Modular oxidation of cytosine modifications and their application in direct and quantitative sequencing of 5-hydroxymethylcytosine
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-acetami...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Journal article |
| Language: | English |
| Published: |
American Chemical Society
2023
|
| _version_ | 1797110062217428992 |
|---|---|
| author | Xu, H Chen, J Cheng, J Kong, L Chen, X Inoue, M Liu, Y Kriaucionis, S Zhao, M Song, C-X |
| author_facet | Xu, H Chen, J Cheng, J Kong, L Chen, X Inoue, M Liu, Y Kriaucionis, S Zhao, M Song, C-X |
| author_sort | Xu, H |
| collection | OXFORD |
| description | 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<sup>+</sup>BF<sub>4</sub><sup>–</sup>) 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. |
| first_indexed | 2024-03-07T07:49:59Z |
| format | Journal article |
| id | oxford-uuid:6ff576e4-2672-42e1-91cc-7365e0f269d7 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T07:49:59Z |
| publishDate | 2023 |
| publisher | American Chemical Society |
| record_format | dspace |
| spelling | oxford-uuid:6ff576e4-2672-42e1-91cc-7365e0f269d72023-07-06T11:57:28ZModular oxidation of cytosine modifications and their application in direct and quantitative sequencing of 5-hydroxymethylcytosineJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:6ff576e4-2672-42e1-91cc-7365e0f269d7EnglishSymplectic ElementsAmerican Chemical Society2023Xu, HChen, JCheng, JKong, LChen, XInoue, MLiu, YKriaucionis, SZhao, MSong, C-XSelective, 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<sup>+</sup>BF<sub>4</sub><sup>–</sup>) 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. |
| spellingShingle | Xu, H Chen, J Cheng, J Kong, L Chen, X Inoue, M Liu, Y Kriaucionis, S Zhao, M Song, C-X 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 |
| work_keys_str_mv | AT xuh modularoxidationofcytosinemodificationsandtheirapplicationindirectandquantitativesequencingof5hydroxymethylcytosine AT chenj modularoxidationofcytosinemodificationsandtheirapplicationindirectandquantitativesequencingof5hydroxymethylcytosine AT chengj modularoxidationofcytosinemodificationsandtheirapplicationindirectandquantitativesequencingof5hydroxymethylcytosine AT kongl modularoxidationofcytosinemodificationsandtheirapplicationindirectandquantitativesequencingof5hydroxymethylcytosine AT chenx modularoxidationofcytosinemodificationsandtheirapplicationindirectandquantitativesequencingof5hydroxymethylcytosine AT inouem modularoxidationofcytosinemodificationsandtheirapplicationindirectandquantitativesequencingof5hydroxymethylcytosine AT liuy modularoxidationofcytosinemodificationsandtheirapplicationindirectandquantitativesequencingof5hydroxymethylcytosine AT kriaucioniss modularoxidationofcytosinemodificationsandtheirapplicationindirectandquantitativesequencingof5hydroxymethylcytosine AT zhaom modularoxidationofcytosinemodificationsandtheirapplicationindirectandquantitativesequencingof5hydroxymethylcytosine AT songcx modularoxidationofcytosinemodificationsandtheirapplicationindirectandquantitativesequencingof5hydroxymethylcytosine |