Nuclease deficiencies alter plasma cell-free DNA methylationprofiles (mouse)
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PROVIDER: EGAS00001004696 | EGA |
REPOSITORIES: EGA
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Project description:The effects of DNASE1L3 or DNASE1 deficiency on cfDNA methylation was explored in plasma of mice deficient in these nucleases and in DNASE1L3-deficient humans. Compared to wildtype cfDNA, cfDNA in Dnase1l3-deficient mice was significantly hypomethylated, while cfDNA in Dnase1-deficient mice was hypermethylated. The cfDNA hypomethylation in Dnase1l3-deficient mice was due to increased fragmentation and representation from open chromatin regions (OCRs) and CpG islands (CGIs). These findings were absent in Dnase1-deficient mice.
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Project description:The dataset contains sequencing data in wildtype, Dnase1-deficient and Dnase1l3-deficient mice. We performed 2 x 75bp paired-end whole genome bisulfite sequencing of pooled plasma cell-free DNA (cfDNA) and buffy coat genomic DNA. The effects of DNASE1L3 or DNASE1 deficiency on cfDNA methylation was explored in plasma of mice deficient in these nucleases.
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Project description:We carried out a genome-wide cfDNA methylation profiling study of pancreatic ductal adenocarcinoma (PDAC) patients by Methylated DNA Immunoprecipitation coupled with high-throughput sequencing (MeDIP-seq). Compared with healthy individuals, 775 differentially methylated regions (DMRs) located in promoter regions were identified in PDAC patients with 761 hypermethylated and 14 hypomethylated regions; meanwhile, 761 DMRs in CpG islands (CGIs) were identified in PDAC patients with 734 hypermethylated and 27 hypomethylated regions (p-value < 35 0.0001). 143 hypermethylated DMRs were further selected which were located in promoter regions and completely overlapped with CGIs. A total of 8 probes from 8 genes were found to fairly distinguish PDAC patients from the healthy individuals, including TRIM73, FAM150A, EPB41L3, SIX3, MIR663, MAPT, LOC100128977 and LOC100130148.
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Project description:T-cell independent type II (TI-II) antigens, such as capsular polysaccharides, have multivalent epitope, which induce B cell activation, plasma cell differentiation and antibody production by strongly cross-linking B cell receptors. However, the mechanism of B cell activation by TI-II antigens remains unclear. In this study, we demonstrate that DNA endonuclease DNase1L3 (also termed DNase g) is required for the TI-II response. The production of antigen-specific antibodies was severely diminished in DNase1L3-deficient mice upon immunization with TI-II antigens, but not with TD antigens. Bone-marrow chimeric mice and B cell transfer experiments revealed that B-cell-intrinsic DNase1L3 was required for the TI-II response. DNase1L3-deficient B cells were defective in cell proliferation and plasma cell differentiation in the TI-II response in vivo as well as in vitro, which was not rescued by co-culture with DNase1L3-sufficient B cells in vitro, disproving an involvement of a secretory DNase1L3. In vitro stimulation with TI-II antigen transiently increased expression of DNase1L3 and its translocation into the nucleus. RNA-seq analysis of ex-vivo B cells having been responded to TI-II antigen in vivo revealed a marked reduction of Myc-target gene sets in DNase1L3-deficient B cells. Expression of IRF4, the gene of which is a target of Myc, was diminished in the ex-vivo DNase1L3-deficient B cells, in which forced expression of IRF4 restored the TI-II response in vivo. These data revealed an unexpected role of DNase1L3 in a missing link between B cell receptor signaling and B cell activation in the TI-II response, giving a valuable clue to molecularly dissect this response.
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Project description:Abnormal epigenetic gene regulation may play a pivotal role in atherogenesis. In particular, global DNA hypomethylation potentially leading to proatherogenic gene expression, occurs in atherosclerotic lesions in humans and animal models. In order to identify genomic sequences targeted for DNA hypomethylation in atherosclerosis, we analysed the methylation status of CpG islands (CGIs) in 45 human arteries with advanced atherosclerotic lesions and 16 normal counterparts by a microarray approach. Methylation data for 10,367 CGIs revealed that a subset (1.5%) of such sequences was hypermethylated in normal arteries, in accordance with data previously obtained in peripheral blood cells. Ninety-four per cent of this CGI subset was demethylated in atherosclerotic tissue, while only 17 of normally hypomethylated CGIs was hypermethylated in diseased tissue. A functional classification of genes physically associated with differentially methylated CGIs revealed a bias towards transcription factors (42%). The latter include HOX members, NOTCH1 and FOXP1, which are known to regulate angiogenesis, dedifferentiation, cell migration and macrophage function. The methylation status of selected CGIs was validated in further 10 subjects for either group. Expression patterns of these factors were compatible with the observed differential methylation. Our data suggest that one of the molecular changes associated with aberrant DNA methylation in advanced atherosclerosis is the regulation of critical transcription factor genes for the induction of a proatherogenic cellular phenotype. Two-condition experiment, i.e. normal vs. atherosclerotic arteries. 16 and 45 normal and atherosclerotic samples, respectively, were pooled and used to interrogate CpG island arrays in triplicate, for a total of six arrays. Each array was co-hybridized with untreated DNA (reference) and hypermethylated DNA obtained by biochemical filtration.
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Project description:Abnormal epigenetic gene regulation may play a pivotal role in atherogenesis. In particular, global DNA hypomethylation potentially leading to proatherogenic gene expression, occurs in atherosclerotic lesions in humans and animal models. In order to identify genomic sequences targeted for DNA hypomethylation in atherosclerosis, we analysed the methylation status of CpG islands (CGIs) in 45 human arteries with advanced atherosclerotic lesions and 16 normal counterparts by a microarray approach. Methylation data for 10,367 CGIs revealed that a subset (1.5%) of such sequences was hypermethylated in normal arteries, in accordance with data previously obtained in peripheral blood cells. Ninety-four per cent of this CGI subset was demethylated in atherosclerotic tissue, while only 17 of normally hypomethylated CGIs was hypermethylated in diseased tissue. A functional classification of genes physically associated with differentially methylated CGIs revealed a bias towards transcription factors (42%). The latter include HOX members, NOTCH1 and FOXP1, which are known to regulate angiogenesis, dedifferentiation, cell migration and macrophage function. The methylation status of selected CGIs was validated in further 10 subjects for either group. Expression patterns of these factors were compatible with the observed differential methylation. Our data suggest that one of the molecular changes associated with aberrant DNA methylation in advanced atherosclerosis is the regulation of critical transcription factor genes for the induction of a proatherogenic cellular phenotype.
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Project description:The biology of cell-free DNA fragmentation and the roles of DNASE1, DNASE1L3 and DFFB
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Project description:The biology of cell-free DNA fragmentation and the roles of
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Project description:We report that full length TET1 (TET1-FL) overexpression fails to induce global DNA demethylation in HEK293T cells. The preferential binding of TET1-FL to hypomethylated CpG islands (CGIs) through its CXXC domain leads to its inhibited 5-hydroxymethylcytosine (5hmC) production as methylation level increases. TET1-FL-induced 5hmC accumulates at CGI edges, while TET1 knockdown induces methylation spreading from methylated edges into hypomethylated CGIs. However, TET1 can regulate gene transcription independent of its dioxygenase catalytic function. Thus, our results identify TET1 as a maintenance DNA demethylase that does not purposely decrease methylation levels, but specifically maintains the DNA hypomethylation state of CGIs in adult cells. hMeDIP-seq analysis of genomic 5-hydroxymethylcytosine in HEK293T cells overexpressing mTET1-CD, TET1-CD, mTET1-FL, or TET1-FL
2014-06-04 | E-GEOD-44036 | biostudies-arrayexpress
Project description:We report that full length TET1 (TET1-FL) overexpression fails to induce global DNA demethylation in HEK293T cells. The preferential binding of TET1-FL to hypomethylated CpG islands (CGIs) through its CXXC domain leads to its inhibited 5-hydroxymethylcytosine (5hmC) production as methylation level increases. TET1-FL-induced 5hmC accumulates at CGI edges, while TET1 knockdown induces methylation spreading from methylated edges into hypomethylated CGIs. However, TET1 can regulate gene transcription independent of its dioxygenase catalytic function. Thus, our results identify TET1 as a maintenance DNA demethylase that does not purposely decrease methylation levels, but specifically maintains the DNA hypomethylation state of CGIs in adult cells.
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