Transcriptome and DNA Methylation Analysis of Goat Pineal Gland During Puberty [RNA-seq]
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ABSTRACT:
PROVIDER: PRJNA980707 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24843920_1.fastq.gz | Fastqsanger.gz | |||
| SRR24843920_2.fastq.gz | Fastqsanger.gz | |||
| SRR24843921_1.fastq.gz | Fastqsanger.gz | |||
| SRR24843921_2.fastq.gz | Fastqsanger.gz | |||
| SRR24843922_1.fastq.gz | Fastqsanger.gz |
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Project description:Epigenetic regulation of gene transcription may play a critical role in the onset of puberty. Previous studies have confirmed that methylation regulates gene transcription in the hypothalamus-pituitary-gonadal axis during puberty initiation, but little is known about the regulation of DNA methylation on gene expression in the pineal gland. This study aims to screen pineal gland candidate genes related to the onset of goat puberty and regulated by genome methylation, to clarify the initiation mechanism of goat puberty and lay the foundation for improving goat reproductive performance. Pineal gland was collected from three female Anhui white goats during prepuberty (2.5 to 3.0 mo) and three during puberty (4.0 to 4.5 mo). Genome-wide hydrogen sulfite sequencing determined the DNA methylation profile, while RNA sequencing determined the transcriptome. The relationship between gene transcription and DNA methylation was determined by joint analysis. We found that there was no significant change in the whole genome methylation level of goat pineal gland before and after puberty, but the methylation pattern changed significantly, indicating that genomic DNA methylation of the pineal gland may be involved in regulating goat puberty initiation. Changes in DNA methylation patterns affected some pineal gland transcriptomes, while the transcriptional level of most genes was not affected by DNA methylation differences. Genes regulated by DNA methylation were mainly involved in metabolic processes, oxidative phosphorylation (OXPHOS), and signaling pathways related to thermogenesis. The differential genes ATP5F1D, CACNB2, and PTEN were significantly regulated by methylation, and the difference multiples of LIN28B, GIP, OPN1SW, and DCC were the most significant, possibly involved in puberty initiation.
2024-11-14 | GSE234298 | GEO
Project description:Epigenetic regulation of gene transcription may play a critical role in the onset of puberty. Previous studies have confirmed that methylation regulates gene transcription in the hypothalamus-pituitary-gonadal axis during puberty initiation, but little is known about the regulation of DNA methylation on gene expression in the pineal gland. This study aims to screen pineal gland candidate genes related to the onset of goat puberty and regulated by genome methylation, to clarify the initiation mechanism of goat puberty and lay the foundation for improving goat reproductive performance. Pineal gland was collected from three female Anhui white goats during prepuberty (2.5 to 3.0 mo) and three during puberty (4.0 to 4.5 mo). Genome-wide hydrogen sulfite sequencing determined the DNA methylation profile, while RNA sequencing determined the transcriptome. The relationship between gene transcription and DNA methylation was determined by joint analysis. We found that there was no significant change in the whole genome methylation level of goat pineal gland before and after puberty, but the methylation pattern changed significantly, indicating that genomic DNA methylation of the pineal gland may be involved in regulating goat puberty initiation. Changes in DNA methylation patterns affected some pineal gland transcriptomes, while the transcriptional level of most genes was not affected by DNA methylation differences. Genes regulated by DNA methylation were mainly involved in metabolic processes, oxidative phosphorylation (OXPHOS), and signaling pathways related to thermogenesis. The differential genes ATP5F1D, CACNB2, and PTEN were significantly regulated by methylation, and the difference multiples of LIN28B, GIP, OPN1SW, and DCC were the most significant, possibly involved in puberty initiation.
2024-11-14 | GSE234928 | GEO
Project description:Transcriptome and DNA Methylation Analysis of Goat Pineal Gland During Puberty
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Project description:Transcriptome and DNA Methylation Analysis of Goat Pineal Gland During Puberty [Bisulfite-seq]
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Project description:Pineal gland is a neuroendocrine gland located at the center of the brain. It protects the body from the effect of toxic compounds and regulates sleep-wake cycle, body temperature and sexual maturity through the secretion of melatonin. Abnormal functioning of pineal glands is known to be associated with Smith-Magenis syndrome, autism spectrum disorder, sleep disorders and Alzheimer’s disease. Characterization of pineal gland proteome will facilitate molecular level investigations on pathophysiological conditions underlying these diseases. We aimed to characterize the proteome of human pineal glands using a high resolution mass spectrometry- based approach. A total of 5,752 proteins were identified from human pineal glands in this study. Of these, 1,108 proteins contained signal peptide domain. We identified 2 novel proteins in this study, which are predicted by computational methods. In addition, a large number of proteins were uniquely identified in this study. A comprehensive list of proteins identified from human pineal glands will aid in unraveling the role of pineal glands in sleep disorders, neuropsychiatric and neurodegenerative diseases.
2017-02-02 | PXD004332 | Pride
Project description:This study determines pineal gland gene expression levels in the NeuroD1 knockout mouse at postnatal day zero. Comparison was performed against pineal gland gene expression levels in 129 wildtype mice also disected at P0. Keywords: Comparison of wildtype versus transgenic pineal gland gene expression
2007-10-13 | GSE6030 | GEO
Project description:Microarray data allowed detection of genes that are highly expressed in the pineal gland. Experiment Overall Design: Adult Tg(aanat2:EGFP)Y8 transgenic zebrafish in which EGFP marks the pineal gland were used for RNA extraction and hybridization on Affymetrix microarrays. Fish were anesthetized in 1.5 mM Tricane (Sigma) and sacrificed by decapitation, and pineal glands were removed under a fluorescent dissecting microscope. Since the pineal gland is a clock-containing organ and levels of certain transcripts may vary throughout the circadian cycle, glands were collected throughout the 24-hr cycle at 4 hr intervals. During the 24-hr cycle the fish were either maintained in a 12-h light/12-h dark cycle (LD) or kept in constant darkness (DD). 12 pineal glands were collected and pooled at each time point at each light condition, and total RNA was extracted (RNeasy, Qiagen).
2009-05-11 | E-GEOD-13196 | biostudies-arrayexpress
Project description:Microarray data allowed detection of genes that are highly expressed in the pineal gland. Keywords: tissue expression pattern
2009-05-01 | GSE13196 | GEO
Project description:NeuroD1 encodes a basic helix-loop-helix transcription factor involved in the development of neural and endocrine structures. NeuroD1 mRNA is highly abundant in the adult mammalian pineal gland and exhibits a developmental expression pattern similar to the retina. This is consistent with the common evolutionary origin of pinealocytes and retinal photoreceptors. Pinealocytes and retinal photoreceptors express a shared set of phototransduction genes and submammalian pinealocytes are photosensitive. In contrast to the retina, the pineal gland is a relatively homogeneous structure, composed 95% of pinealocytes. This makes the pineal gland a particularly useful model for understanding photoreceptor cell biology. The loss of NeuroD1 in the retina results in progressive photoreceptor degeneration and the molecular mechanisms underlying this retinal degeneration phenotype remain unknown. Similarly, the role that NeuroD1 plays in the pineal gland is unknown. To determine the function of NeuroD1 in the pineal gland and retina, a Cre/loxP recombination strategy was used to selectively target a NeuroD1 floxed allele and generate NeuroD1 conditional knockout (cKO) mice. Tissue specificity was conferred using Cre recombinase expressed under the control of the promoter of Crx, a transcription factor selectively expressed in the pineal gland and retina. Pineal and retinal tissues from two-month-old NeuroD1 cKO and control animals were used in microarray studies to identify candidate genes responsible for the photoreceptor degeneration phenotype.
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Project description:Microarray data allowed detection of genes that have circadian expression pattern in the zebrafish pineal gland
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