Waveband Specific Transcriptional Control of Select Genetic Pathways in Xiphophorus maculatus Skin
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ABSTRACT:
PROVIDER: PRJNA447434 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6912030_1.fastq.gz | Fastqsanger.gz | |||
| SRR6912030_2.fastq.gz | Fastqsanger.gz | |||
| SRR6912040_1.fastq.gz | Fastqsanger.gz | |||
| SRR6912040_2.fastq.gz | Fastqsanger.gz | |||
| SRR6912050_1.fastq.gz | Fastqsanger.gz |
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Project description:Changes in the transcriptional profiles of Xiphophorus maculatus skin was assessed by RNA-Seq after exposure to fluorescent (i.e., FL, 4,100K or “cool white”), or narrow wavelength regions of light between 300-600 nm (i.e., 50 nm or 10 nm regions, herein termed ”wavebands”). Exposure to varied 50 nm wavebands allowed identification of waveband specific transcriptional modulation within gene sets representing discrete functional pathways within Xiphophorus skin. For example, exposure to either 350-400 or 450-500 nm wavebands resulted in opposite transcriptional effects in necrosis and apoptosis gene sets that predict selective differential suppression or activation of these pathways (i.e., 350-400 nm; necrosis suppression, apoptosis activation, and 450-500 nm; apoptosis suppression, necrosis activation). Further investigation of waveband specific transcription employing successive 10 nm waveband exposures within the genetically responsive 500-550 nm waveband show; (a) greater numbers of genes may be transcriptionally modulated after 10 nm exposures, than observed for either 50 nm or FL exposures. (b) the 10 nm wavebands incite greater functional specificity than either 50 nm or FL exposures. (c) The principal genetic effects of FL are primarily due to the 30 nm between 500 to 530 nm.
2018-04-30 | GSE112473 | GEO
Project description:RNA from Xiphophorus maculatus (X. maculatus) are isolated and sequenced for annotation of enhanced X. maculatus genome
2017-11-28 | GSE107449 | GEO
Project description:BACKGROUND:Evolution occurred exclusively under the full spectrum of sunlight. Conscription of narrow regions of the solar spectrum by specific photoreceptors suggests a common strategy for regulation of genetic pathways. Fluorescent light (FL) does not possess the complexity of the solar spectrum and has only been in service for about 60 years. If vertebrates evolved specific genetic responses regulated by light wavelengths representing the entire solar spectrum, there may be genetic consequences to reducing the spectral complexity of light. RESULTS:We utilized RNA-Seq to assess changes in the transcriptional profiles of Xiphophorus maculatus skin after exposure to FL ("cool white"), or narrow wavelength regions of light between 350 and 600 nm (i.e., 50 nm or 10 nm regions, herein termed "wavebands"). Exposure to each 50 nm waveband identified sets of genes representing discrete pathways that showed waveband specific transcriptional modulation. For example, 350-400 or 450-500 nm waveband exposures resulted in opposite regulation of gene sets marking necrosis and apoptosis (i.e., 350-400 nm; necrosis suppression, apoptosis activation, while 450-500 nm; apoptosis suppression, necrosis activation). Further investigation of specific transcriptional modulation employing successive 10 nm waveband exposures between 500 and 550 nm showed; (a) greater numbers of genes may be transcriptionally modulated after 10 nm exposures, than observed for 50 nm or FL exposures, (b) the 10 nm wavebands induced gene sets showing greater functional specificity than 50 nm or FL exposures, and (c) the genetic effects of FL are primarily due to 30 nm between 500 and 530 nm. Interestingly, many genetic pathways exhibited completely opposite transcriptional effects after different waveband exposures. For example, the epidermal growth factor (EGF) pathway exhibits transcriptional suppression after FL exposure, becomes highly active after 450-500 nm waveband exposure, and again, exhibits strong transcriptional suppression after exposure to the 520-530 nm waveband. CONCLUSIONS:Collectively, these results suggest one may manipulate transcription of specific genetic pathways in skin by exposure of the intact animal to specific wavebands of light. In addition, we identify genes transcriptionally modulated in a predictable manner by specific waveband exposures. Such genes, and their regulatory elements, may represent valuable tools for genetic engineering and gene therapy protocols.
| S-EPMC5946439 | biostudies-literature
Project description:Xiphophorus maculatus Transcriptome or Gene expression
| PRJNA191034 | ENA
Project description:RNA-Seq of spontaneous melanoma in Xiphophorus interspecies hybrids, and paired normal skin samples from the same melanoma-bearing animals were performed.
2018-05-01 | GSE113622 | GEO
Project description:In both Xiphophorus fishes and humans, males are reported to have a higher incidence of melanoma than females. To better understand sex-specific differences in the molecular genetic response to UVB, we performed RNA-Seq experiments in skin of female and male Xiphophorus maculatus Jp 163 B following UVB doses of 8 or 16kJ/m(2) exposure. Male X. maculatus differentially express a significantly larger number of transcripts following exposure to 16kJ/m(2) UVB (1293 genes) compared to 8kJ/m(2) UVB (324 genes). Female skin showed differential gene expression in a larger number of transcripts following 8kJ/m(2) UVB (765) than did males; however, both females and males showed similar numbers of differentially expressed genes at 16kJ/m(2) UVB (1167 and1293, respectively). Although most modulated transcripts after UVB exposure represented the same dominant pathways in both females and males (e.g., DNA repair, circadian rhythm, and fatty acid biosynthesis), we identified genes in several pathways that exhibited opposite modulation in female vs. male skin (e.g., synaptic development, cell differentiation, wound healing, and glucose metabolism). The oppositely modulated genes appear related through uncoupling protein 3 (UCP3) that is involved with the regulation of fatty acid oxidation and serves to balance glucose and lipid metabolism. Overall, these results identify gender-specific differences in UVB-induced genetic profiles in the skin of females and males and show female and male X. maculatus respond to UVB differently through pathways involved in reactive oxygen species, wound healing, and energy homeostasis.
| S-EPMC4662892 | biostudies-literature
Project description:Xiphophorus fishes represent a model often utilized to study UVB induced tumorigenesis. Recently, varied genetic responses to UVB exposure have been documented in the skin of female and male Xiphophorus, as have differences in UVB response in the skin of different parental species and for interspecies hybrids produced from crossing them. Additionally, it has been shown that exposure to "cool white" fluorescent light induces a shift in the genetic profiles of Xiphophorus skin that is nearly as robust as the UVB response, but involves a fundamentally different set of genes. Given these results and the use of Xiphophorus interspecies hybrids as an experimental model for UVB inducible melanoma, it is of interest to characterize genes that may be transcriptionally modulated in a wavelength specific manner. The global molecular genetic response of skin upon exposure of the intact animal to specific wavelengths of light has not been investigated. Herein, we report results of RNA-Seq experiments from the skin of male Xiphophorus maculatus Jp 163 B following exposure to varied 50nm wavelengths of light ranging from 300-600nm. We identify two specific wavelength regions, 350-400nm (88 genes) and 500-550nm (276 genes), that exhibit transcriptional modulation of a significantly greater number of transcripts than any of the other 50nm regions in the 300-600nm range. Observed functional sets of genes modulated within these two transcriptionally active light regions suggest different mechanisms of gene modulation.
| S-EPMC4662885 | biostudies-literature