DNA methylation-sensitive transcription factors and bivalency orchestrate transposon expression in the absence of DNA methylation [Retrotransposon expression in conditional NRF1 mutant testes]
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1188036 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Silencing of young retrotransposons by Cytosine DNA methylation is essential for spermatogenesis. Failure to methylate retrotransposon promoters leads to their reactivation, meiotic catastrophe and infertility. How transposons become reactivated and why their reactivation follows spermatogenic developmental patterns remains unclear. Here, we show that specific retrotransposon families exhibit distinct expression patterns and chromatin landscapes throughout spermatogenesis when DNA methylation is absent from their promoters. We find a strong correlation between the loss of bivalent H3K4me3-H3K27me3 chromatin modifications and the transition from low retrotransposon expression in spermatogonia to reactivation in meiotic spermatocytes. Using a combination of DNA pulldowns, mass spectrometry and chromatin profiling by CUT&Tag, we identify the DNA methylation-sensitive transcription factor NRF1 as a potential regulator of unmethylated retrotransposons in spermatogenesis. Germline conditional ablation of Nrf1 reduced the upregulation of IAPs in the absence of DNA methylation and rescued the accumulation of IAP-derived Pol protein to wild type germ cell levels. Our study demonstrates that a combination of chromatin modifications and a DNA methylation-sensitive TF regulates young retrotransposons upon loss of repressive DNA methylation in germ cells, suggesting these interactions may be a core strategy used by retrotransposons to proliferate in the germline after evading silencing by DNA methylation.
2025-08-08 | GSE282279 | GEO
Project description:Eukaryotic transcription factors (TFs) are key determinants of gene activity, yet they bind only a fraction of their corresponding DNA sequence motifs in any given cell type. Chromatin has the potential to restrict accessibility of binding sites; however, in which context chromatin states are instructive for TF binding remains mainly unknown. To explore the contribution of DNA methylation to constrained TF binding, we mapped DNase-I-hypersensitive sites in murine stem cells in the presence and absence of DNA methylation. Methylation-restricted sites are enriched for TF motifs containing CpGs, especially for those of NRF1. In fact, the TF NRF1 occupies several thousand additional sites in the unmethylated genome, resulting in increased transcription. Restoring de novo methyltransferase activity initiates remethylation at these sites and outcompetes NRF1 binding. This suggests that binding of DNA-methylationsensitive TFs relies on additional determinants to induce local hypomethylation. In support of this model, removal of neighbouring motifs in cis or of a TF in trans causes local hypermethylation and subsequent loss of NRF1 binding. This competition between DNA methylation and TFs in vivo reveals a case of cooperativity between TFs that acts indirectly via DNA methylation. Methylation removal by methylation-insensitive factors enables occupancy of methylation-sensitive factors, a principle that rationalizes hypomethylation of regulatory regions. DNase-seq (2 replicates) in mouse embryonic stem cells with (WT) and without DNA methylation (DNMT TKO). RNA-seq (3 replicates) in WT and DNMT TKO cells and in DNMT TKO cells after treatment with control siRNA or siRNA targeting Nrf1. H3K27ac ChIP-seq (2 replicates) in WT and DNMT TKO cells. NRF1 ChIP-seq (2 replicates) in WT and DNMT TKO cells, in WT upon culture in different conditions (adaptation to 2i and back to serum), upon transient overexpression of NRF1 and after differentiation into neuronal progenitor cells (NP). Whole-genome bisulfite sequencing in DNMT TKO cells and in WT upon culture in different conditions (adaptation to 2i and back to serum). NRF1 ChIP-seq (2 replicates) in human HMEC and HCC1954 cells.
2015-12-16 | E-GEOD-67867 | biostudies-arrayexpress
Project description:Silencing of young retrotransposons by Cytosine DNA methylation is essential for spermatogenesis. Failure to methylate retrotransposon promoters leads to their reactivation, meiotic catastrophe and infertility. How transposons become reactivated and why their reactivation follows spermatogenic developmental patterns remains unclear. Here, we show that specific retrotransposon families exhibit distinct expression patterns and chromatin landscapes throughout spermatogenesis when DNA methylation is absent from their promoters. We find a strong correlation between the loss of bivalent H3K4me3-H3K27me3 chromatin modifications and the transition from low retrotransposon expression in spermatogonia to reactivation in meiotic spermatocytes. Using a combination of DNA pulldowns, mass spectrometry and chromatin profiling by CUT&Tag, we identify the DNA methylation-sensitive transcription factor NRF1 as a potential regulator of unmethylated retrotransposons in spermatogenesis. Germline conditional ablation of Nrf1 reduced the upregulation of IAPs in the absence of DNA methylation and rescued the accumulation of IAP-derived Pol protein to wild type germ cell levels. Our study demonstrates that a combination of chromatin modifications and a DNA methylation-sensitive TF regulates young retrotransposons upon loss of repressive DNA methylation in germ cells, suggesting these interactions may be a core strategy used by retrotransposons to proliferate in the germline after evading silencing by DNA methylation.
2025-08-08 | GSE282278 | GEO
Project description:Eukaryotic transcription factors (TFs) are key determinants of gene activity, yet they bind only a fraction of their corresponding DNA sequence motifs in any given cell type. Chromatin has the potential to restrict accessibility of binding sites; however, in which context chromatin states are instructive for TF binding remains mainly unknown. To explore the contribution of DNA methylation to constrained TF binding, we mapped DNase-I-hypersensitive sites in murine stem cells in the presence and absence of DNA methylation. Methylation-restricted sites are enriched for TF motifs containing CpGs, especially for those of NRF1. In fact, the TF NRF1 occupies several thousand additional sites in the unmethylated genome, resulting in increased transcription. Restoring de novo methyltransferase activity initiates remethylation at these sites and outcompetes NRF1 binding. This suggests that binding of DNA-methylationsensitive TFs relies on additional determinants to induce local hypomethylation. In support of this model, removal of neighbouring motifs in cis or of a TF in trans causes local hypermethylation and subsequent loss of NRF1 binding. This competition between DNA methylation and TFs in vivo reveals a case of cooperativity between TFs that acts indirectly via DNA methylation. Methylation removal by methylation-insensitive factors enables occupancy of methylation-sensitive factors, a principle that rationalizes hypomethylation of regulatory regions.
2015-12-16 | GSE67867 | GEO
Project description:DNA methylation-sensitive transcription factors and bivalency orchestrate transposon expression in the absence of DNA methylation.
| PRJNA1188030 | ENA
Project description:DNA methylation-sensitive transcription factors and bivalency orchestrate transposon expression in the absence of DNA methylation [Postnatal Retrotransposon expression in spermatogenesis]
| PRJNA1188038 | ENA
Project description:Silencing of young retrotransposons by Cytosine DNA methylation is essential for spermatogenesis. Failure to methylate retrotransposon promoters leads to their reactivation, meiotic catastrophe and infertility. How transposons become reactivated and why their reactivation follows spermatogenic developmental patterns remains unclear. Here, we show that specific retrotransposon families exhibit distinct expression patterns and chromatin landscapes throughout spermatogenesis when DNA methylation is absent from their promoters. We find a strong correlation between the loss of bivalent H3K4me3-H3K27me3 chromatin modifications and the transition from low retrotransposon expression in spermatogonia to reactivation in meiotic spermatocytes. Using a combination of DNA pulldowns, mass spectrometry and chromatin profiling by CUT&Tag, we identify the DNA methylation-sensitive transcription factor NRF1 as a potential regulator of unmethylated retrotransposons in spermatogenesis. Germline conditional ablation of Nrf1 reduced the upregulation of IAPs in the absence of DNA methylation and rescued the accumulation of IAP-derived Pol protein to wild type germ cell levels. Our study demonstrates that a combination of chromatin modifications and a DNA methylation-sensitive TF regulates young retrotransposons upon loss of repressive DNA methylation in germ cells, suggesting these interactions may be a core strategy used by retrotransposons to proliferate in the germline after evading silencing by DNA methylation.
2025-08-08 | GSE282277 | GEO
Project description:Silencing of young retrotransposons by Cytosine DNA methylation is essential for spermatogenesis. Failure to methylate retrotransposon promoters leads to their reactivation, meiotic catastrophe and infertility. How transposons become reactivated and why their reactivation follows spermatogenic developmental patterns remains unclear. Here, we show that specific retrotransposon families exhibit distinct expression patterns and chromatin landscapes throughout spermatogenesis when DNA methylation is absent from their promoters. We find a strong correlation between the loss of bivalent H3K4me3-H3K27me3 chromatin modifications and the transition from low retrotransposon expression in spermatogonia to reactivation in meiotic spermatocytes. Using a combination of DNA pulldowns, mass spectrometry and chromatin profiling by CUT&Tag, we identify the DNA methylation-sensitive transcription factor NRF1 as a potential regulator of unmethylated retrotransposons in spermatogenesis. Germline conditional ablation of Nrf1 reduced the upregulation of IAPs in the absence of DNA methylation and rescued the accumulation of IAP-derived Pol protein to wild type germ cell levels. Our study demonstrates that a combination of chromatin modifications and a DNA methylation-sensitive TF regulates young retrotransposons upon loss of repressive DNA methylation in germ cells, suggesting these interactions may be a core strategy used by retrotransposons to proliferate in the germline after evading silencing by DNA methylation.
2025-08-08 | GSE282276 | GEO
Project description:Competition between DNA methylation and transcription factors determines binding of NRF1
| PRJNA281090 | ENA
Project description:Epigenetic priming factors establish a permissive epigenetic landscape which is not required until a later developmental or physiological time point, temporally uncoupling the presence of these factors with their phenotypic effects. One classic example of epigenetic priming is in the context of bivalent chromatin, found in pluripotent stem cells and early embryos at key developmental gene promoters marked by both activating-associated H3K4me3 and repressive-associated H3K27me3 histone modifications. It is currently unknown how these bivalent domains are targeted, or precisely how they impact on lineage commitment. Here we show that the small heterodimerising non-enzymatic DNA binding proteins Developmental Pluripotency Associated 2 (Dppa2) and 4 (Dppa4) act as epigenetic priming factors to establish bivalency at a subset of developmental genes. Dppa2/4 localise to the +1 nucleosome position of bivalent genes and while they are not required for pluripotency in embryonic stem cells (ESCs), double knockout cells fail to exit pluripotency and to differentiate efficiently, with delays in upregulating bivalently marked lineage genes. Proteomics reveal that Dppa2/4 interact on chromatin with members of the COMPASS and Polycomb complexes important for H3K4me3 and H3K27me3 deposition, respectively. Epigenetic profiling reveals a striking loss of H3K4me3, H3K27me3, and their associated enzymatic machinery at a significant subset of bivalent promoters in Dppa2/4 mutants, in addition to loss of H2A.Z and chromatin accessibility. In wild-type ESCs, these “Dppa2/4-dependent” bivalent promoters are characterised by low H3K4me3 enrichment and breadth, near-absent expression levels and initiating but not elongating RNA polymerase. Notably, Dppa2/4-dependent promoters are less evolutionarily conserved suggesting that they lack additional safeguard measures to maintain bivalency at these genes in the absence of Dppa2/4. Concomitantly with the loss of bivalency, Dppa2/4-dependent bivalent promoters gain DNA methylation and consequently are no longer able to be effectively activated upon ESC differentiation, leading to defects in cell fate acquisition. Our findings reveal a targeting principle for bivalency to developmental gene promoters poising them for future lineage specific gene activation.
2020-05-26 | PXD014981 | Pride