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Quantitative profiling of DNA 6mA at single-base resolution using NAME-seq

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Escherichia coli Homo sapiens Chlamydomonas reinhardtii Helicobacter pylori

PROVIDER: GSE215170 | GEO | 2025/10/09

REPOSITORIES: GEO

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Quantitative profiling of DNA 6mA at single-base resolution using NAME-seq II

Project description:DNA N6-methyladenine (6mA) is the most widespread type of DNA methylation in prokaryotes. However, the prevalence of 6mA in eukaryotes has recently been challenged due to the limitations of current 6mA detection techniques. Here, we present a chemical-based sequencing method, Nitrite-assisted Amino MEthylation sequencing (NAME-seq), for quantitative, whole-genome mapping of 6mA at single-base resolution. NAME-seq combines nitrite conversion of 6mA to nitrosylated-6mA (6mA-NO) with Klenow Fragment (3'→5' exo-) random priming to induce a 6mA-to-T transversion specifically. We apply NAME-seq to two bacterial species and show that, compared to SMRT-seq, NAME-seq results in a more specific and robust detection of 6mA. NAME-seq can also accurately map 6mA in the C. reinhardtii genome at single-base resolution. Additionally, we show that NAME-seq can be combined with conventional DIP-seq to detect 6mA in the Dam-methylated human genome with high specificity. Therefore, we further perform DIP-NAME-seq to profile 6mA in WT and TASOR KO K562 cell line and revealed that 6mA is enriched at specific motifs (HYYHAG and CACACA) and H3K9me3 regions. In summary, we demonstrate NAME-seq is a specific and sensitive sequencing method for quantitative 6mA mapping at single base resolution across different model organisms.

2025-10-09 | GSE215169 | GEO

Quantitative profiling of DNA 6mA at single-base resolution using NAME-seq I

2025-10-09 | GSE215168 | GEO

Quantitative profiling of DNA 6mA at single-base resolution using NAME-seq

Project description:Quantitative profiling of DNA 6mA at single-base resolution using NAME-seq

| PRJNA889028 | ENA

Quantitative profiling of DNA 6mA at single-base resolution using NAME-seq II

Project description:Quantitative profiling of DNA 6mA at single-base resolution using NAME-seq II

| PRJNA889029 | ENA

Quantitative profiling of DNA 6mA at single-base resolution using NAME-seq I

Project description:Quantitative profiling of DNA 6mA at single-base resolution using NAME-seq I

| PRJNA889030 | ENA

Quantitative sequencing of 5-formylcytosine in DNA at single-base resolution

2014-04-08 | GSE56572 | GEO

Quantitative sequencing of 5-formylcytosine in DNA at single-base resolution.

Project description: Not available

| S-EPMC4188980 | biostudies-literature

Quantitative sequencing of 5-formylcytosine in DNA at single-base resolution

Project description:Cytosine base modifications 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) and 5-formylcytosine (5fC) are present in mammalian DNA. Here, reduced bisulfite sequencing is developed for quantitatively sequencing 5fC at single-base resolution. This method is then applied with oxidative bisulfite sequencing to gain a map of 5mC, 5hmC and 5fC in mouse embryonic stem cells. 12 samples, reduced representation bisulphite treatment: 4 replicates each for bisulphite (BS), oxidative BS (oxBS) and reduced BS (redBS) for the detection of 5mC, 5hmC and 5fC. Mouse (strain B6C) embryonic stem cells.

2014-04-08 | E-GEOD-56572 | biostudies-arrayexpress

Single-base resolution analysis of active DNA demethylation using methylase-assisted bisulfite sequencing

Project description:Active DNA demethylation in mammals involves TET-mediated iterative oxidation of 5-methylcytosine (5mC)/5-hydroxymethylcytosine (5hmC) and subsequent excision repair of highly oxidized cytosine bases 5-formylcytosine (5fC)/5-carboxylcytosine (5caC) by Thymine DNA glycosylase (TDG). However, quantitative and high-resolution analysis of active DNA demethylation activity remains challenging. Here we describe M.SssI methylase-assisted bisulfite sequencing (MAB-seq), a method that directly maps 5fC/5caC at single-base resolution. Genome-wide MAB-seq allows systematic identification of 5fC/5caC in Tdg-depleted embryonic stem cells, thereby generating a base-resolution map of active DNA demethylome. A comparison of 5fC/5caC and 5hmC distribution maps indicates that catalytic processivity of TET enzymes correlates with local chromatin accessibility. MAB-seq also reveals strong strand asymmetry of active demethylation within palindromic CpGs. Integrating MAB-seq with other base-resolution mapping methods enables quantitative measurement of cytosine modification states at key transitioning steps of active demethylation pathway, and reveals a regulatory role of 5fC/5caC excision repair in active DNA demethylation cascade.

2014-11-02 | GSE62631 | GEO

Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using a DNA deaminase

Project description:Here we present APOBEC-coupled epigenetic sequencing (ACE-seq), a bisulfite-free method for localizing 5-hydroxymethylcytosine (5hmC) at single-base resolution with low DNA input. The method builds on the observation that AID/APOBEC family DNA deaminase enzymes can potently discriminate between cytosine modification states and exploits the non-destructive nature of enzymatic, rather than chemical, deamination. ACE-seq yielded high-confidence 5hmC profiles with at least 1,000-fold less DNA input than conventional methods. Applying ACE-seq to generate a base-resolution map of 5hmC in tissue-derived cortical excitatory neurons, we found that 5hmC was almost entirely confined to CG dinucleotides. The whole-genome map permitted cytosine, 5-methylcytosine (5mC) and 5hmC to be parsed and revealed genomic features that diverged from global patterns, including enhancers and imprinting control regions with high and low 5hmC/5mC ratios, respectively. Enzymatic deamination overcomes many challenges posed by bisulfite-based methods, thus expanding the scope of epigenome profiling to include scarce samples and opening new lines of inquiry regarding the role of cytosine modifications in genome biology.

2018-10-08 | GSE116016 | GEO

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