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Whole-genome DNA methylation analysis for purified WT, Pld6 KO, and Dnmt3l KO spermatogonia

ABSTRACT: DNA methylomes were obtained to analyze methylation levels of retrotransposons as welll as the genome-wide methylation levels.

ORGANISM(S): Mus musculus

PROVIDER: GSE70888 | GEO | 2017/07/20

SECONDARY ACCESSION(S): PRJNA289872

REPOSITORIES: GEO

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The effect of the Pld6 and Dnmt3l mutations on DNA methylation and expression of retrotransposons in mouse male germ cells

Project description:Mammalian genomes harbor millions of retrotransposon copies, some of which are transpositionally active. In mouse prospermatogonia, PIWI-interacting small RNAs called piRNAs combat retrotransposon activity. The piRNA system guides de novo DNA methylation at retrotransposon promoters, but it remains unclear whether DNA methylation is involved in retrotransposon silencing in prospermatogonia. We performed a genome-wide study of DNA methylation and RNA abundance for retrotransposons in developing mouse male germ cells, using Pld6/Mitopld and Dnmt3l knockout (KO) mice deficient in piRNA biogenesis and de novo DNA methylation, respectively. The Dnmt3l mutation greatly reduced DNA methylation at most retrotransposons but its effect on their RNA abundance was low in prospermatogonia. In the Pld6 mutants, only few retrotransposons exhibited reduced DNA methylation but many were more upregulated at the RNA level than in the Dnmt3l mutants. Moreover, the retrotransposon upregulation by the Pld6 mutation was observed even in the Dnmt3l KO background. Thus, in prospermatogonia, post-transcriptional RNA digestion by the piRNA system plays a more important role in retrotransposon regulation than transcriptional silencing by DNA methylation. However, their relative importance was changed in meiotic spermatocytes where hypomethylation of retrotransposons increased their expression by up to 100-fold in both mutants. Interestingly, retrotransposon activation disrupted the transcriptome integrity because intergenic and intronic retrotransposon sequences, in particular, the antisense promoter of LINE-1, drive expression of nearby genes.

2017-07-20 | GSE70891 | GEO

Gene and retrotransposon expression analysis for WT, Pld6 KO, and Dnmt3l KO male germ cells during spermatogenesis

Project description:mRNA sequencing analysis of P0 testes and FACS-purified leptotene/zygotene (L/Z) spermatocytes

2017-07-20 | GSE70889 | GEO

Gene and retrotransposon expression analysis in the F1 hybrid background of B6 and MSM for WT, Pld6 KO, and Dnmt3l KO male germ cells

Project description:mRNA sequencing analysis of FACS-purified leptotene/zygotene (L/Z) spermatocytes

2017-07-20 | GSE78905 | GEO

Dnmt3L-histone H3 binding is necessary for male fertility and non-CG methylation

Project description:Patterns of DNA methylation are established during gametogenesis. The catalytically-inactive adaptor Dnmt3L is crucial to ensure this occurs correctly. In vitro, Dnmt3L binds to the N terminal tail of histone H3 but the function of this interaction during development is unknown. Here we show that Dnmt3L-histone H3 interaction is necessary for spermatogenesis. Mutant animals exhibit reduced fertility, defective methylation establishment at retrotransposons coupled with their reactivation and meiotic catastrophe. The spermatogonial stem cell pool is also defective, with mutant cells displaying marked changes in gene expression. Genome-wide methylation analysis reveals reductions in CG methylation as well as severe loss of non-CG methylation suggesting that non-CG methylation is specifically sensitive to the ability of Dnmt3L to bind histone H3. MethylC-Seq of wild-type and Dnmt3LA/A 1dpp prospermatagonia

2015-01-14 | E-GEOD-58066 | biostudies-arrayexpress

Loss of spermatogonia and wide-spread DNA methylation defects in newborn male mice deficient in DNMT3L.

Project description:BackgroundFormation of haploid spermatozoa capable of fertilization requires proper programming of epigenetic information. Exactly how DNMT3L (DNA methyltransferase 3-Like), a postulated regulator of DNA methyltransferase activity, contributes to DNA methylation pattern acquisition during gametogenesis remains unclear. Here we report on the role of DNMT3L in male germ cell development.ResultsA developmental study covering the first 12 days following birth was conducted on a Dnmt3L mutant mouse model; lower germ cell numbers and delayed entry into meiosis were observed in Dnmt3L-/- males, pointing to a mitotic defect. A temporal expression study showed that expression of Dnmt3L is highest in prenatal gonocytes but is also detected and developmentally regulated during spermatogenesis. Using a restriction enzyme qPCR assay (qAMP), DNA methylation analyses were conducted on postnatal primitive type A spermatogonia lacking DNMT3L. Methylation levels along 61 sites across chromosomes 4 and X decreased significantly by approximately 50% compared to the levels observed in Dnmt3L+/+ germ cells, suggesting that many loci throughout the genome are marked for methylation by DNMT3L. More so, hypomethylation was more pronounced in regions of lower GC content than in regions of higher GC content.ConclusionTaken together, these data suggest that DNMT3L plays a more global role in genomic methylation patterning than previously believed.

| S-EPMC2212652 | biostudies-literature

The effect of the Pld6 and Dnmt3l mutations on DNA methylation and expression of retrotransposons in mouse male germ cells

Project description:The effect of the Pld6 and Dnmt3l mutations on DNA methylation and expression of retrotransposons in mouse male germ cells

| PRJNA289866 | ENA

Dnmt3L-histone H3 binding is necessary for male fertility and non-CG methylation

2015-01-14 | GSE58066 | GEO

Dnmt1 has de novo activity targeted to transposable elements

Project description:DNA methylation plays a critical role in development, particularly in repressing retrotransposons. The mammalian methylation landscape is dependent on the combined activities of the canonical maintenance enzyme Dnmt1 and the de novo Dnmts, 3a and 3b. Here we demonstrate that Dnmt1 displays de novo methylation activity in vitro and in vivo with specific retrotransposon targeting. We used whole-genome bisulfite and long-read Nanopore sequencing in genetically engineered methylation depleted embryonic stem cells to provide an in-depth assessment and quantification of this activity. Utilizing additional knockout lines and molecular characterization, we show that Dnmt1's de novo methylation activity depends on Uhrf1 and its genomic recruitment overlaps with targets that enrich for Trim28 and H3K9 trimethylation. Our data demonstrate that Dnmt1 can de novo add and maintain DNA methylation, especially at retrotransposons and that this mechanism may provide additional stability for long-term repression and epigenetic propagation throughout development.

2021-06-29 | PXD025736 | Pride

Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates

Project description:During germ cell and preimplantation development, mammalian cells undergo nearly complete reprogramming of DNA methylation patterns. We profiled the methylomes of human and chimp sperm as a basis for comparison to methylation patterns of ES cells. While the majority of promoters escape methylation in both ES cells and sperm, the corresponding hypomethylated regions show substantial structural differences. Repeat elements are heavily methylated in both germ and somatic cells; however, retrotransposons from several subfamilies evade methylation more effectively during male germ cell development, while other subfamilies show the opposite trend. Comparing methylomes of human and chimp sperm revealed a subset of differentially methylated promoters and strikingly divergent methylation in retrotransposon subfamilies, with an evolutionary impact that is apparent in the underlying genomic sequence. Thus, the features that determine DNA methylation patterns differ between male germ cells and somatic cells, and elements of these features have diverged between humans and chimpanzees.

2011-09-01 | GSE30340 | GEO

RNA-seq data of Spermatogonia cells of Tet1-ko and WT

Project description:We analyzed 3 repeats of 12 samples of mouse spermatogonia cells including 3-month-old WT and 3 month-old Tet1, 11-month-old WT and 11-month-old Tet1, aimed to find Tet1 function on male fertility.

2020-01-18 | GSE140014 | GEO

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