Quantifying propagation of DNA methylation and hydroxymethylation with iDEMS
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA797183 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17616155_1.fastq.gz | Fastqsanger.gz | |||
| SRR17616155_2.fastq.gz | Fastqsanger.gz | |||
| SRR17616156_1.fastq.gz | Fastqsanger.gz | |||
| SRR17616156_2.fastq.gz | Fastqsanger.gz | |||
| SRR17616157_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
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Project description:DNA methylation is a critical epigenetic mark in mammalian cells. Many aspects of DNA methylation maintenance have been characterized, however the exact kinetics of post-replicative methylation maintenance remain a subject of debate. Here we develop isolation of DNA by EdU-labelling for Mass Spectrometry (iDEMS), a highly sensitive, quantitative mass spectrometry-based method for measuring DNA modifications on metabolically labelled DNA. iDEMS reveals an unexpectedly hemi-methylated landscape on nascent DNA. Combining iDEMS with metabolic labelling reveals that methylation maintenance is outpaced by cell division in mouse embryonic stem cells. Our approach shows hydroxymethylation is perpetually asymmetric between sister strands in favor of the parental, template strand. iDEMS can be coupled with immunoprecipitation of chromatin proteins, revealing features of DNA methylation-histone modification crosstalk and suggesting a model for interplay between methylation and nucleosome assembly. iDEMS therefore elucidates long-standing questions about DNA modification propagation and provides an important orthogonal technology to understanding this process in dynamic cellular contexts.
2022-10-24 | GSE193681 | GEO
Project description:Analysis of nucleosides (dC, dG, 5mdC and 5hmdC) using mass spectrometry and digested DNA samples.
Experimental data description:
- 12 h restoration (corresponding to EDFig2 b, EDFig5 b,c,h), E14 mESCs, labelled samples and followed for 12h, total DNA and stranded, 4 biological replicates (rep1, rep2, rep3 and rep4) and 2 technical replicates (_1, _2).
- KST061-62-63 (corresponding to Fig1 e-f, Fig2 b-g, Fig5 b-e, EDFig5 a,f), E14 mESCs, labelled samples and followed for 8h, total DNA and stranded, 3 biological replicates (KST061, KST062 and KST063) and 2 technical replicates (_1, _2).
- KST73-74-75 (corresponding to EDFig5 d,e,g), NIH3T3 cell line, labelled samples and followed for 8h, total DNA and stranded, 3 biological replicates (KST073, KST074 and KST075) and 2 technical replicates (_1, _2).
- KST76-77-78 (corresponding to Fig6 b-e, EDFig6 b-c), E14 mESCs, ChIP mass spectrometry samples for several histone modifications antibodies, total DNA and ChIP DNA, 3 biological replicates (KST076, KST077 and KST078) and 2 technical replicates (_1, _2).
- KST035 (corresponding to Fig1 c-d), E14 mESCs, DNA abundance and methylation levels, 2 technical replicates (_1, _2)
- KST045-46-47 (corresponding to Fig3 b, EDFig3 a), E14 mESCs, labelled early S phase samples and followed for 8h, total DNA and EdU+ pull down, 3 biological replicates (KST045, KST046 and KST047) and 2 technical replicates (_1, _2).
- KST050-51-52 (corresponding to Fig3 c, EDFig3 b), E14 mESCs, labelled late S phase samples and followed for 8h, total DNA and EdU+ pull down, 3 biological replicates (KST050, KST051 and KST052) and 2 technical replicates (_1, _2).
- KST056-57-60 (corresponding to EDFig4 a), E14 mESCs, cell cycle phases sorted using EdU labelling, 3 biological replicates (KST056, KST057 and KST060) and 2 technical replicates (_1, _2).
Standard curve data used for quantification are named as MM1-MM10, 2 technical replicates (_1, _2).
2022-10-21 | MSV000090568 | MassIVE
Project description:DNA methylation is a critical epigenetic mark in mammalian cells. Many aspects of DNA methylation maintenance have been characterized; however, the exact kinetics of post-replicative methylation maintenance remain a subject of debate. Here we develop isolation of DNA by 5-ethynyl-deoxyuridine labelling for mass spectrometry (iDEMS), a highly sensitive, quantitative mass spectrometry-based method for measuring DNA modifications on metabolically labelled DNA. iDEMS reveals an unexpectedly hemi-methylated landscape on nascent DNA. Combining iDEMS with metabolic labelling reveals that methylation maintenance is outpaced by cell division in mouse embryonic stem cells. Our approach shows that hydroxymethylation is perpetually asymmetric between sister strands in favour of the parental, template strand. iDEMS can be coupled with immunoprecipitation of chromatin proteins, revealing features of DNA methylation-histone modification crosstalk and suggesting a model for interplay between methylation and nucleosome assembly. iDEMS therefore elucidates long-standing questions about DNA modification propagation and provides an important orthogonal technology to understanding this process in dynamic cellular contexts.
| S-EPMC9859752 | biostudies-literature
Project description:Background: Despite the significant global loss of DNA hydroxymethylation marks in prostate cancer tissues, the locus-specific role of hydroxymethylation in prostate tumorigenesis is unknown. We characterized hydroxymethylation and methylation marks by performing whole-genome next generation sequencing in representative normal and prostate cancer-derived cell lines in order to determine functional pathways and key genes regulated by these epigenomic modifications in cancer. Results: Our cell line model shows disruption of hydroxymethylation distribution in cancer, with global loss and highly specific gain in promoter and CpG island regions. Significantly, we observed locus-specific retention of hydroxymethylation marks in specific intronic and intergenic regions which may play a novel role in the regulation of gene expression in critical functional pathways, such as BARD1 signaling and steroid hormone receptor signaling in cancer. We confirm a modest correlation of hydroxymethylation with expression in intragenic regions in prostate cancer, while identifying an original role for intergenic hydroxymethylation in differentially expressed regulatory pathways in cancer. We also demonstrate a successful strategy for the identification and validation of key candidate genes from differentially regulated biological pathways in prostate cancer. Conclusion: Our results indicate a distinct function for aberrant hydroxymethylation within each genomic feature in cancer, suggesting a specific and complex role for the deregulation of hydroxymethylation in tumorigenesis, similar to methylation. Subsequently, our characterization of key cellular pathways exhibiting dynamic enrichment patterns for methylation and hydroxymethylation marks may allow us to identify differentially epigenetically modified target genes implicated in prostate cancer tumorigenesis. Methylation profiles of representative normal prostate cell line RWPE-1 and prostate adenocarcinoma cell line 22Rv1 were generated by MBD capture followed by high-throughput sequencing on the HiSeq 2500 (Illumina), in triplicate. Hydroxymethylation profiles of RWPE-1 and 22Rv1 were generated by hMeSeal followed by high-throughput sequencing on the HiSeq 2500 (one replicate each). Additional hydroxymethylation profiling for RWPE-1 was generated by hMeDIP followed by high-throughput sequencing on the HiSeq 2000 (Illumina).
2016-03-15 | E-GEOD-74464 | biostudies-arrayexpress
Project description:Neuronal DNA modifications differ from those in other cells, including methylation outside CpG context and abundant 5-hydroxymethylation whose relevance for neuronal identities are unclear. Striatal projection neurons expressing D1 or D2 dopamine receptors allow addressing this question, as they share many characteristics but differ in their gene expression profiles, connections, and functional roles. We compare translating mRNAs and DNA modifications in these two populations. DNA methylation differences occur predominantly in large genomic clusters including differentially expressed genes, potentially important for D1 and D2 neurons. Decreased gene body methylation is associated with higher gene expression. Hydroxymethylation differences are more scattered and affect transcription factor binding sites, which can influence gene expression. We also find a strong genome-wide hydroxymethylation asymmetry between the two DNA strands, particularly pronounced at expressed genes and retrotransposons. These results identify novel properties of neuronal DNA modifications and unveil epigenetic characteristics of striatal projection neurons heterogeneity.
2022-11-11 | GSE186572 | GEO
Project description:Global distribution of DNA hydroxymethylation and DNA methylation in chronic lymphocytic leukemia
| PRJNA450999 | ENA
Project description:Extensive DNA methylation in promoter regions is observed in gastric cancer with Epstein-barr virus (EBV) infection and EBV infection is the cause to induce this extensive hypermethylaiton phenotype in gastric epithelial cells. From transcriptome analysis, we found that TET2, one of the demethylase enzymes, was downregulated by EBV infection in gastric epithelial cell line MKN7. TET2 was overexpressed in a gastric epithelial cell line, GES1, to see its function and the hydroxymethylation, a byproduct of DNA demethylation, acquired genes by TET2 overexpression and methylation acquired genes by EBV infection were significantly overlapped. These suggested that hydroxymethylation by TET2 could function to keep unmethylated status of genes before EBV infection, and TET2 depression could contribute to methylation acquisition of these target genes after EBV infection.
2017-04-28 | GSE84897 | GEO
Project description:Unified analysis of DNA methylation, hydroxymethylation and chromatin accessibility through targeted DNA labeling
| PRJNA970248 | ENA
Project description:Background: Despite the significant global loss of DNA hydroxymethylation marks in prostate cancer tissues, the locus-specific role of hydroxymethylation in prostate tumorigenesis is unknown. We characterized hydroxymethylation and methylation marks by performing whole-genome next generation sequencing in representative normal and prostate cancer-derived cell lines in order to determine functional pathways and key genes regulated by these epigenomic modifications in cancer. Results: Our cell line model shows disruption of hydroxymethylation distribution in cancer, with global loss and highly specific gain in promoter and CpG island regions. Significantly, we observed locus-specific retention of hydroxymethylation marks in specific intronic and intergenic regions which may play a novel role in the regulation of gene expression in critical functional pathways, such as BARD1 signaling and steroid hormone receptor signaling in cancer. We confirm a modest correlation of hydroxymethylation with expression in intragenic regions in prostate cancer, while identifying an original role for intergenic hydroxymethylation in differentially expressed regulatory pathways in cancer. We also demonstrate a successful strategy for the identification and validation of key candidate genes from differentially regulated biological pathways in prostate cancer. Conclusion: Our results indicate a distinct function for aberrant hydroxymethylation within each genomic feature in cancer, suggesting a specific and complex role for the deregulation of hydroxymethylation in tumorigenesis, similar to methylation. Subsequently, our characterization of key cellular pathways exhibiting dynamic enrichment patterns for methylation and hydroxymethylation marks may allow us to identify differentially epigenetically modified target genes implicated in prostate cancer tumorigenesis.
2016-03-15 | GSE74464 | GEO
Project description:Background Alzheimer’s disease is a progressive neurodegenerative disorder that is hypothesized to involve epigenetic dysfunction. Previous studies of DNA modifications in Alzheimer’s disease have been unable to distinguish between DNA methylation and DNA hydroxymethylation. DNA hydroxymethylation has been shown to be enriched in the human brain, although its role in Alzheimer’s disease has not yet been fully explored. Here we utilize oxidative bisulfite conversion, in conjunction with the Illumina Infinium Human Methylation 450K microarray, to identify neuropathology-associated differential DNA methylation and DNA hydroxymethylation in the entorhinal cortex. Results We identified one experiment-wide significant differentially methylated position residing in the WNT5B gene. Next, we investigated pathology-associated regions consisting of multiple adjacent loci. We identified one significant differentially hydroxymethylated region consisting of four probes spanning 104 bases in the FBXL16 gene. We also identified two significant differentially methylated regions: one consisting of two probes in a 93 base-pair region in the ANK1 gene and the other consisting of six probes in a 99 base-pair region in the ARID5B gene. We also highlighted three regions that show alterations in unmodified cytosine: two probes in a 39 base-pair region of ALLC, two probes in a 69 base-pair region in JAG2, in addition to the same six probes in ARID5B that were differentially methylated. Finally we replicated significant ANK1 disease-associated hypermethylation and hypohydroxymethylation patterns across eight CpG sites in an extended 118 base-pair region in an independent cohort using oxidative-bisulfite pyrosequencing. Conclusions Our study represents the first epigenome-wide association study of both DNA methylation and hydroxymethylation in Alzheimer’s disease entorhinal cortex. We demonstrate that previous estimates of DNA hypermethylation in ANK1 in Alzheimer’s disease were underestimates as it is confounded by hypohydroxymethylation.
2019-03-05 | GSE105109 | GEO