Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Whole genome bisulfite sequencing of apoptotic and male-differentiated subpopulations of E13.5 wild-type murine male germ cells

ABSTRACT: Heterogeneity within murine prospermatogonia manifests as certain populations either die or survive during a developmentally scheduled apoptotic event at E13.5. We have identified that this apoptosis is clonal, suggesting that apoptotic fate is heritably enforced among populations of germ cells. To determine how subpopulations of germ cells differ, we used single-cell RNA sequencing to identify two diametric states: an apoptotic (AP) versus a male-differentiated (MD) subpopulation that differ primarily by the expression of critical male-differentiation genes known to be epigenetically regulated. We isolated AP and MD germ cells from E13.5 male embryos for whole genome bisulfite sequencing to compare how methylation differs between these populations. We find that AP germ cells are relatively hypermethylated at a whole-genome level and, importantly, are significantly hypermethylated at specific genome-reprogramming responsive (GRR) loci. Because these GRR genes facilitate male differentiation, we conclude that inappropriate demethylation as germ cells epigentically reprogram in the period preceding apoptosis produces an aberrantly male-differentiated clone that is fated for elimination. This quality-control paradigm therefore links fidelitous epigenetic reprogramming to germ cell selection.

ORGANISM(S): Mus musculus

PROVIDER: GSE155122 | GEO | 2020/11/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Whole genome bisulfite sequencing of apoptotic and male-differentiated subpopulations of E13.5 wild-type murine male germ cells

Project description:Whole genome bisulfite sequencing of apoptotic and male-differentiated subpopulations of E13.5 wild-type murine male germ cells

| PRJNA648720 | ENA

Expression profiling of FACS-purified fetal germ cells

Project description:We used microarrays to profile global gene expression changes of Pou5f1-GFP-positive germ cells between E11.5 to E15.5. Germ cells were FACS-purified from gonadal single cell suspension based on Pou5f1-GFP expression. Three timepoints were included in this study: E11.5 (male/female), E13.5 (male) and E15.5 (male). For each timepoint, three biological replicates were analyzed. The Pou5f1-GFP-negative (non-germ cell) fraction of E13.5 (male) gonads was also included as a control.

2013-01-25 | E-GEOD-38126 | biostudies-arrayexpress

Whole transcriptome RNAseq analysis of germ cells in Inhba and Inha fetal testis

Project description:We performed bulk RNA-Seq on male fetal germ cells isolated from E13.5 and E15.5 testes from activin A-deficient mice (Inhba KO), and from E13.5 testes from mice with greater activin A bioactivity (Inha KO). The aim of this expereiment was to determine how chronic altered activin A bioactivity altered the germline transcriptome.

2022-05-26 | GSE201520 | GEO

Whole genome bisulfite sequencing of E13.0 and E13.5 Tex14 mutant, heterozygote and wild-type murine female germ cells

Project description:Meiosis is critical to generating oocytes however, the mechanisms regulating the switch from mitotic primordial germ cells (PGCs) to meiotic germ cells are poorly understood in females. We showed that the onset of meiosis in the fetal murine ovary propagates via intercellular bridges between developing germ cells by using Tex14 mutant (Tex14-/-) mice. Tex14-/- germ cells, which lack intercellular bridges, initiates meiosis prematurely and they more rapidly extinguish pluripotency-associated transcripts (such as Dppa3) upon entering meiosis. Considering the involvement of Dppa3 in methylation process as well as the importance of epigenetic reprogramming for gamete formation and meiosis, we isolated Tex14 wild-type, heterozygous and mutant germ cells from E13.0 and E13.5 ovaries for whole genome bisulfite sequencing. We compared how methylation differs between age-matched wild-type/heterozygous controls and mutants. We find that DNA methylation across the genome is not affected in Tex14 mutant germ cells however, promoters of Germline Reprogramming Responsive (GRR) genes and younger L1 genes are hypomethylated. These results suggest that cytoplasmic sharing via intercellular bridges slows and coordinates the cell state transition from pluripotency to meiosis potentially by diluting regulatory factors of epigenetic reprogramming.

2021-04-06 | GSE165010 | GEO

H3K27me3 maintains the transcription program during epigenetic reprogramming in the mouse germ line [RNA-seq]

Project description:To investigate the role of EZH2 in transcription regulation in mouse primordial germ cells, we isolated Ctrl and Ezh2 CKO male and female PGCs at E13.5. Our data demonstrates that EZH2-mediated H3K27me3 is required for regulating the expression of meiotic genes in the female germ cells. Furthermore, RNA-seq analysis shows that EZH2 is essential for transcriptional repression of retrotransposons.

2021-09-27 | GSE141181 | GEO

Apelin Stimulation of the Perivascular MuSC Niche Enhances Endogenous Repair in Muscular Dystrophy

Project description:Impaired skeletal muscle stem cell (MuSC) function has long been suspected to contribute to the pathogenesis of muscular dystrophy (MD). Here we describe that defects in the endothelial cell (EC) compartment of the perivascular stem cell niche in three different types of MD are associated with inefficient mobilization of MuSCs following tissue damage. Using chemoinformatic analysis, we identified the 13 amino acid form of the peptidic hormone apelin (AP-13) as a candidate for systemic stimulation of skeletal muscle ECs. In dystrophic mice, administration of AP-13 generates a pro-myogenic EC-rich niche that supports MuSC function and markedly improves tissue regeneration, muscle strength, and physical performance. Moreover, we demonstrate that EC specific knockout of the AP-13 receptor leads to regenerative defects that phenocopy major pathological features of MD. Altogether, we provide in vivo proof-of-concept that enhancing endogenous repair by targeting the perivascular niche is a viable therapeutic avenue for MD and characterize AP-13 as a novel drug candidate for systemic treatment of stem cell dysfunction.

2024-03-20 | GSE240983 | GEO

In vivo epigenomic profiling of germ cells reveals germ cell molecular signatures [ChIP-Seq]

Project description:The limited number of in vivo germ cells poses an impediment to genome-wide studies. Here, we applied a small-scale ChIP-Seq method on purified mouse fetal germ cells to generate genome-wide maps of four histone modifications (H3K4me3, H3K27me3, H3K27ac and H2BK20ac), facilitating the identification of active and repressed cis-regulatory elements in germ cells in vivo. Comparison of active chromatin state between somatic, embryonic stem cells (ESC) and germ cells revealed promoters and enhancers needed for stem cell maintenance and germ cell development. The nuclear receptor Nr5a2 motif is enriched at a subset of cis-regulatory regions and we confirm its role in germ cell differentiation. Interestingly, germ cells have comparatively more H3K27me3-marked sites that are absent in ESC and other somatic cell types. These repressed regions are enriched for retrotransposons and MHC genes and this indicates that these loci are specifically silenced in germ cells. Together, our study provides the first genome-wide histone modification maps of in vivo germ cells and revealed the molecular chromatin signatures unique to germ cells. Germ cells were FACS-purified from gonadal single cell suspension based on Pou5f1-GFP expression. ChIP-seq of Histone modification was done for two timepoints in this study: E11.5 (male/female), E13.5 (male). For E13.5 timepoint, two biological replicates were analyzed. In order to validate small scale ChIP-seq method limited number of ES cells were used to check consistency of ChIP-seq data.

2013-01-25 | E-GEOD-38164 | biostudies-arrayexpress

MicroRNAs-wide analysis of primordial germ and somatic cells reveals sexual and developmental differential functional regulation in mouse embryonic gonads

Project description:We have characterized by small-RNAseq the miRNA expression pattern of mouse male and female Primordial Germ Cells (PGCs) and somatic stromal cells from gonads at E11.5, E12.5 and E13.5. MiRNA accumulation was higher in somatic cells than in PGCs and more stable across the different developmental stages analyzed. Differential expression analyses showed differences in the regulation of key miRNA clusters such as miR-199-214, miR-182-183-96 and miR-34c-5p whose targets have defined roles in both germ and somatic cells in gonadal sexual determination. Extensive analyses of miRNA sequences revealed an increase in non-canonical isoforms in PGCs at E12.5 compared to E11.5 and E13.5 and a dramatic change in isomiR expression and non-template 3' nucleotide additions in female PGCs at E13.5 respect to the other samples.

2018-02-28 | GSE98713 | GEO

Mus musculus

Project description:miRNA expression profiling of enriched male germ cell populations

| PRJNA153721 | ENA

A male infertility mutation switches NANOS1 activity from anti-apoptotic to pro-apoptotic

Project description:While Nanos-mediated maintenance of germ cells in Drosophila and mice has been related to regulation of apoptosis, the relevance of these findings to human physiology is uncertain. We show here that the NM_199461.4(NANOS1_v001):c.[100C>A;240_242del]; NM_199461.4(NANOS1_i001):p.[(Pro34Thr);(Ser83del)] double mutation, which has previously been associated with a lack of germ cells in the testes of infertile patients, causes NANOS1 to functionally switch from being anti-apoptotic to pro-apoptotic in the human male germ cell line TCam-2.

2019-08-01 | GSE134802 | 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