiment is to examine the effect of exposing mature leaves to high CO2 or low light or both on the gene expression profile of developing leaves. We already have data for maize that changes in gene expression profile occur within 4h and that there are a variety of temporal responses that differ between individual gene transcripts. We have also demonstrated that Arabidopsis leaf development is altered by these systemmic signals and that lesions in the jasmonate and ethylene signalling pathways block these responses. Our experimental design is shown below:; We have 4 treatments and 7 timepoints. (0, 2, 4, 12, 24, 48, 96 h); We would sample from 5 individual plants that would be pooled for each RNA preparation. This would require 28 chips and this would include extra replication of the 0 time-point control (deemed by many as nessary). Experimental details:; All plants were germinated for 7 days under the following conditions:; Humax multi-purpose compost, ambient carbon dioxide (370 ppm) and ambient light (250 µmol/m/s), constant temperature of 20°C and a 10 h photoperiod (8 am until 6 pm). After a week the the seedlings were potted up into 104-cell plug trays for a further 2 weeks and then potted up into 10 cm pots and the bottom part of the signalling cuvette system attached (see Lake et al., Nature 10th May 2001 Vol. 411, pp 154). Twenty four, 4 week old plants, then had the top part of the signalling system attached, trapping leaf insertions 5-13. Humidified, ambient air was passed through them at 500 mls/min via an oil-free air compressor. The three target leaves (19-21) were then marked with non-toxic, acrylic paint. After a 24 h period (the plants were sealed into the cuvettes from 10 am until 10am) of adjustment, the experiment was started by harvesting the target leaves from 4 plants and immediately freezing the tissue in liquid nitrogen to give the 0 h sample before RNA extraction. The remaining 20 plants were divided into 4 groups of five and given one of the following treatments:; Ambient carbon dioxide/ambient light (Control) (A); Elevated carbon dioxide (750 ppm)/ambient light (E); Ambient carbon dioxide/low light (50 µmol/m/s) (AS); Elevated carbon dioxide/low light (ES); - For the Elevated CO2, elevated CO2 was pumped in using a CT room next door set to same temperature but with a CO2 cylinder inside and the same pump as used in the ambient room to supply the elevated CO2 laden, humidified air into the signalling room using rubber tubing. - Shade treatment consisted of neutral density filter (Cat. 210 0.6ND, Lee Filters) that had a hole cut in the middle to allow the middle developing leaves to grow through. A timecourse of 2, 4, 12, 24, 48 and 96 h were carried out each using a batch of 24 plants. This whole process was repeated with another batch of 24 plants at the same developmental stage to give a 2, 4, 12, 24, 48 and 96 hour sample from each of the four treatments. The whole timecourse was then repeated 4 times. For the mature leaves:; We had 8 chips left over so we devised this little experiment to assess the gene changes that were occurring in the enclosed, treated, mature leaves that were signalling the environment to the young developing leaves. Experimenter name = Simon Coupe; Experimenter phone = 0114 222 4115; Experimenter fax = 0114 222 0002; Experimenter institute = University of Sheffield; Experimenter address = Animal and Plant Sciences; Experimenter address = University of Sheffield; Experimenter address = Western Bank; Experimenter address = Sheffield; Experimenter zip/postal_code = S10 2TN; Experimenter country = UK Experiment Overall Design: 28 samples were used in this experiment
2008-06-14 | E-GEOD-5638 | biostudies-arrayexpress
Project description:We were awarded a BBSRC grant about a year ago to undertake some affymetrix gene chip profiling of light and CO2 systemic signalling in Arabidopsis. The design of the proposed experiment is given below and the appropriate funding has been provided by the BBSRC. The aim of the project is to identify the temporal profile of those genes that respond to light and CO2 systemic signals in developing leaves. Moreover, as thes two signals have opposing effects on leaf development to ascertain whether they involve similar or parallel signalling pathways. The experiment is to examine the effect of exposing mature leaves to high CO2 or low light or both on the gene expression profile of developing leaves. We already have data for maize that changes in gene expression profile occur within 4h and that there are a variety of temporal responses that differ between individual gene transcripts. We have also demonstrated that Arabidopsis leaf development is altered by these systemmic signals and that lesions in the jasmonate and ethylene signalling pathways block these responses. Our experimental design is shown below:; We have 4 treatments and 7 timepoints. (0, 2, 4, 12, 24, 48, 96 h); We would sample from 5 individual plants that would be pooled for each RNA preparation. This would require 28 chips and this would include extra replication of the 0 time-point control (deemed by many as nessary). Experimental details:; All plants were germinated for 7 days under the following conditions:; Humax multi-purpose compost, ambient carbon dioxide (370 ppm) and ambient light (250 µmol/m/s), constant temperature of 20°C and a 10 h photoperiod (8 am until 6 pm). After a week the the seedlings were potted up into 104-cell plug trays for a further 2 weeks and then potted up into 10 cm pots and the bottom part of the signalling cuvette system attached (see Lake et al., Nature 10th May 2001 Vol. 411, pp 154). Twenty four, 4 week old plants, then had the top part of the signalling system attached, trapping leaf insertions 5-13. Humidified, ambient air was passed through them at 500 mls/min via an oil-free air compressor. The three target leaves (19-21) were then marked with non-toxic, acrylic paint. After a 24 h period (the plants were sealed into the cuvettes from 10 am until 10am) of adjustment, the experiment was started by harvesting the target leaves from 4 plants and immediately freezing the tissue in liquid nitrogen to give the 0 h sample before RNA extraction. The remaining 20 plants were divided into 4 groups of five and given one of the following treatments:; Ambient carbon dioxide/ambient light (Control) (A); Elevated carbon dioxide (750 ppm)/ambient light (E); Ambient carbon dioxide/low light (50 µmol/m/s) (AS); Elevated carbon dioxide/low light (ES); - For the Elevated CO2, elevated CO2 was pumped in using a CT room next door set to same temperature but with a CO2 cylinder inside and the same pump as used in the ambient room to supply the elevated CO2 laden, humidified air into the signalling room using rubber tubing. - Shade treatment consisted of neutral density filter (Cat. 210 0.6ND, Lee Filters) that had a hole cut in the middle to allow the middle developing leaves to grow through. A timecourse of 2, 4, 12, 24, 48 and 96 h were carried out each using a batch of 24 plants. This whole process was repeated with another batch of 24 plants at the same developmental stage to give a 2, 4, 12, 24, 48 and 96 hour sample from each of the four treatments. The whole timecourse was then repeated 4 times. For the mature leaves:; We had 8 chips left over so we devised this little experiment to assess the gene changes that were occurring in the enclosed, treated, mature leaves that were signalling the environment to the young developing leaves. Experimenter name = Simon Coupe; Experimenter phone = 0114 222 4115; Experimenter fax = 0114 222 0002; Experimenter institute = University of Sheffield; Experimenter address = Animal and Plant Sciences; Experimenter address = University of Sheffield; Experimenter address = Western Bank; Experimenter address = Sheffield; Experimenter zip/postal_code = S10 2TN; Experimenter country = UK Experiment Overall Design: 26 samples were used in this experiment
2008-06-14 | E-GEOD-5636 | biostudies-arrayexpress