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Gene expression analysis of control and Dnd1-cKO germ cells at E12.5 and E13.5.

ABSTRACT: Gene expression analysis of control and Dnd1-cKO germ cells at E12.5 and E13.5.

PROVIDER: PRJNA905391 | ENA |

REPOSITORIES: ENA

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Gene expression analysis of control and Dnd1-cKO germ cells at E12.5 and E13.5.

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Gene expression analysis of control and Dnd1-cKO germ cells at E11.5.

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Project description:During embryonic development, large-scale reprogramming occurs in primordial germ cells (PGCs) at the level of both DNA demethylation and histone modifications. While much is known about epigenetic changes, it still remains unclear how this chromatin state impacts the transcriptome and development of the germline. We have used cell-number normalised (CNN) RNA-seq to document the striking upregulation of the germ cell transcriptome at E13.5 compared to neighboring somatic cells of the embryonic gonad. We provide a novel, genome-wide analysis of hypertranscription during development, documenting the global amplification of the majority of the E13.5 PGC transcriptome. Upregulated transcripts in PGCs include those for ribosome biogenesis, translation and chromatin remodelling, as well as all transposable element families. These data reveal the significant hyperactivity of the germ cell transcriptome.

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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

The RNA Binding Protein Dead End1 Is Differentially Expressed in Male Germ Cells During Late Gestation and Targets Chromatin Modifiers and Translational Machinery

Project description:DND1 is essential to maintain germ cell identity. Loss of Dnd1 function results in trans-differentiation of germ cells to somatic fates in zebrafish or the formation of teratomas in mice. To explore the mechanistic role of DND1, we recently developed a transgenic mouse line in which a functional fusion protein between DND1 and GFP is expressed from the endogenous locus (Dnd1GFP). Surprisingly, we found that this reporter distinguishes two male germ cell populations (MGCs) during late gestation cell cycle arrest (G0). Most MGCs express low levels of DND1-GFP, but 5-12% of the population express high levels of DND1-GFP. An RNA-seq time course during late gestation revealed that Dnd1 transcript levels as well as transcript levels for multiple epigenetic regulators are 5-10-fold higher in DND1-GFP-hi cells. Furthermore, using antibodies against DND1-GFP for RNA immunoprecipitation (RIP) time course sequencing during late gestation, we identified multiple epigenetic and translational regulators that are binding targets of DND1 during G0. Among these targets are DNA methyltransferases (Dnmts), the enzyme Setdb1 that imposes the nuclear lamina associated repressive histone mark (H3K9me3), five Tudor domain proteins (Tdrds), four actin dependent regulators (Smarcs), and a group of ribosomal and Golgi proteins. These data suggest that DND1 binds to transcripts of a group of epigenetic enzymes and gates their translation during MGC G0 arrest in late gestation.

2022-10-18 | GSE197610 | GEO

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