FTDC1/2, oocyte-specific cofactors of DNMT1 required for epigenetic regulation and embryonic development (Bisulfite-Seq)
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1035096 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26655501_1.fastq.gz | Fastqsanger.gz | |||
| SRR26655501_2.fastq.gz | Fastqsanger.gz | |||
| SRR26655503_1.fastq.gz | Fastqsanger.gz | |||
| SRR26655503_2.fastq.gz | Fastqsanger.gz | |||
| SRR26655505_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:FTDC1/2, oocyte-specific cofactors of DNMT1 required for epigenetic regulation and embryonic development
| PRJNA1031544 | ENA
Project description:In order to obtain genome-wide profiles, base-resolution methylomes of oocytes, 4-cells and blastocysts were generated using the bisulfite sequencing (BS-seq) method for few samples. We find that global loss of DNA methylation during preimplantation development in Ftdc1-/-and Ftdc2-/- mice. Such a loss of methylation upon Ftdc1 or Ftdc2 inactivation is truly global and occurs across all chromosomes and genomic features examined, such as exon, intron, transposon and etc. To refine the analysis, we identified 7,311 and 6,208 hypomethylated differentially methylated regions (hypo-DMRs) and no hypermethylated DMRs (hyper-DMRs) in Ftdc1- and Ftdc2-null blastocyst compared to WT, respectively. To test whether FTDC1/2 deficiency and the observed global hypomethylation have an impact on transcriptional activity, we conducted RNA-sequencing in WT and Ftdc1- or Ftdc2-null blastocysts. 1,886 and 1,073 differentially expressed genes were identified in Ftdc1-/-(up 945, down 941) and Ftdc2-/- embryos (up 945, down 941). Gene ontology (GO) analysis showed that these DEGs are primarily enriched in gastrulation, autophagy, adhesion, and immune system-related pathways. To assess the potential effects of FTDC1/2 deficiency on histone modifications, our genome-wide profiles of H3K9me3 in blastocysts revealed that FTDC1/2 depletion results in the massive loss of H3K9me3. In contrast, H3K9me3 was correspondingly reduced in those hypo-DMRs in Ftdc1-/- and Ftdc2-/- embryos.
2025-05-18 | GSE246910 | GEO
Project description:In order to obtain genome-wide profiles, base-resolution methylomes of oocytes, 4-cells and blastocysts were generated using the bisulfite sequencing (BS-seq) method for few samples. We find that global loss of DNA methylation during preimplantation development in Ftdc1-/-and Ftdc2-/- mice. Such a loss of methylation upon Ftdc1 or Ftdc2 inactivation is truly global and occurs across all chromosomes and genomic features examined, such as exon, intron, transposon and etc. To refine the analysis, we identified 7,311 and 6,208 hypomethylated differentially methylated regions (hypo-DMRs) and no hypermethylated DMRs (hyper-DMRs) in Ftdc1- and Ftdc2-null blastocyst compared to WT, respectively. To test whether FTDC1/2 deficiency and the observed global hypomethylation have an impact on transcriptional activity, we conducted RNA-sequencing in WT and Ftdc1- or Ftdc2-null blastocysts. 1,886 and 1,073 differentially expressed genes were identified in Ftdc1-/-(up 945, down 941) and Ftdc2-/- embryos (up 945, down 941). Gene ontology (GO) analysis showed that these DEGs are primarily enriched in gastrulation, autophagy, adhesion, and immune system-related pathways. To assess the potential effects of FTDC1/2 deficiency on histone modifications, our genome-wide profiles of H3K9me3 in blastocysts revealed that FTDC1/2 depletion results in the massive loss of H3K9me3. In contrast, H3K9me3 was correspondingly reduced in those hypo-DMRs in Ftdc1-/- and Ftdc2-/- embryos.
2025-05-18 | GSE246099 | GEO
Project description:Whole-genome bisulfite sequencing of Dnmt1/3a/3b triple knockout (TKO) embryonic stem cells with or without expression of exogenous Dnmt1 before and after cell differentiation.
2025-01-16 | GSE200166 | GEO
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
Project description:DNA methylation is a key epigenetic modification involved in regulating gene expression and maintaining genomic integrity. Somatic patterns of DNA methylation are largely static, apart from focal dynamics at gene regulatory elements. To further advance our understanding of the role of DNA methylation in human development and disease, we inactivated all three catalytically active DNA methyltransferases in human embryonic stem cells (ESCs) using CRISPR/Cas9 genome editing. Disruption of DNMT3A or DNMT3B individually, as well as of both enzymes in tandem, creates viable, pluripotent cell lines with distinct effects on their DNA methylation landscape as assessed by whole-genome bisulfite sequencing. Surprisingly, in contrast to mouse, deletion of DNMT1 resulted in rapid cell death in human ESCs. To overcome the immediate lethality, we generated a doxycycline (DOX) responsive tTA-DNMT1* rescue line and readily obtained homozygous DNMT1 mutant lines. However, DOX-mediated repression of the exogenous DNMT1* initiates rapid, global loss of DNA methylation, followed by extensive cell death, demonstrating that DNA methylation is essential for human ESCs cultured in standard conditions. In summary, our data provide a comprehensive characterization of DNMT mutant ESCs, including single base genome-wide maps of their targets. RRBS methylation profiling of a time course of DNMT1* withdrawal in human ES cells
2015-03-30 | E-GEOD-63279 | biostudies-arrayexpress
Project description:Lung endoderm development occurs through a series of finely coordinated transcriptional processes that are regulated by epigenetic mechanisms. However, the role of DNA methylation in regulating lung endoderm development remains poorly understood. We demonstrate that DNA methyltransferase 1 (Dnmt1) is required for early branching morphogenesis of the lungs and for restraining epithelial fate specification. Loss of Dnmt1 leads to an early branching defect, a loss of proximal endodermal cell differentiation, and an expansion of the distal endoderm compartment. Dnmt1 deficiency also leads to precocious distal endodermal cell differentiation with premature expression of alveolar type 2 cell restricted genes. These data reveal an important requirement for Dnmt1 mediated DNA methylation in early lung development to promote proper branching morphogenesis, maintain proximal endodermal cell fate, and suppress premature activation of the distal epithelial fate.
2020-01-24 | GSE129177 | GEO
Project description:DNA methylation is a key epigenetic modification involved in regulating gene expression and maintaining genomic integrity. Somatic patterns of DNA methylation are largely static, apart from focal dynamics at gene regulatory elements. To further advance our understanding of the role of DNA methylation in human development and disease, we inactivated all three catalytically active DNA methyltransferases in human embryonic stem cells (ESCs) using CRISPR/Cas9 genome editing. Disruption of DNMT3A or DNMT3B individually, as well as of both enzymes in tandem, creates viable, pluripotent cell lines with distinct effects on their DNA methylation landscape as assessed by whole-genome bisulfite sequencing. Surprisingly, in contrast to mouse, deletion of DNMT1 resulted in rapid cell death in human ESCs. To overcome the immediate lethality, we generated a doxycycline (DOX) responsive tTA-DNMT1* rescue line and readily obtained homozygous DNMT1 mutant lines. However, DOX-mediated repression of the exogenous DNMT1* initiates rapid, global loss of DNA methylation, followed by extensive cell death, demonstrating that DNA methylation is essential for human ESCs cultured in standard conditions. In summary, our data provide a comprehensive characterization of DNMT mutant ESCs, including single base genome-wide maps of their targets.
2015-03-30 | GSE63279 | GEO
Project description:Purpose: This study aims to identify the differentially methylated regions in target genes in embryonic cardiomyocytes following the knockdown of DNMT1 expression. Methods: Primary cardiomyocytes were isolated from mouse embryonic day (E) 13.5 ventricles, and cultured for 48 h at 37°C to reach 70-80% confluency. Cells were transfected with either Qiagen FlexiTube GeneSolution (with 4 siRNAs) DNMT1 siRNA (#GS13433) or AllStars negative control siRNA (#1027281) at 12 nM using lipofectamine RNAiMAX (n=3 per treatment). At 72 h after transfection, cells were released with Accutase (Innovative Cell Technologies, San Diego, CA) and dissociated with Accumax (Innovative Cell Technologies). To sort cardiomyocytes, dissociated cells were stained with anti-VCAM1 antibody conjugated with allophycocyanin (APC; BioLegend, San Diego, CA), followed by magnetic sorting using anti-APC microbeads and magnetic assisted cell sorting (MACS) columns (Miltenyi Biotec, Bergisch Gladbach, Germany). DNA was extracted with the Quick-gDNA™ MicroPrep kit (Zymo Research, Irvine, CA). Genomic DNA was treated with sodium metabisulfite for bisulfite conversion. Target gene regions for fifteen target genes (two promoter regions per gene) were PCR-amplified from the bisulfite-converted DNA with ZymoTaq™ PreMix (Hot start DNA taq polymerase, ZYMO Research, Irvine, CA). The fifteen genes include Myh6, Myh7, Myh7b, Nppa, Nppb, Tnnc1, Tnni3, Tnnt2, Camta1, Camta2, Cdkn1A, Cdkn1B, Cdkn1C, Mef2c, and Mef2d. PCR products were cleaned with the ZR-96 DNA Clean & Concentrator™-5 kit (ZYMO Research). PCR products from the same genomic DNA sample were pooled at equal concentration ratio and made into an indexed sequencing library with the Nextera XT DNA Library Preparation kit and the Nextera XT Index Kit (Illumina, San Diego, CA). The Illumina-adapted libraries were pooled at equal molar ratio, spiked with 20% PhiX control libraries (Illumina), and sequenced with one 1x150 cycles run (v3) on a MiSeq sequencer (Illumina). The fastq files generated from MiSeq were uploaded to the UF Research Computing Galaxy instance developed by the University of Florida. The data were cleaned with the following steps: removed sequencing artifacts, trimmed 5’ or 3’ ends with low scores, removed adaptor contamination, and filtered low quality reads by the FastQC program. A reference genome with the amplicon sequences was built and bisulfite converted in silico with Bismark Bisulfite Mapper. The high quality sequence reads were aligned to the reference genome using Bowtie 2. Cytosine methylation counting was performed with the Bismark methylation extractor. Differential methylation was analyzed with the Methylkit package. CpG sites with false discovery rate (FDR) less than 0.05 and absolute percent methylation difference greater than 5% were considered as significant. Results: Following knockdown of DNMT1 for 72 h, differentially methylated regions were identified in the promoter CpG sites of Myh6, Myh7, Myh7b, Tnnc1, Tnni3, Tnnt2, Nppa, Nppb, Mef2c, Mef2d, Camta2, Cdkn1A, and Cdkn1C.
2019-05-12 | GSE81464 | GEO
Project description:Identification of the all RNA species associated with DNMT1. Using a comparative genome-scale approach we identified and correlated the RNA species physically associated with DNMT1 and proximal to the annotated genes to the methylation status of the corresponding loci and expression levels of the respective genes. This comparative approach delineated the first -DNMT1 centered- 'epitranscriptome' map, a comprehensive map cross-referencing DNMT1-interacting transcripts to (i) DNA methylation and (ii) gene expression profile. Relationship between DNMT1-RNA interactions, DNA methylation and gene expression
2012-12-01 | E-GEOD-32162 | biostudies-arrayexpress