Transcriptome-scale spatial gene expression in rat arcuate nucleus during puberty
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PROVIDER: PRJEB48453 | ENA |
REPOSITORIES: ENA
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Project description:Identification of puberty-associated cell composition and characterization of the unique transcriptional signatures across different cells are beneficial to specific neurons isolation and advanced understanding their functions. In this study, the whole brains of female SD rats aged PND-25, 35 and 45were performed 10 μm serial tissue sections transversely to expose ARC regions (bregma: -2.52 to 2.92 mm, interaural: 6.08 to 6.48 mm) according to Allen Brain Atlas and processed by spatial transcriptomics sequencing.
2021-11-07 | E-MTAB-10976 | biostudies-arrayexpress
Project description:To better understand the epigenetic mechanism underlying pubertal onset, the hypothalamic genome-wide chromatin accessibility patterns in mouse arcuate nucleus at early and late pubertal stages were explored. Female mice have been widely used in multiple studies on pubertal development as they present the similar molecular behaviors in HPG axis and stable cycles of menstrual calendar like human. Hypothalamic ARC underwent a huge epigenetic and genetic reprogramming to adapt to the response and feedback on sexual hormones during the stages of early pubertal (2-5-week of age) and late puberty (5-8-week of age) . We harvested 4- and 8-week hypothalamic ARC and employed ATAC-seq on a genome-wide scale. Combined with previous RRBS, RRHP and RNA-seq, the connections between DNA (hydroxyl)methylation in retroelements and gene expression were studied, emphasizing the importance of epigenetic alterations in regulating transcription in puberty onset.
2021-04-02 | E-MTAB-10263 | biostudies-arrayexpress
Project description:Chromatin accessibility in mouse hypothalamic arcuate nucleus in puberty onset
| PRJEB43863 | ENA
Project description:BackgroundA variety of neurons in hypothalamus undergo a complicated regulation on transcription activity of multiple genes for hypothalamic-pituitary-gonadal axis activation during pubertal development. Identification of puberty-associated cell composition and characterization of the unique transcriptional signatures across different cells are beneficial to isolation of specific neurons and advanced understanding of their functions.MethodsThe hypothalamus of female Sprague-Dawley rats in postnatal day-25, 35 and 45 were used to define the dynamic spatial atlas of gene expression in the arcuate nucleus (ARC) by 10× Genomics Visium platform. A surface protein expressed selectively by kisspeptin neurons was used to sort neurons by flow cytometric assay in vitro. The transcriptome of the isolated cells was examined using Smart sequencing.ResultsFour subclusters of neurons with similar gene expression signatures in ARC were identified. Only one subcluster showed the robust expression of Kiss1, which could be isolated by a unique membrane surface biomarker Solute carrier family 18 member A3 (SLC18A3). Moreover, genes in different subclusters presenting three expression modules distinctly functioned in each pubertal stage. Different types of cells representing distinct functions on glial or neuron differentiation, hormone secretion as well as estradiol response precisely affect and coordinate with each other, resulting in a complicated regulatory network for hypothalamic-pituitary-gonadal axis initiation and modulation.ConclusionOur data revealed a comprehensive transcriptomic overview of ARC within different pubertal stages, which could serve as a valuable resource for the study of puberty and sexual development disorders.
| S-EPMC8781439 | biostudies-literature
Project description:To better understand the epigenetic mechanism underlying pubertal onset, the hypothalamic genome-wide DNA methylation and hydroxymethylation patterns as well as the transcription profiles in mouse arcuate nucleus at early and late pubertal stages were explored. Female mice have been widely used in multiple studies on pubertal development as they present the similar molecular behaviors in HPG axis and stable cycles of menstrual calendar like human. Hypothalamic ARC underwent a huge epigenetic and genetic reprogramming to adapt to the response and feedback on sexual hormones during the stages of early pubertal (2-5-week of age) and late puberty (5-8-week of age) . We harvested 4- and 8-week hypothalamic ARC and employed RNA-seq, reduced representation bisulfite sequencing (RRBS) and hydroxymethylation profiling (RRHP) on a genome-wide scale. We identified a large number of differential expressed genes (DEGs) and differential 5(h)mC signals across the whole genome. We discovered novel connections between DNA (hydroxyl)methylated modification and gene expression, emphasizing the importance of epigenetic alterations in regulating transcription in puberty onset.
2020-08-21 | E-MTAB-9421 | biostudies-arrayexpress
Project description:To better understand the epigenetic mechanism underlying pubertal onset, the hypothalamic genome-wide DNA methylation and hydroxymethylation patterns as well as the transcription profiles in mouse arcuate nucleus at early and late pubertal stages were explored. Female mice have been widely used in multiple studies on pubertal development as they present the similar molecular behaviors in HPG axis and stable cycles of menstrual calendar like human. Hypothalamic ARC underwent a huge epigenetic and genetic reprogramming to adapt to the response and feedback on sexual hormones during the stages of early pubertal (2-5-week of age) and late puberty (5-8-week of age) . We harvested 4- and 8-week hypothalamic ARC and employed RNA-seq, reduced representation bisulfite sequencing (RRBS) and hydroxymethylation profiling (RRHP) on a genome-wide scale. We identified a large number of differential expressed genes (DEGs) and differential 5(h)mC signals across the whole genome. We discovered novel connections between DNA (hydroxyl)methylated modification and gene expression, emphasizing the importance of epigenetic alterations in regulating transcription in puberty onset.
2020-08-20 | E-MTAB-9420 | biostudies-arrayexpress
Project description:Transcriptome and DNA (hydro)methylation in mouse hypothalamic arcuate nucleus in puberty onset.
| PRJEB39790 | ENA
Project description:Transcriptome and DNA (hydro)methylation in mouse hypothalamic arcuate nucleus in puberty onset
| PRJEB39815 | ENA
Project description:DNA methylation was assessed in genomic DNA obtained from the arcuate nucleus of heifers fed to gain body weight at high (HG, n = 4) and low (LG, n = 4) rates from 4.5 to 8.5 mo of age. A methyl-CpG binding domain-based (MBD) protein assay was performed to capture fragments of methylated DNA (methylated-enriched DNA). Input (total) and methylated-enriched DNA were labeled with two different dyes and co-hybridized to a custom-designed oligonucleotide array targeted to genes associated with nutritional inputs and the control of puberty. The ratio of the log2 (enriched/input) of the normalized intensities, were determined. Data was analyzed comparing values of HG versus LG heifers. Two nutritional schedules: HG (n=4 heifers) and LG (n=4 heifers); one array per heifer; methylated enriched DNA (enriched) and total DNA (input) co-hybridyzed into each array Methylated-enriched DNA obtained from a methyl-CpG binding domain-based (MBD) protein assay
2016-02-11 | E-GEOD-77782 | biostudies-arrayexpress
Project description:Glucocorticoids (GCs) are widely prescribed to treat inflammatory and autoimmune conditions. However, patients often develop adverse metabolic effects, including hyperphagia, obesity, and hyperglycemia.The arcuate nucleus has an established role in the central control of energy balance. In this study we examined the transcriptomic response of the arcuate nucleus to oral corticosterone treatment. Gene expression changes were measured after 2 days and 4 weeks of Cort treatment in ad libitum fed C57BL6/J mice.
2019-04-01 | GSE128148 | GEO