DNA methylomes of ovaries during pubertal transition in gilts
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB32261 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3288583_1.fastq.gz | Fastqsanger.gz | |||
| ERR3288583_2.fastq.gz | Fastqsanger.gz | |||
| ERR3288584_1.fastq.gz | Fastqsanger.gz | |||
| ERR3288584_2.fastq.gz | Fastqsanger.gz |
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Project description:BACKGROUND:In female mammals, the initiation of puberty, coupling with the dramatically morphological changes in ovaries, indicates the sexual and follicular maturation. Previous studies have suggested that the disrupted DNA methylation results in the delayed puberty. However, to date, the changes in ovarian methylomes during pubertal transition have not been investigated. In this study, using gilts as a pubertal model, the genome-wide DNA methylation were profiled to explore their dynamics during pubertal transition across Pre-, In- and Post-puberty. RESULTS:During pubertal transition, the follicles underwent maturation and luteinization, coupled with the significant changes in the mRNA expression of DNMT1 and DNMT3a. DNA methylation levels of In-puberty were higher than that of Pre- and Post-puberty at the locations of genes and CpG islands (CGIs). Analysis of the DNA methylation changes identified 12,313, 20,960 and 17,694 differentially methylated CpGs (DMCs) for the comparisons of Pre- vs. In-, In vs. Post-, and Pre- vs. Post-puberty, respectively. Moreover, the CGIs, upstream and exonic regions showed a significant underrepresentation of DMCs, but the CGI shores, CGI shelves, intronic, downstream and intergenic regions showed a significant overrepresentation of DMCs. Furthermore, biological functions of these methylation changes enriched in PI3K-Akt signaling pathway, GnRH signaling pathway, and Insulin secretion, and the mRNA expressions of several genes of these signaling pathway, including MMP2, ESR1, GSK3B, FGF21, IGF1R, and TAC3, were significantly changed across Pre-, In- and Post-puberty in ovaries. CONCLUSIONS:During pubertal transition in gilts, the DNA methylation changes of ovaries were likely to affect the transcription of genes related to PI3K-Akt signaling pathway, GnRH signaling pathway, and Insulin secretion. These observations can provide new insight into the epigenetic mechanism of follicular and sexual maturation during pubertal transition in mammals.
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Project description:DNA methylomes of pituitaries during the onset of puberty in gilts
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Project description:DNA methylomes of hypothalamus during the onset of puberty in gilts
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Project description:The pituitary gland exhibits sex differences in its function. Diseases associated with dysregulation of the pituitary are also sex-biased in prevalence. Previous qPCR profiling of puberty-related genes in the pituitary gland revealed increasingly sex-biased expression of genes profiled across pubertal transition. Here, we performed small RNA-seq on total RNA extracted from C57BL/6J mouse pituitary gland of both sexes mice at 4 ages spanning pubertal transition (postnatal days 12, 22, 27, 32) (6 replicates per sex at each age) to examine microRNA (miRNA) regulation of sex differences in gene expression observed. Total RNA was sent to SickKids TCAG core to construct small RNA-seq libraries using NEBNext Small RNA Library Prep Kit according to manufacterer’s protocol. Resulting single-end libraries were sequenced at TCAG core on the Illumina HiSeq 2500 v4 flow cell with SR50 bp. Data obtained was processed using miRDeep2 pipeline to align small RNA-seq reads to the mouse genome (mm10) and to filter for miRNAs.
2022-10-12 | E-MTAB-9460 | biostudies-arrayexpress
Project description:The pituitary gland exhibits sex differences in its function. Diseases associated with dysregulation of the pituitary are also sex-biased in prevalence. Previous qPCR profiling of puberty-related genes in the pituitary gland revealed increasingly sex-biased expression of genes profiled across pubertal transition. Here, we performed 3’-UTR-seq on pituitary gland from both sexes of C57BL/6J mice at 5 ages spanning pubertal transition (postnatal days 12, 22, 27, 32, 37) (6 replicates per sex at each age) to examine genome-wide sex-biased trends in gene expression and potential regulatory mechanisms of these sex differences. QuantSeq 3’mRNA-seq libraries were constructed from total RNA using an automated method with Agilent NGS Workstation. Resulting single-end libraries were sequenced at SickKids TCAG core on the Illumina v4 flow cell with SR50 bp cycles extended to 68 bp. A customized pipeline was developed and used for analysis of reads obtained (see paper for details). Processed reads were mapped to mouse genome (mm10).
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Project description:The timing of puberty in mammals marks the point at which reproduction becomes possible. Abnormalities in the timing of puberty may exert a series of negative effects on subsequent health outcomes. Alternative splicing (AS) has not only emerged as a significant factor in the transcription of genes but it is also reported to play a role in the timing of puberty. However, to date, the changes and dynamics of AS during the onset of puberty is extremely seldom explored. In the present study, we used gilts as a research model to investigated the dynamics of AS and differentially expressed AS (DEAS) events within the hypothalamus-pituitary-ovary (HPO) axis across pre-, in-, and post-puberty. We detected 3,390, 6,098, and 9,085 DEAS events in the hypothalamus, pituitary, and ovary when compared across pre-, in-, and post-pubertal stages, respectively. Within the entire HPO axis, we also identified 22,889, 22,857, and 21,055 DEAS events in the pre-, in-, and post-pubertal stages, respectively. Further analysis revealed that the differentially spliced genes (DSGs) associated with staged DEAS events were likely to be enriched in the oxytocin signaling pathway, thyroid hormone signaling pathway, GnRH signaling pathway, and oocyte meiosis signaling pathway. The DSGs associated with DEAS events across the entire HPO axis were enriched in endocytosis signaling pathway, the MAPK signaling pathway, and the Rap1 signaling pathway. Moreover. the ASs of TAC1, TACR3, CYP19A1, ESR1, ESRRA, and FSHR were likely to regulate the functions of the certain HPO tissues during the onset of puberty. Collectively, the AS dynamics and DEAS events were comprehensively profiled in hypothalamus, pituitary, and ovary across the pre-, in-, and post-pubertal stages in pigs. These findings may enhance our knowledge of how puberty is regulated by AS and shed new light on the molecular mechanisms underlying the timing of puberty in mammals.
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Project description:Herein we identified 301 (176 up- and 125 downregulated) differentially abundant proteins (DAPs) in the ovaries of pubertal and prepubertal Anhui white goats (P < 0.05) using quantitative proteomics techniques based on LC–MS/MS and iTRAQ. Gene ontology functional enrichment analysis revealed that several DAPs enriched in biological processes were related to cellular process, biological regulation, metabolic process, and response to stimulus. Further, Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis indicated that DAPs were enriched in olfactory translation, glutathione metabolism, and calcium signaling pathways.
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Project description:The hypothalamus is a functionally and cellularly complex tissue controlling many developmental processes, including puberty. While key hormonal aspects of puberty regulation in the hypothalamus are well established, understanding the genes, cell-types, and epigenetic mechanisms underlying and regulating puberty is limited. Here, we performed 3’-UTR-seq on the hypothalamus from both sexes of C57BL/6J mice at 5 ages spanning pubertal transition (postnatal days 12, 22, 27, 32, 37) (4-5 replicates per sex at each age) to examine genome-wide age- and sex-biased trends in gene expression in a cell-type aware manner. Sample collection, RNA extraction, and sequencing was completed using the same protocols and on the same mice as PMID: 3622112 (E-MTAB-9459). QuantSeq 3’mRNA-seq libraries were constructed from total RNA using an automated method with Agilent NGS Workstation. The resulting single-end libraries were sequenced at SickKids TCAG core on the Illumina v4 flow cell with SR50 bp cycles extended to 68 bp. A customized pipeline was developed and used for the analysis of reads obtained (PMID: 36221127 for details). Processed reads were mapped to mouse genome (mm10).
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