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Modular Oxidation of Cytosine Modifications and Their Application in Direct and Quantitative Sequencing of 5-Hydroxymethylcytosine
[Image: see text] Selective, efficient, and controllable oxidation of cytosine modifications is valuable for epigenetic analyses, yet only limited progress has been made. Here, we present two modular chemical oxidation reactions: conversion of 5-hydroxymethylcytosine (5hmC) into 5-formylcytosine (5f...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2023
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10080677/ https://www.ncbi.nlm.nih.gov/pubmed/36961225 http://dx.doi.org/10.1021/jacs.3c01663 |
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author | Xu, Haiqi Chen, Jinfeng Cheng, Jingfei Kong, Linzhen Chen, Xiufei Inoue, Masato Liu, Yibin Kriaucionis, Skirmantas Zhao, Meiping Song, Chun-Xiao |
author_facet | Xu, Haiqi Chen, Jinfeng Cheng, Jingfei Kong, Linzhen Chen, Xiufei Inoue, Masato Liu, Yibin Kriaucionis, Skirmantas Zhao, Meiping Song, Chun-Xiao |
author_sort | Xu, Haiqi |
collection | PubMed |
description | [Image: see text] Selective, efficient, and controllable oxidation of cytosine modifications is valuable for epigenetic analyses, yet only limited progress has been made. Here, we present two modular chemical oxidation reactions: conversion of 5-hydroxymethylcytosine (5hmC) into 5-formylcytosine (5fC) using 4-acetamido-2,2,6,6-tetramethylpiperidine-1-oxoammonium tetrafluoroborate (ACT(+)BF(4)(–)) and further transformation of 5fC into 5-carboxycytosine (5caC) through Pinnick oxidation. Both reactions are mild and efficient on double-stranded DNA. We integrated these two oxidations with borane reduction to develop chemical-assisted pyridine borane sequencing plus (CAPS+), for direct and quantitative mapping of 5hmC. Compared with CAPS, CAPS+ improved the conversion rate and false-positive rate. We applied CAPS+ to mouse embryonic stem cells, human normal brain, and glioblastoma DNA samples and demonstrated its superior sensitivity in analyzing the hydroxymethylome. |
format | Online Article Text |
id | pubmed-10080677 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-100806772023-04-08 Modular Oxidation of Cytosine Modifications and Their Application in Direct and Quantitative Sequencing of 5-Hydroxymethylcytosine Xu, Haiqi Chen, Jinfeng Cheng, Jingfei Kong, Linzhen Chen, Xiufei Inoue, Masato Liu, Yibin Kriaucionis, Skirmantas Zhao, Meiping Song, Chun-Xiao J Am Chem Soc [Image: see text] Selective, efficient, and controllable oxidation of cytosine modifications is valuable for epigenetic analyses, yet only limited progress has been made. Here, we present two modular chemical oxidation reactions: conversion of 5-hydroxymethylcytosine (5hmC) into 5-formylcytosine (5fC) using 4-acetamido-2,2,6,6-tetramethylpiperidine-1-oxoammonium tetrafluoroborate (ACT(+)BF(4)(–)) and further transformation of 5fC into 5-carboxycytosine (5caC) through Pinnick oxidation. Both reactions are mild and efficient on double-stranded DNA. We integrated these two oxidations with borane reduction to develop chemical-assisted pyridine borane sequencing plus (CAPS+), for direct and quantitative mapping of 5hmC. Compared with CAPS, CAPS+ improved the conversion rate and false-positive rate. We applied CAPS+ to mouse embryonic stem cells, human normal brain, and glioblastoma DNA samples and demonstrated its superior sensitivity in analyzing the hydroxymethylome. American Chemical Society 2023-03-24 /pmc/articles/PMC10080677/ /pubmed/36961225 http://dx.doi.org/10.1021/jacs.3c01663 Text en © 2023 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Xu, Haiqi Chen, Jinfeng Cheng, Jingfei Kong, Linzhen Chen, Xiufei Inoue, Masato Liu, Yibin Kriaucionis, Skirmantas Zhao, Meiping Song, Chun-Xiao Modular Oxidation of Cytosine Modifications and Their Application in Direct and Quantitative Sequencing of 5-Hydroxymethylcytosine |
title | Modular Oxidation of
Cytosine Modifications and Their
Application in Direct and Quantitative Sequencing of 5-Hydroxymethylcytosine |
title_full | Modular Oxidation of
Cytosine Modifications and Their
Application in Direct and Quantitative Sequencing of 5-Hydroxymethylcytosine |
title_fullStr | Modular Oxidation of
Cytosine Modifications and Their
Application in Direct and Quantitative Sequencing of 5-Hydroxymethylcytosine |
title_full_unstemmed | Modular Oxidation of
Cytosine Modifications and Their
Application in Direct and Quantitative Sequencing of 5-Hydroxymethylcytosine |
title_short | Modular Oxidation of
Cytosine Modifications and Their
Application in Direct and Quantitative Sequencing of 5-Hydroxymethylcytosine |
title_sort | modular oxidation of
cytosine modifications and their
application in direct and quantitative sequencing of 5-hydroxymethylcytosine |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10080677/ https://www.ncbi.nlm.nih.gov/pubmed/36961225 http://dx.doi.org/10.1021/jacs.3c01663 |
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