Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nucleome programming is required for the foundation of totipotency in mammalian germline development [ChIP-Seq]

ABSTRACT: Germ cells are unique in engendering totipotency, yet the mechanisms underlying this capacity remain elusive. Here, we perform comprehensive and in-depth nucleome analysis of mouse germ-cell development in vitro, encompassing pluripotent precursors, primordial germ cells (PGCs) before and after epigenetic reprogramming, and spermatogonia/spermatogonial stem cells (SSCs). Although epigenetic reprogramming, including genome-wide DNA de-methylation, creates broadly open chromatin with abundant enhancer-like signatures, the augmented chromatin insulation safeguards transcriptional fidelity. These insulatory constraints are then erased en masse for spermatogonial development. Notably, despite distinguishing epigenetic programming, including global DNA re-methylation, the PGCs-to-spermatogonia/SSCs development entails further euchromatization. This accompanies substantial erasure of lamina-associated domains, generating spermatogonia/SSCs with a minimal peripheral attachment of chromatin except for pericentromeres—an architecture conserved in primates. Accordingly, faulty nucleome maturation, including persistent insulation and improper euchromatization, leads to impaired spermatogenic potential. Given that PGCs after epigenetic reprogramming serve as oogenic progenitors as well, our findings elucidate a principle for the nucleome programming that creates gametogenic progenitors in both sexes, defining a basis for nuclear totipotency.

ORGANISM(S): Mus musculus

PROVIDER: GSE183826 | GEO | 2022/06/15

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Nucleome programming is required for the foundation of totipotency in mammalian germline development [ATAC-Seq]

Project description:Germ cells are unique in engendering totipotency, yet the mechanisms underlying this capacity remain elusive. Here, we perform comprehensive and in-depth nucleome analysis of mouse germ-cell development in vitro, encompassing pluripotent precursors, primordial germ cells (PGCs) before and after epigenetic reprogramming, and spermatogonia/spermatogonial stem cells (SSCs). Although epigenetic reprogramming, including genome-wide DNA de-methylation, creates broadly open chromatin with abundant enhancer-like signatures, the augmented chromatin insulation safeguards transcriptional fidelity. These insulatory constraints are then erased en masse for spermatogonial development. Notably, despite distinguishing epigenetic programming, including global DNA re-methylation, the PGCs-to-spermatogonia/SSCs development entails further euchromatization. This accompanies substantial erasure of lamina-associated domains, generating spermatogonia/SSCs with a minimal peripheral attachment of chromatin except for pericentromeres—an architecture conserved in primates. Accordingly, faulty nucleome maturation, including persistent insulation and improper euchromatization, leads to impaired spermatogenic potential. Given that PGCs after epigenetic reprogramming serve as oogenic progenitors as well, our findings elucidate a principle for the nucleome programming that creates gametogenic progenitors in both sexes, defining a basis for nuclear totipotency.

2022-06-15 | GSE183801 | GEO

Nucleome programming is required for the foundation of totipotency in mammalian germline development [Hi-C]

2022-06-15 | GSE184129 | GEO

Nucleome programming is required for the foundation of totipotency in mammalian germline development [NET-CAGE]

2022-06-15 | GSE183807 | GEO

Multiomics Approach to Profiling Development of the Spermatogonial Stem Cell Niche Focused on Sertoli cell Maturation

Project description:Spermatogonial stem cells are the foundation of spermatogenesis and as such can serve as a tool for the treatment of infertility in prepubertal cancer survivors. Spermatogonial stem cells are unique as they develop from primordial germ cells (PGCs), which colonize the developing tubules as immature SSC precursors. It has been controversial, when SSCs are maturing to an adult-like stem cell and recent research has found that prepubertal SSCs are actually metabolically distinct from adult SSCs until puberty. Sertoli cells picture a major part of the SSC niche and undergo drastic changes with puberty and polarize to compartmentalize the seminiferous epithelium with formation of tight junctions to a tight basal part where SSCs reside and an apical part with more differentiated stages of spermatogenesis. In the study were mapping the progression of Sertoli cells maturation events to the metabolic changes SSCs undergo during prepubertal development.

2023-02-24 | PXD037764 | Pride

Transcription and Imprinting Dynamics in Developing Postnatal Male Germline Stem Cells

Project description:Paternal imprinting initiates in primordial germ cells (PGCs), and is considered largely completed at birth. The resulting postnatal spermatogonial stem cells (SSCs) thenself-renew and proliferate to populate the testicular niche, with sexual maturation enabling productive gametogenesis. mRNA profiles of neonatal wild type (WT) mice testis were generated by deep sequencing using Illumina HiSeq 2000 Examination of 2 different histone modifications in mouse spermatogonia Please note that ChIPSeq_Kitplus samples are samples isolated with MACS CD117 microbeads from Miltenyi and ChIPSeq_Kitminus are samples that were not positively selected for Kit.

2015-11-09 | E-GEOD-62355 | biostudies-arrayexpress

The histone demethylase KDM1A is essential for the maintenance and differentiation of spermatogonial stem cells and progenitors

Project description:Little is known of the fundamental processes governed by epigenetic mechanisms in the supplier cells of spermatogenesis, the spermatogonial stem cells (SSCs). The histone H3 lysine demethylase KDM1A is expressed in spermatogonia. We hypothesized that KDM1A serves in transcriptional regulation of SSCs and fertility. Using a conditional deletion of Kdm1a [conditional knockout (cKO)] in mouse spermatogonia, we determined that Kdm1a is essential for spermatogenesis as adult cKO males completely lack germ cells. Analysis of postnatal testis development revealed that undifferentiated and differentiating spermatogonial populations form in Kdm1a-cKO animals, yet the majority fail to enter meiosis. Loss of germ cells in the cKO was rapid with none remaining by postnatal day (PND) 21. To gain insight into the mechanistic implications of Kdm1a ablation, we isolated PND 6 spermatogonia enriched for SSCs and analyzed their transcriptome by RNA sequencing. Loss of Kdm1a was associated with altered transcription of 1206 genes. Importantly, differentially expressed genes between control and Kdm1a-cKO animals included those that are essential for SSC and progenitor maintenance and spermatogonial differentiation. The complete loss of fertility and failure to establish spermatogenesis indicate that Kdm1a is a master controller of gene transcription in spermatogonia and is required for SSC and progenitor maintenance and differentiation.

2019-02-16 | GSE126607 | GEO

H3K4me2 Chromatin Immunoprecipitation sequencing analysis of chicken Embryonic stem cells, Primordial germ cells and Spermatogonial stem cells

Project description:We report the chromatin status in chicken Embryonic stem cells（ESCs）, Primordial germ cells (PGCs) and Spermatogonial stem cells (SSCs). H3K4me2 antibody was used to collect DNA sequences through CHIP experiments, and the DNA was analyzed by next-generation sequencing. We mapped the genome-wide chromatin maps of chicken ESCs, PGCs, and SSCs. We found that the entire genome of H3K4me2 in ESCs, PGCs, and SSCs was erased and then reconstructed. Most of the enriched genes were related to the cell lineage. It is mainly enriched in distal intergenic. H3K4me2 in the promoter first enriches in ESCs, then decreases in PGCs. The enrichment rebuilds in SSCs. This study provides a basis for analyzing the differences of chromatin status in ESCs, PGCs, and SSCs.

2020-03-21 | GSE147255 | GEO

Transcription and Imprinting Dynamics in Developing Postnatal Male Germline Stem Cells

2015-11-09 | GSE62355 | GEO

Neonatal and adult human testis defined at the single-cell level

Project description:Spermatogenesis has been well studied in rodents and invertebrates, but remains poorly understood in humans. As a step towards illuminating human spermatogenesis, we used single-cell RNA-sequencing (scRNAseq) analysis to analyze neonatal and adult human testes. Clustering analysis of neonatal testes revealed 3 germ subsets, including cells with characteristics of primordial germ cells (PGCs), and more differentiated cells with gene expression profiles similar with adult spermatogonial stem cells (SSCs). We identified markers for these neonatal subsets, including protein markers for the PGC-like (PGCL) subset. Clustering analysis of the adult testis revealed 9 germ and 3 somatic cell subsets. Among the germ cell clusters are 4 undifferentiated spermatogonia (SPG) states, each marked by specific genes. One of the SPG states has characteristics suggesting it is enriched for SSCs. We identified protein markers specific for this state, including cell-surface proteins that we used to enrich for these cells. We mapped the timeline of male germ cell development from PGCs through fetal germ cells to differentiating adult SPG stages. We also defined somatic cell subsets in the human testis and traced their developmental trajectories. Together, our data provides a blueprint for understanding the development of the male germline and supporting somatic cells in humans. The germ cell subset markers we identified are candidates to be used for clinical applications, including SSC therapy for treating infertility.

2018-12-22 | GSE124263 | GEO

Differentially expressed genes in undifferentiated spermatogonia at single cell level following a low dose of busulfan

Project description:Spermatogonial stem cells are responsible for sustaining gametes production and male fertiliy in men. However, germ cells including SSCs are highly sensitive to chemotherapies and radiations, placing male cancer patients at high risk of treatment-induce infertility. We have previously shown that the undifferentiated spermatogonial population of mouse testis is functionally heterogeneous and contain both stem cells and committed progenitor cells. Using mouse model of chemotherapy-induced germline damage and recovery, we aim to define molecular charactersitics, dynamics and heterogeneity of undifferentiated spermatogonia during germline regeneration compared to homeostatic undifferentiated spermatogonia.

2022-03-04 | GSE182924 | GEO

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