Whole genome bisulfite sequencing of apoptotic and male-differentiated subpopulations of E13.5 wild-type murine male germ cells
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PROVIDER: PRJNA648720 | ENA |
REPOSITORIES: ENA
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Project description: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.
2020-11-01 | GSE155122 | GEO
Project description:A male infertility mutation switches NANOS1 activity from anti-apoptotic to pro-apoptotic
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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.
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Project description:We created mice, which are deficient for Myc specifically in cardiac myocytes by crossing crossed Myc-floxed mice (Mycfl/fl) and MLC-2VCre/+ mice. Serial analysis of earlier stages of gestation revealed that Myc-deficient mice died prematurely at E13.5-14.5. Morphological analyses of E13.5 Myc-null embryos showed normal ventricular size and structure; however, decreased cardiac myocyte proliferation and increased apoptosis was observed. BrdU incorporation rates were also decreased significantly in Myc-null myocardium. Myc-null mice displayed a 3.67-fold increase in apoptotic cardiomyocytes by TUNEL assay. We examined global gene expression using oligonucleotide microarrays. Numerous genes involved in mitochondrial death pathways were dysregulated including Bnip3L and Birc2. Keywords: wildtype vs Myc-null
2007-06-30 | GSE7162 | GEO
Project description:We created mice, which are deficient for Myc specifically in cardiac myocytes by crossing crossed Myc-floxed mice (Mycfl/fl) and MLC-2VCre/+ mice. Serial analysis of earlier stages of gestation revealed that Myc-deficient mice died prematurely at E13.5-14.5. Morphological analyses of E13.5 Myc-null embryos showed normal ventricular size and structure; however, decreased cardiac myocyte proliferation and increased apoptosis was observed. BrdU incorporation rates were also decreased significantly in Myc-null myocardium. Myc-null mice displayed a 3.67-fold increase in apoptotic cardiomyocytes by TUNEL assay. We examined global gene expression using oligonucleotide microarrays. Numerous genes involved in mitochondrial death pathways were dysregulated including Bnip3L and Birc2. Hearts were taken from wide type and Myc-null Mouse embryos at E13.5 under the dissecting scope. Cardiac myocyte RNA was isolated using TRIZOL®Reagent Total RNA (100 ng) was hybridized to the Sentrix® MouseRef-8 Expression BeadChip that contains probes for ~24,000 transcripts. GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A. The data were analyzed with Illumina Inc. BeadStudio version 1.5.0.34 and normalized by rank invariant method.
2010-06-10 | E-GEOD-7162 | biostudies-arrayexpress
Project description:Epigenetic reprogramming, characterized by loss of cytosine methylation and histone modifications, occurs during mammalian development in primordial germ cells (PGCs). Here we provide a detailed map of cytosine methylation on a large portion of the genome in developing male and female PGCs isolated from mouse embryos. We mapped DNA methylation in E13.5 PGCs isolated by FACS sorting from Oct4-GFP male and female embryos. As a control, we also mapped DNA methylation in E7.5 epiblasts from wich PGCs derive from. MeDIP and Input samples were hybridized to Nimblegen HD2 MM8 promoter deluxe arrays covering 12 kb of all gene promoters. Experiments were performed in duplicates for E7.5 epiblasts and triplicates for E13.5 PGCs.
2012-01-31 | E-GEOD-31572 | biostudies-arrayexpress
Project description:Purpose: The purpose of this study is to compare the transcriptome expression profiles of E13.5 Foxf2-/-;Osr2RFP/+ and control palatal mesenchyme by using RNA-seq analysis. Methods: Foxf2+/- female mice were crossed with Foxf2+/-;Osr2RFP/+ male mice.The embryos were harvested at E13.5. The pair of palatal shelves were dissected from each Osr2-RFP+ embryo. The RFP+ palatal mesenchyme cells were isolated by using fluorescence-activated cell sorting (FACS). RNA-seq analysis was carried out using the FACS-isolated palatal mesenchyme from Foxf2-/-;Osr2RFP/+, Foxf2+/-;Osr2RFP/+ and Osr2RFP/+embryos, respectively.
2015-12-28 | GSE67015 | GEO
Project description:By using His6-tagged recombinant human secretagogin in the presence of Ca2+ (100 µM), we isolated its putative interacting partners from mouse embryonic (E13.5) pancreata and identified their amino acid sequences by mass spectrometry. Next to previously described interacting partners (participating in vesicle-mediated transport, cytoskeletal organization and members of chaperonin-containing complex), we found a substantial group of proteins involved in proteasomal catabolic process including 15 different subunits of the 26S proteasome. Our data support that secretagogin protects Pdx1 from proteasomal degradation to control a transcriptional program required for β cell specification.
2018-06-13 | PXD009516 | Pride
Project description:We have employed whole genome microarray expression profiling to identify genes regulated by Sall1 in the kidney. Kidneys at E13.5 were obtained from inducible Sall1 deletion 24 hrs after tamoxifen treatment (2 set).
2014-03-24 | E-GEOD-45841 | biostudies-arrayexpress