Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

17 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chromatin accessibility in mouse hypothalamic arcuate nucleus in puberty onset

ABSTRACT: 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.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Mus musculus

SUBMITTER: Yihang Shen

PROVIDER: E-MTAB-10263 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcriptome and DNA (hydro)methylation in mouse hypothalamic arcuate nucleus in puberty onset.

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

Transcriptome and DNA (hydro)methylation in mouse hypothalamic arcuate nucleus in puberty onset

2020-08-21 | E-MTAB-9421 | biostudies-arrayexpress

Endogenous brain ARC complexes

Project description:Arc is an activity regulated neuronal protein yet little is known about its protein interactions, assembly into multiprotein complexes, role in human disease and cognition. We applied an integrated proteomic and genetic strategy using targeted tagging of a Tandem Affinity Purification (TAP) tag and Venus fluorescent protein into the endogenous Arc gene in mice, biochemical and proteomic characterization of native complexes in wild type and knockout mice, and human genetic analyses of disease and intelligence. TAP tagging enabled efficient purification of complexes and identification of many novel Arcinteracting proteins, of which PSD95 was the most abundant. PSD95 was essential for Arc assembly into 1.5 MDa complexes and activity-dependent recruitment to excitatory synapses. Integrating human genetic data with proteomic data showed postsynaptic Arc- PSD95 complexes are enriched in schizophrenia, intellectual disability, autism and epilepsy mutations and normal variants in intelligence. Arc-PSD95 postsynaptic complexes are a molecular substrate for the convergence of normal and pathological genetic variants impacting on human cognitive function.

2017-10-19 | PXD007283 | Pride

Integrative proteomic and phosphoproteomic analysis in the female goat hypothalamus to study the onset of puberty

Project description:Puberty marks the end of childhood and achieve sexual maturation and fertility. The role of hypothalamic proteins in regulating puberty onset is unclear. We performed a comprehensive differential proteomics and phosphoproteomics analysis in prepubertal and pubertal goats to determine the roles of hypothalamic proteins and phosphoproteins during the onset of puberty.

2023-04-06 | PXD041426 | iProX

Testosterone-dependent and independent transcriptional networks in the hypothalamus of Gpr54 and Kiss1 knockout male mice

Project description:Humans and mice with loss of function mutations in GPR54 (KISS1R) or kisspeptin (KISS1) do not progress through puberty, caused by a failure to release GnRH. The transcriptional networks regulated by these proteins in the hypothalamus have yet to be explored by genome-wide methods. Using micro-dissected hypothalamic tissues to isolate RNA from our mice, we first set out to define the transcriptional differences among the wild type and knockout mice. Since the GPR54-kisspeptin axis is subject to hormonal feedback and the knockout mice are pre-pubertal, we also tested the hormonal dependence/independence of each differentially expressed transcript. To avoid variation in gene expression due to fluctuations in the levels of circulating hormones during the female estrous cycle, only male mice were used in this study. 17 samples were successfully hybridized; 4 GKO, 5 KKO, 3 WT 3 weeks old, 5 WT 6 weeks old. We compared GKO to KKO, GKO to WT, KKO to WT and all KO to all WT.

2011-08-21 | E-GEOD-28383 | biostudies-arrayexpress

Transcriptome-scale spatial gene expression in rat arcuate nucleus during puberty

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

Integrated transcriptomics and proteomics analyses reveal anthelmintic mechanism of arctigenin against Gyrodactylus kobayashii

Project description:The widespread resistance of parasitic worms to commonly used anthelmintics highlights the urgent need for development of new effective chemicals. Arctigenin (ARC) is a natural lignin compound that exhibits excellent anthelminthic efficacy against infections of Gyrodactylus, but knowledge about the mechanism of action is far from clear. In the present study, high-throughput RNA-sequencing was integrated with iTRAQ quantitative proteomics analysis to explore the anthelmintic mechanism and possible molecular targets of ARC against Gyrodactylus kobayashii.

2020-05-26 | PXD010913 | Pride

Detection of Arc/Arg3.1 oligomers in rat brain: constitutive and synaptic activity-evoked dimer expression in vivo

Project description:The immediate early gene product activity-regulated cytoskeleton-associate protein (Arc or Arg3.1) is a major regulator long-term synaptic plasticity with critical roles in postnatal cortical development and memory formation. However, the molecular basis of Arc function is not defined. Arc is a hub protein with interaction partners in the postsynaptic neuronal compartment and nucleus. In vitro biochemical and biophysical analysis of purified recombinant Arc show formation of low-order oligomers and larger particles including retrovirus-like capsids. Here, we provide evidence for naturally occurring Arc oligomers in mammalian brain. Using in situ protein crosslinking to trap weak Arc-Arc interactions, we identified in various preparations a prominent Arc immunoreactive band on SDS-PAGE of molecular mass corresponding to a dimer. While heavier Arc species or putative trimers and tetramers were detected, they were of lower abundance. In the dentate gyrus (DG) of adult anesthetized rats, induction of long-term potentiation (LTP) by high-frequency stimulation (HFS) of medial perforant synapses or by brief intrahippocampal infusion of BDNF led to a massive increase in Arc dimer expression. Arc immunoprecipitation of crosslinked DG tissue showed enhanced expression of dimer during four hours of LTP maintenance. Mass spectrometric proteomic analysis of immunoprecipitated, gel-excised bands corroborated detection of Arc dimer. Furthermore, Arc dimer was constitutively expressed in naïve cortical, hippocampal and DG tissue, with lowest levels in the DG. Taken together the results implicate Arc dimers as the predominant low-oligomeric form in mammalian brain, exhibiting regional differences in its constitutive expression and pronounced enhanced expression during DG LTP.

2023-07-20 | PXD039612 | Pride

The Dynamic Transcriptional Cell Atlas of Testis Development During Human Puberty

Project description:The human testis undergoes dramatic developmental and structural changes during puberty, including proliferation and maturation of niche/somatic cells, and the onset of spermatogenesis. Here, we profiled and analyzed single-cell transcriptomes of ~10,000 testicular cells from four boys spanning puberty, and compared to infants and adults. During puberty, undifferentiated spermatogonia first expand and then differentiate, prior to gametogenesis. Notably, we identify a common pre-pubertal progenitor for Leydig and myoid cells, and reveal candidate factors/pathways for pubertal differentiation. Furthermore, pre-pubertal Sertoli cells form two states that differ in mitochondrial/metabolic transcription, which converge to a single mature population during puberty. Roles for testosterone in Sertoli cell maturation, antimicrobial peptide secretion and spermatogonial differentiation are revealed through analyses of testosterone-suppressed transgender female testis and via in vitro seminiferous tubule culturing. Overall, our transcriptional atlas of the developing human testis provides major insights into developmental changes and key factors/pathways that accompany male puberty.

2020-01-13 | GSE134144 | GEO

Transcription profiling of human MCF7 cells treated with ARC (NSC 188491)

Project description:ARC (NSC 188491, SMA-491), 4-amino-6-hydrazino-7-beta-d-ribofuranosyl-7H-pyrrolo-(2,3-d)-pyrimidine-5-carboxamide, is a nucleoside analog with profound in vitro anti-cancer activity. First identified in a high-throughput screen for inhibitors of p21 mRNA expression, subsequent experiments showed that ARC also repressed expression of hdm2 and survivin, leading to its classification as a global inhibitor of transcription 1. The following Hu U133 plus 2.0 arrays represent single time point (24 hour) gene expression analysis of transcripts altered by ARC treatment. Arrays for the other compounds (sangivamycin and doxorubicin) are included as comparators. Experiment Overall Design: MCF7 cells treated with ARC, Sangivamycin or Doxorubicin for 24 hours.

2008-11-15 | E-GEOD-13477 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data