Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1243995 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR32914304_1.fastq.gz | Fastqsanger.gz | |||
| SRR32914304_2.fastq.gz | Fastqsanger.gz | |||
| SRR32914305_1.fastq.gz | Fastqsanger.gz | |||
| SRR32914305_2.fastq.gz | Fastqsanger.gz |
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Project description:We developed a novel in-vitro experimental method to characterize the protein-DNA interaction specificity and methylation sensitivity, we called Methyl-Spec-seq. In this data set, mouse HOXB13 (F1-F3) was used as a positive control example to show that Methyl-Spec-seq can determine the relative binding energy for variants with different methylation property, i.e., unmethylated, top hemimethylated, bottom hemimethylated, duplex methylated by either chemical synthesis or enzymatic treatment.
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Project description:We developed a novel in-vitro experimental method to characterize the protein-DNA interaction specificity and methylation sensitivity, we called Methyl-Spec-seq. In this data set, mouse ZFP57 (F1-F3) was used as a positive control example to show that Methyl-Spec-seq can determine the relative binding energy for variants with different methylation property, i.e., unmethylated, top hemimethylated, bottom hemimethylated, duplex methylated by either chemical synthesis or enzymatic treatment.
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Project description:We developed a novel in-vitro experimental method to characterize the protein-DNA interaction specificity and methylation sensitivity, we called Methyl-Spec-seq. In this data set, mouse AP1 was used as a positive control example to show that Methyl-Spec-seq can determine the relative binding energy for variants with different methylation property, i.e., unmethylated, top hemimethylated, bottom hemimethylated, duplex methylated by either chemical synthesis or enzymatic treatment.
2017-10-11 | GSE98669 | GEO
Project description:We developed a novel in-vitro experimental method to characterize the protein-DNA interaction specificity and methylation sensitivity, we called Methyl-Spec-seq. In this data set, mouse ZFP57 (F1-F3) was used as a positive control example to show that Methyl-Spec-seq can determine the relative binding energy for variants with different methylation property, i.e., unmethylated, top hemimethylated, bottom hemimethylated, duplex methylated by either chemical synthesis or enzymatic treatment.
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Project description:Bisulphite sequencing enables DNA methylation analysis of every cytosine residue. We have optimized conditions for combining chromatin immunoprecipation (ChIP) with high throughput bisulphite sequencing to study the relationship between histone modifications and DNA methylation. Paired-end bisulphite sequencing of H3K27me3-ChIP DNA for LNCaP and PrEC cell lines
2012-01-18 | E-GEOD-30558 | biostudies-arrayexpress
Project description:To improve our understanding of the relationships between methylation and expression we profiled mRNA expression and single-base resolution methylation levels for two breast cancer cell lines, MCF7 and T47D. Expression was profiled using RNA-seq. Methylation was assayed using Methyl-MAPS, which uses methylation-sensitive and -dependent restriction enzyme digests followed by high-throughput sequencing to identify methylation levels at individual CpGs (Edwards et al. 2010, Genome Research). DNA Methylation was assayed for two breast cancer cell lines using Methyl-MAPS.
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Project description:Background: To better understand the role DNA methylation plays in regulating gene expression in the developng heart and furthermore the role it plays in heart development we performed genome wide DNA methylation profiling of embryonic hearts at embryonic day (E)11.5 and E14.5 using methyl sensitive tiny fragment enrichment coupled with massive parallel sequencing by using the methyl-sensitive restriction enzyme HpyCH4IV, recognition site 'ACGT'. Results: We found that global methylation remains stable at analyzed 'ACGT' sites (1.64 million site) in developing hearts between E11.5 and E14.5. However, differential methylation was identified at individual loci enriched at genes involved in heart development suggesting a role for DNA methylation in the developing heart. Used Methyl Sensitive Tiny Fragment Enrichment/Massive Parallel Sequencing (MSFE/MPS) to assay methylation at 'ACGT' sites throughout the genome and generate a developmental profile of DNA methylation in the embryonic heart and to identify differences between developing mouse hearts at E11.5 and E14.5.
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Project description:In eukaryotes, heterochromatin is characterized by numerous epigenetic marks, including DNA methylation. Spreading of these marks into nearby active genes must be avoided in order to maintain appropriate gene expression. Here, we uncover Arabidopsis Methyl-CpG-Binding Domain 7 (MBD7) and Increased DNA Methylation 3 (IDM3) as anti-silencing factors that prevent transgene repression and genome-wide DNA hypermethylation. MBD7 preferentially binds to highly methylated, CG-dense regions associated with non-CG methylation and physically associates with other anti-silencing factors, including the histone acetyltransferase IDM1, IDM2, and IDM3. IDM1 and IDM2 were previously shown to facilitate active DNA demethylation by the 5-methylcytosine DNA glycosylase/lyase ROS1. Thus, MBD7 tethers the IDM proteins to methylated DNA, which enables the function of DNA demethylases that in turn establish chromatin boundaries and limit DNA methylation. Whole genome methylation maps of idm3-3, mbd7-2(CS876032) and Col-0 WT were generated using BS-seq
2015-01-29 | E-GEOD-59712 | biostudies-arrayexpress
Project description:We report the application of methyl-binding protein sequencing (MBD-seq) to global identify aberrant methylation between cisplatin sensitive and resistant ovarian cancer cell lines Detection of aberrant methylation states between cisplatin sensitive and resistant cell lines
2012-04-10 | E-GEOD-31418 | biostudies-arrayexpress
Project description:DNA methylation is catalysed by DNA methyltransferases (DNMTs) and is necessary for a correct embryonic development. On the other hand, the DNA demethylation is mediated by the Ten Eleven Translocation (Tet) proteins through oxidation of 5-methyl cytosine (5mC) to 5-hydroxyl (5hmC), 5-formyl (5fC) and 5-carboxyl (5caC) cytosine, and by the Thymine-DNA glycosylase (TDG) that excises the 5fC and 5caC. In embryonic stem cells (ESCs), gene promoters are maintained in an hypomethylated state, but the dynamics of this phenomenon still remains unknown. Here we present a genome-wide approach, named methylation-assisted bisulfite sequencing (MAB-Seq) that enables single-base resolution mapping of 5fC and 5caC and measuring of their relative abundance. Application of this method to mouse ESCs exposed the presence of 5fcaC residues on the hypomethylated promoters of the expressed genes, revealing an active DNA demethylation mechanism since the loss of TDG leads to an increase of 5fC/5caC. We also show that TDG is actually bound on these regions and that co-localizes and interacts with Tet1. We moreover demonstrate, by reduced representation of bisulfite sequencing (RRBS), that active promoters are actually demethylated by a Tet-dependent mechanism and that Dnmt1 and Dnmt3a are responsible of this DNA methylation. Our work shows the whole-genome map of 5fC and 5caC at single base resolution in ESCs, it demonstrates in detail the DNA methylation dynamics occurring on expressed gene promoters and identifies the key players of this mechanism. Furthermore, we provide a new tool (MAB-Seq) that can be broadly used in all biological contexts for epigenetics study involving identification and quantification of 5fC and 5caC at single base resolution. Methylation-assisted bisulfite sequencing (MAB-Seq) of E14 embryonic stem cells (ESCs), Biotag ChIP-Seq of Tdg and Reduced representation Bisulfite Sequencing (RRBS) in E14 ESCs.
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