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Base-resolution detection of N4-methylcytosine in genomic DNA using 4mC-TAB-seq

ABSTRACT: Base-resolution detection of N4-methylcytosine in genomic DNA using 4mC-TAB-seq

PROVIDER: PRJNA267586 | ENA |

REPOSITORIES: ENA

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Base-resolution detection of N4-methylcytosine in genomic DNA using 4mC-TAB-seq

Project description:N4-methylcytosine is a major DNA modification integral to restriction-modification (R-M) systems in bacterial genomes. Here we describe 4mC-Tet-Assisted Bisulfite-sequencing (4mC-TAB-seq), a method that accurately and rapidly reveals the genome-wide locations of N4-methylcytosines at single-base resolution. By coupling Tet-mediated oxidation with a modified sodium bisulfite conversion reaction, unmodified cytosines and 5-methylcytosines are read out as thymines, whereas N4-methylcytosines are read out as cytosines revealing their positions throughout the genome. 4mC-TAB-seq

2015-07-11 | E-GEOD-63371 | biostudies-arrayexpress

Base-resolution detection of N4-methylcytosine in genomic DNA using 4mC-TAB-seq

2015-07-11 | GSE63371 | GEO

Bisulfite-free and single-base resolution mapping of N4-methylcytosine in genomic DNA by APOBEC3A-mediated deamination sequencing

Project description:Bisulfite-free and single-base resolution mapping of N4-methylcytosine in genomic DNA by APOBEC3A-mediated deamination sequencing

| PRJNA785432 | ENA

Genome-wide mapping of N4-methylcytosine at single-base resolution by APOBEC3A-mediated deamination sequencing

Project description:N 4-methylcytosine (4mC) is a natural DNA modification occurring in thermophiles and plays important roles in restriction-modification (R-M) systems in bacterial genomes. However, the precise location and sequence context of 4mC in the whole genome are limited. In this study, we developed an APOBEC3A-mediated deamination sequencing (4mC-AMD-seq) method for genome-wide mapping of 4mC at single-base resolution. In the 4mC-AMD-seq method, cytosine and 5-methylcytosine (5mC) are deaminated by APOBEC3A (A3A) protein to generate uracil and thymine, both of which are read as thymine in sequencing, while 4mC is resistant to deamination and therefore read as cytosine. Thus, the readouts of cytosines from sequencing could manifest the original 4mC sites in genomes. With the 4mC-AMD-seq method, we achieved the genome-wide mapping of 4mC in Deinococcus radiodurans (D. radiodurans). In addition, we confirmed that 4mC, but not 5mC, was the major modification in the D. radiodurans genome. We identified 1586 4mC sites in the genome of D. radiodurans, among which 564 sites were located in the CCGCGG motif. The average methylation levels in the CCGCGG motif and non-CCGCGG sequence were 70.0% and 22.8%, respectively. We envision that the 4mC-AMD-seq method will facilitate the investigation of 4mC functions, including the 4mC-involved R-M systems, in uncharacterized but potentially useful strains.

2021-12-15 | GSE189965 | GEO

Single-base resolution methylome of 5-methylcytosine in mammalian transcriptome

Project description:Single-base resolution methylome of 5-methylcytosine in mammalian transcriptome

| PRJNA301456 | ENA

Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution

Project description:Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution

| PRJNA448064 | ENA

Single-base resolution methylome of 5-Methylcytosine in human and mouse transcriptome

Project description:Single-base resolution methylome of 5-Methylcytosine in human and mouse transcriptome

| PRJNA362514 | ENA

Base-resolution detection of N4-methylcytosine in genomic DNA using 4mC-Tet-assisted-bisulfite- sequencing.

Project description: Not available

| S-EPMC4666385 | biostudies-literature

Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution

Project description:We report a new bisulfite-free 5mC and 5hmC base-resolution sequencing method: TET Assisted Pyridine borane Sequencing (TAPS). TAPS relies on mild reactions and detects DNA modifications directly, without affecting unmodified cytosines. We applied this method for the first time to whole genome sequencing in E14 mESC cell line. For comparsion we prepared whole-genome bisulfite sequencing in the same cell line. Compared with bisulfite sequencing, TAPS results in higher mapping rates, more even coverage and lower sequencing cost, enabling more informative and cheaper methylome analyses. We expect TAPS to become the new standard in epigenetic DNA sequencing.

2018-12-24 | GSE112520 | GEO

Nanopore sequencing and data analysis for base-resolution genome-wide 5-methylcytosine profiling

Project description:Whole-genome bisulfite sequencing (WGBS) is currently the gold standard for DNA methylation (5-methylcytosine, 5mC) profiling, however the destructive nature of sodium bisulfite results in DNA fragmentation and subsequent biases in sequencing data. Such issues have led to the development of bisulfite-free methods for 5mC detection. Nanopore sequencing is a long read non-destructive approach that directly analyzes DNA and RNA fragments in real time. Recently, computational tools have been developed that enable base-resolution detection of 5mC from Oxford Nanopore sequencing data. In this chapter we provide a detailed protocol for preparation, sequencing, read assembly and analysis of genome-wide 5mC using Nanopore sequencing technologies.

2021-12-03 | GSE179673 | GEO

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