Molecular regulation of photoinduced seasonal changes in Japanese Quail (Coturnix japonica) energy rheostasis.
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1129079 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29622528_1.fastq.gz | Fastqsanger.gz | |||
| SRR29622529_1.fastq.gz | Fastqsanger.gz | |||
| SRR29622530_1.fastq.gz | Fastqsanger.gz | |||
| SRR29622531_1.fastq.gz | Fastqsanger.gz | |||
| SRR29622532_1.fastq.gz | Fastqsanger.gz |
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Project description:The neuroendocrine regulation of seasonal energy homeostasis and rheostasis are widely studied. However, the molecular pathways underlying tissue-specific adaptations remain poorly described. We conducted an experiment to examine long-term rheostatic changes in energy stability using the well-characterized photoperiodic response of the Japanese quail. We exposed quails to photoperiodic transitions simulating the annual photic cycle and examined the morphology and fat deposition in liver, and white adipose tissue. To identify molecular substrates during the vernal transition in lipid accumulation, we conducted transcriptomic analyses of white adipose and liver tissues. We identified transcripts involved in adipocyte growth (Cysteine Rich Angiogenic Inducer 61, Very Low Density Lipoprotein Receptor) and obesity-linked disease resistance (Insulin-Like Growth Factor Binding Protein 2, Apolipoprotein D) increase expression in anticipation of body mass gain. In the liver, under long photoperiods, transcripts involved in fatty acid (FA) synthesis (Fatty Acid Synthase, Fatty Acid Desaturase 2) were down-regulated. Parallel upregulation of hepatic Fatty Acid Translocase and Pyruvate Dehydrogenase Kinase 4 expression suggests increased circulatory FA uptake and a switch from glucose to FA utilization. Overall, we have identified tissue-specific biochemical and molecular changes that drive photoperiod-induced adipogenesis in quails. These findings can be use to determine conserved pathways that enable animals to accumulate fat without developing metabolic diseases.
2024-07-01 | GSE270939 | GEO
Project description:In this study, we used RNA-seq to identify differences in gene expression patterns in ovarian follicles of female Japanese quail (Coturnix coturnix japonica) that produce large versus small eggs relative to their body size. A high quality reference genome is currently under construction by the Quail Genome Consortium (BioProject ID: PRJNA292031).
2015-10-11 | E-MTAB-3945 | biostudies-arrayexpress
Project description:Japanese quail (Coturnix coturnix japonica) reach sexual maturity early, breed rapidly and successfully, and cost less and require less space than other birds raised for their meat and eggs. Given the value of this species for commercial production and experimental use as well as recent increasing demand, more studies are necessary to determine chromosomal regions and genes associated with gender and breed-differentiation in the species. Identification of sex-related genes can help target chromosomal regions for molecular sexing purposes. This study employed Trinity and edgeR for transcriptome analysis of next-generation RNA-seq data, which included 4 tissues obtained from 3 different breeds of Japanese quail (wild, miniature, and jumbo). The initial goal was to identify genes related to sexual dimorphism, as well as potential novel candidate genes for molecular sexing. Analysis and interpretation of differentially expressed genes shared between female and male tissue contrast groups provided insight into sex-related differences. Several of the genes identified in the present study as significant sex-related genes have been previously found in avian gene expression analyses (e.g. NIPBL, UBAP2), and other genes found differentially expressed in this study and not previously associated with sex-related differences may be considered potential candidates for molecular sexing (e.g. TERA, MYP0, PPR17, CASQ2). Additionally, other genes likely associated with neuronal and brain development (e.g. CHKA, NYAP), as well as body development and size differentiation (e.g. ANKRD26, GRP87) in quail were identified. Expression of homeobox protein regulating genes in the sex-related contrast group revealed two genes (HXC4, ISL1) that may regulate sex-specific anatomical development. Results of these analyses expand the currently limited pool of knowledge on the genetic features of the quail breed and could allow for more effective molecular sexing as well as selective breeding for traits important in commercial production. This study employed Trinity and edgeR for transcriptome analysis of next-generation RNA-seq data, which included 4 tissues obtained from 3 different breeds of Japanese quail (wild, miniature, and jumbo).
2015-12-10 | E-GEOD-64961 | biostudies-arrayexpress
Project description:Japanese quail (Coturnix coturnix japonica) reach sexual maturity early, breed rapidly and successfully, and cost less and require less space than other birds raised for their meat and eggs. Given the value of this species for commercial production and experimental use as well as recent increasing demand, more studies are necessary to determine chromosomal regions and genes associated with gender and breed-differentiation in the species. Identification of sex-related genes can help target chromosomal regions for molecular sexing purposes. This study employed Trinity and edgeR for transcriptome analysis of next-generation RNA-seq data, which included 4 tissues obtained from 3 different breeds of Japanese quail (wild, miniature, and jumbo). The initial goal was to identify genes related to sexual dimorphism, as well as potential novel candidate genes for molecular sexing. Analysis and interpretation of differentially expressed genes shared between female and male tissue contrast groups provided insight into sex-related differences. Several of the genes identified in the present study as significant sex-related genes have been previously found in avian gene expression analyses (e.g. NIPBL, UBAP2), and other genes found differentially expressed in this study and not previously associated with sex-related differences may be considered potential candidates for molecular sexing (e.g. TERA, MYP0, PPR17, CASQ2). Additionally, other genes likely associated with neuronal and brain development (e.g. CHKA, NYAP), as well as body development and size differentiation (e.g. ANKRD26, GRP87) in quail were identified. Expression of homeobox protein regulating genes in the sex-related contrast group revealed two genes (HXC4, ISL1) that may regulate sex-specific anatomical development. Results of these analyses expand the currently limited pool of knowledge on the genetic features of the quail breed and could allow for more effective molecular sexing as well as selective breeding for traits important in commercial production.
2015-12-10 | GSE64961 | GEO
Project description:Annual cycles in daylength provide an initial predictive environmental cue that plants and animals use to time seasonal biology. Seasonal changes in photoperiodic information acts to entrain endogenous programs in physiology to optimize an animal’s fitness. Attempts to identify the neural and molecular substrates of photoperiodic time measurement in birds have, to date, focussed on blunt changes in light exposure during a restricted period of photoinducibility. The objectives of these studies were first to characterise a molecular seasonal clock in Japanese quail and second, to identify the key transcripts involved in endogenously generated interval timing that underlies photosensitivity in birds. We hypothesized that the mediobasal hypothalamus (MBH) provides the neuroendocrine control of photoperiod-induced changes in reproductive physiology, and that the pars distalis of the pituitary gland contains an endogenous internal timer for the short photoperiod dependent development of reproductive photosensitivity. Here we report distinct seasonal waveforms of transcript expression in the MBH, and pituitary gland and discovered the patterns were not synchronized across tissues. Follicle-stimulating hormone-β (FSHβ) expression increased during the simulated spring equinox, prior to photoinduced increases in prolactin, thyrotropin-stimulating hormone-β and testicular growth. Diurnal analyses of transcript expression showed sustained elevated levels of FSHβ under conditions of the spring equinox, compared to autumnal equinox, short (<12L) and long (>12L) photoperiods. FSHβ expression increased in quail held in non-stimulatory short photoperiod, indicative of the initiation of an endogenously programmed interval timer. These data identify that FSHβ establishes a state of photosensitivity for the external coincidence timing of seasonal physiology. The independent regulation of FSHβ expression provides an alternative pathway through which other supplementary environmental cues, such as temperature, can fine tune seasonal reproductive maturation and involution.
2023-09-04 | GSE241774 | GEO
Project description:Annual cycles in daylength provide an initial predictive environmental cue that plants and animals use to time seasonal biology. Seasonal changes in photoperiodic information acts to entrain endogenous programs in physiology to optimize an animal’s fitness. Attempts to identify the neural and molecular substrates of photoperiodic time measurement in birds have, to date, focussed on blunt changes in light exposure during a restricted period of photoinducibility. The objectives of these studies were first to characterise a molecular seasonal clock in Japanese quail and second, to identify the key transcripts involved in endogenously generated interval timing that underlies photosensitivity in birds. We hypothesized that the mediobasal hypothalamus (MBH) provides the neuroendocrine control of photoperiod-induced changes in reproductive physiology, and that the pars distalis of the pituitary gland contains an endogenous internal timer for the short photoperiod dependent development of reproductive photosensitivity. Here we report distinct seasonal waveforms of transcript expression in the MBH, and pituitary gland and discovered the patterns were not synchronized across tissues. Follicle-stimulating hormone-β (FSHβ) expression increased during the simulated spring equinox, prior to photoinduced increases in prolactin, thyrotropin-stimulating hormone-β and testicular growth. Diurnal analyses of transcript expression showed sustained elevated levels of FSHβ under conditions of the spring equinox, compared to autumnal equinox, short (<12L) and long (>12L) photoperiods. FSHβ expression increased in quail held in non-stimulatory short photoperiod, indicative of the initiation of an endogenously programmed interval timer. These data identify that FSHβ establishes a state of photosensitivity for the external coincidence timing of seasonal physiology. The independent regulation of FSHβ expression provides an alternative pathway through which other supplementary environmental cues, such as temperature, can fine tune seasonal reproductive maturation and involution.
2023-09-04 | GSE241772 | GEO
Project description:Since Japanese quail and chicken belong to the same order Galliforms, DNA sequence of both species are highly conserved and proved to be applicable for various analyses each other. Quail are commonly used to address physiological questions for reasons of economy. To test whether chicken microarrays are useful to quail samples, we compared hybridization signals of chicken and quail genomic DNA on Affymetrix chicken genome array. Keywords: comparative genomic hybridization
2008-03-11 | GSE8016 | GEO
Project description:To understand molecular mechanism of stripe patterning in the embryonic skin of Japanese quail, we compared gene expression profile between black stripe and yelllow stripe by using RNA seq method. Most of differential expression genes were known pigmentation-related genes, but some are unknown role in pigment pattern formation.
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Project description:Our research focus is to study the genetic etiology and molecular mechanisms of glaucoma, a disease characterized by death of the retinal ganglion cell. The QNR/D cells, the only well validated retinal ganglion cell line, are derived from the neuroretina of quail (Coturnix coturnix japonica) embryos at 7 days gestation, and contain RGC (80%) and amacrine cell (20%) populations. With the aim of investigating the effect of candidate gene on glaucoma, the QNR/D cells were transfected in four different conditions. The RNA-Sequencing analysis on these transfected cell lines to identify the related proteins with differential expression profiles.
2016-03-01 | E-MTAB-3832 | biostudies-arrayexpress
Project description:Since Japanese quail and chicken belong to the same order Galliforms, DNA sequence of both species are highly conserved and proved to be applicable for various analyses each other. Quail are commonly used to address physiological questions for reasons of economy. To test whether chicken microarrays are useful to quail samples, we compared hybridization signals of chicken and quail genomic DNA on Affymetrix chicken genome array. Experiment Overall Design: Genomic DNA of female chicken and quail were extracted individually from liver of three birds and hybridized on Affymetrix microarrays. Samples were analyzed in triplicate set of array (three biological replicates).
2008-11-06 | E-GEOD-8016 | biostudies-arrayexpress