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Status |
Public on Mar 15, 2023 |
Title |
Modular oxidation of cytosine modifications and their application in direct and quantitative sequencing of 5-hydroxymethylcytosine |
Organisms |
Homo sapiens; Mus musculus |
Experiment type |
Methylation profiling by high throughput sequencing
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Summary |
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) utilizing 4-acetamido-2,2,6,6-tetramethylpiperidine-1-oxoammonium tetrafluoroborate (ACT+ BF4–) 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 chemical-assisted pyridine borane sequencing (CAPS), CAPS+ improved the conversion rate and false-positive rate. We applied CAPS+ to mouse embryonic stem cells (mESCs) DNA, human normal brain and glioblastoma DNA samples, and demonstrated its superior sensitivity in analyzing the hydroxymethylome
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Overall design |
Whole genome sequencing of 5 hydroxymethylcytosine applying CAPS+ in mESCs (two replicates) and human brain samples (normal brain and glioblastoma).
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Contributor(s) |
Xu H, Chen J, Cheng J, Kong L, Chen X, Inoue M, Liu Y, Zhao M, Song C |
Citation(s) |
36961225 |
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Submission date |
Sep 23, 2022 |
Last update date |
May 02, 2023 |
Contact name |
Linzhen Kong |
E-mail(s) |
linzhen.kong@ndm.ox.ac.uk
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Organization name |
Ludwig Institute for Cancer Research
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Department |
Nuffield Department of Medicine
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Lab |
Dr. Chunxiao Song's group
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Street address |
University of Oxford Old Road Campus Research Building
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City |
Oxford |
ZIP/Postal code |
OX3 7FZ |
Country |
United Kingdom |
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Platforms (2) |
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Samples (4)
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Relations |
BioProject |
PRJNA883609 |