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

2014 ◽  
Vol 32 (12) ◽  
pp. 1231-1240 ◽  
Author(s):  
Hao Wu ◽  
Xiaoji Wu ◽  
Li Shen ◽  
Yi Zhang
Keyword(s):  
Bisulfite Sequencing ◽  
Dna Demethylation ◽  
Single Base ◽  
Active Dna Demethylation ◽  
Resolution Analysis ◽  
Single Base Resolution

scholarly journals Gene specific-loci quantitative and single-base resolution analysis of 5-formylcytosine by compound-mediated polymerase chain reaction

2018 ◽  
Vol 9 (15) ◽  
pp. 3723-3728 ◽  
Author(s):  
Yafen Wang ◽  
Chaoxing Liu ◽  
Xiong Zhang ◽  
Wei Yang ◽  
Fan Wu ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Demethylation ◽  
Chain Reaction ◽  
Single Base ◽  
Active Dna Demethylation ◽  
Key Players ◽  
Resolution Analysis ◽  
Single Base Resolution ◽  
Polymerase Chain

5-Formylcytosine (5fC) is known as one of the key players in the process of active DNA demethylation and displays essential epigenetic functions in mammals.

scholarly journals Bisulfite-free, single base-resolution analysis of 5-hydroxymethylcytosine in genomic DNA by chemical-mediated mismatch

2019 ◽  
Vol 10 (2) ◽  
pp. 447-452 ◽  
Author(s):  
Yafen Wang ◽  
Xiong Zhang ◽  
Fan Wu ◽  
Zonggui Chen ◽  
Xiang Zhou
Keyword(s):  
Genomic Dna ◽  
Dna Demethylation ◽  
Nuclear Reprogramming ◽  
Single Base ◽  
Active Dna Demethylation ◽  
Resolution Analysis ◽  
Single Base Resolution

5-Hydroxymethylcytosine (5hmC) is known as one of the vital players in nuclear reprogramming and the process of active DNA demethylation.

scholarly journals Mirror Bisulfite Sequencing: A Method for Single-Base Resolution of Hydroxymethylcytosine

2018 ◽  
Vol 90 (22) ◽  
pp. 13200-13206
Author(s):  
Darany Tan ◽  
Tzu Hung Chung ◽  
Xueguang Sun ◽  
Xi-Yu Jia
Keyword(s):  
Bisulfite Sequencing ◽  
Single Base ◽  
Single Base Resolution

scholarly journals Retraction Note: DNA methylome profiling at single-base resolution through bisulfite sequencing of 5mC-immunoprecipitated DNA

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Zhen Jia ◽  
Yueyi Shi ◽  
Lei Zhang ◽  
Yipeng Ren ◽  
Tong Wang ◽  
...  
Keyword(s):  
Bisulfite Sequencing ◽  
Single Base ◽  
Dna Methylome ◽  
Single Base Resolution

scholarly journals EM-seq: Detection of DNA Methylation at Single Base Resolution from Picograms of DNA

2019 ◽  
Author(s):  
Romualdas Vaisvila ◽  
V. K. Chaithanya Ponnaluri ◽  
Zhiyi Sun ◽  
Bradley W. Langhorst ◽  
Lana Saleh ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Bisulfite Sequencing ◽  
Nucleotide Composition ◽  
Whole Genome ◽  
Sequencing Data ◽  
Genomic Features ◽  
Single Base ◽  
Bisulfite Treatment ◽  
Genome Bisulfite Sequencing ◽  
Single Base Resolution

AbstractBisulfite sequencing is widely used to detect 5mC and 5hmC at single base resolution. However, bisulfite treatment damages DNA resulting in fragmentation, loss of DNA and biased sequencing data. To overcome this, we developed Enzymatic Methyl-seq (EM-seq), an enzymatic based approach that uses as little as 100 pg of DNA. EM-seq outperformed bisulfite converted libraries in all metrics examined including coverage, duplication, sensitivity and nucleotide composition. EM-seq libraries displayed even GC distribution, improved correlation across input amounts as well as increased representation of genomic features. These data indicate that EM-seq is more accurate and reliable than whole genome bisulfite sequencing (WGBS).

scholarly journals Mirror bisulfite sequencing — a method for single-base resolution of hydroxymethylcytosine

2015 ◽  
Author(s):  
Xueguang Sun ◽  
Darany Tan ◽  
Tzu Hung Chung ◽  
Xi-Yu Jia
Keyword(s):  
Bisulfite Sequencing ◽  
Biological Role ◽  
Human Tissues ◽  
Bisulfite Conversion ◽  
Single Base ◽  
Cpg Site ◽  
Genome Wide ◽  
Single Base Resolution ◽  
Dna Strand

While the role of 5-methylcytosine has been well studied, the biological role of 5-hydroxymethylcytosine still remains unclear due to the limited methods available for single-base detection of 5-hydroxymethylcytosine (5hmC). Here, we present Mirror bisulfite sequencing detects 5-hydroxymethylcytosines at a single CpG site by synthesizing a DNA strand to mirror the parental strand. This semi-conservative duplex is sequentially treated with β-glucosyltransferase and M.SssI methylase. A glucosyl-5hmCpG in the parental strand inhibits methylation of the mirroring CpG site, and after bisulfite conversion, a thymine in the mirroring strand indicates a 5hmCpG site in the parental strand whereas a cytosine indicates a non-5hmC site. Using this method, the 5hmC levels of various human tissues and paired liver tissues were mapped genome-wide.

Quantification and Single-Base Resolution Analysis of N1-Methyladenosine in mRNA by Ligation-Assisted Differentiation

2020 ◽  
Vol 92 (3) ◽  
pp. 2612-2619 ◽  
Author(s):  
Jiang-Hui Ding ◽  
Cheng-Jie Ma ◽  
Meng-Yuan Chen ◽  
Bei Chen ◽  
Bi-Feng Yuan ◽  
...  
Keyword(s):  
Single Base ◽  
Resolution Analysis ◽  
Single Base Resolution
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