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Bisulfite-free and single-nucleotide resolution sequencing of DNA epigenetic modification of 5-hydroxymethylcytosine using engineered deaminase

The discovery of 5-hydroxymethylcytosine (5hmC) in mammalian genomes is a landmark in epigenomics study. Similar to 5-methylcytosine (5mC), 5hmC is viewed as a critical epigenetic modification. Deciphering the functions of 5hmC necessitates the location analysis of 5hmC in genomes. Here, we proposed...

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Detalles Bibliográficos
Autores principales: Xie, Neng-Bin, Wang, Min, Ji, Tong-Tong, Guo, Xia, Ding, Jiang-Hui, Yuan, Bi-Feng, Feng, Yu-Qi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Royal Society of Chemistry 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9200132/
https://www.ncbi.nlm.nih.gov/pubmed/35774177
http://dx.doi.org/10.1039/d2sc01052f
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author Xie, Neng-Bin
Wang, Min
Ji, Tong-Tong
Guo, Xia
Ding, Jiang-Hui
Yuan, Bi-Feng
Feng, Yu-Qi
author_facet Xie, Neng-Bin
Wang, Min
Ji, Tong-Tong
Guo, Xia
Ding, Jiang-Hui
Yuan, Bi-Feng
Feng, Yu-Qi
author_sort Xie, Neng-Bin
collection PubMed
description The discovery of 5-hydroxymethylcytosine (5hmC) in mammalian genomes is a landmark in epigenomics study. Similar to 5-methylcytosine (5mC), 5hmC is viewed as a critical epigenetic modification. Deciphering the functions of 5hmC necessitates the location analysis of 5hmC in genomes. Here, we proposed an engineered deaminase-mediated sequencing (EDM-seq) method for the quantitative detection of 5hmC in DNA at single-nucleotide resolution. This method capitalizes on the engineered human apolipoprotein B mRNA-editing catalytic polypeptide-like 3A (A3A) protein to produce differential deamination activity toward cytosine, 5mC, and 5hmC. In EDM-seq, the engineered A3A (eA3A) protein can deaminate C and 5mC but not 5hmC. The original C and 5mC in DNA are deaminated by eA3A to form U and T, both of which are read as T during sequencing, while 5hmC is resistant to deamination by eA3A and is still read as C during sequencing. Therefore, the remaining C in the sequence manifests the original 5hmC. By EDM-seq, we achieved the quantitative detection of 5hmC in genomic DNA of lung cancer tissue. The EDM-seq method is bisulfite-free and does not require DNA glycosylation or chemical treatment, which offers a valuable tool for the straightforward and quantitative detection of 5hmC in DNA at single-nucleotide resolution.
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spelling pubmed-92001322022-06-29 Bisulfite-free and single-nucleotide resolution sequencing of DNA epigenetic modification of 5-hydroxymethylcytosine using engineered deaminase Xie, Neng-Bin Wang, Min Ji, Tong-Tong Guo, Xia Ding, Jiang-Hui Yuan, Bi-Feng Feng, Yu-Qi Chem Sci Chemistry The discovery of 5-hydroxymethylcytosine (5hmC) in mammalian genomes is a landmark in epigenomics study. Similar to 5-methylcytosine (5mC), 5hmC is viewed as a critical epigenetic modification. Deciphering the functions of 5hmC necessitates the location analysis of 5hmC in genomes. Here, we proposed an engineered deaminase-mediated sequencing (EDM-seq) method for the quantitative detection of 5hmC in DNA at single-nucleotide resolution. This method capitalizes on the engineered human apolipoprotein B mRNA-editing catalytic polypeptide-like 3A (A3A) protein to produce differential deamination activity toward cytosine, 5mC, and 5hmC. In EDM-seq, the engineered A3A (eA3A) protein can deaminate C and 5mC but not 5hmC. The original C and 5mC in DNA are deaminated by eA3A to form U and T, both of which are read as T during sequencing, while 5hmC is resistant to deamination by eA3A and is still read as C during sequencing. Therefore, the remaining C in the sequence manifests the original 5hmC. By EDM-seq, we achieved the quantitative detection of 5hmC in genomic DNA of lung cancer tissue. The EDM-seq method is bisulfite-free and does not require DNA glycosylation or chemical treatment, which offers a valuable tool for the straightforward and quantitative detection of 5hmC in DNA at single-nucleotide resolution. The Royal Society of Chemistry 2022-05-26 /pmc/articles/PMC9200132/ /pubmed/35774177 http://dx.doi.org/10.1039/d2sc01052f Text en This journal is © The Royal Society of Chemistry https://creativecommons.org/licenses/by-nc/3.0/
spellingShingle Chemistry
Xie, Neng-Bin
Wang, Min
Ji, Tong-Tong
Guo, Xia
Ding, Jiang-Hui
Yuan, Bi-Feng
Feng, Yu-Qi
Bisulfite-free and single-nucleotide resolution sequencing of DNA epigenetic modification of 5-hydroxymethylcytosine using engineered deaminase
title Bisulfite-free and single-nucleotide resolution sequencing of DNA epigenetic modification of 5-hydroxymethylcytosine using engineered deaminase
title_full Bisulfite-free and single-nucleotide resolution sequencing of DNA epigenetic modification of 5-hydroxymethylcytosine using engineered deaminase
title_fullStr Bisulfite-free and single-nucleotide resolution sequencing of DNA epigenetic modification of 5-hydroxymethylcytosine using engineered deaminase
title_full_unstemmed Bisulfite-free and single-nucleotide resolution sequencing of DNA epigenetic modification of 5-hydroxymethylcytosine using engineered deaminase
title_short Bisulfite-free and single-nucleotide resolution sequencing of DNA epigenetic modification of 5-hydroxymethylcytosine using engineered deaminase
title_sort bisulfite-free and single-nucleotide resolution sequencing of dna epigenetic modification of 5-hydroxymethylcytosine using engineered deaminase
topic Chemistry
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9200132/
https://www.ncbi.nlm.nih.gov/pubmed/35774177
http://dx.doi.org/10.1039/d2sc01052f
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