Adolescent alcohol exposure alters DNA and RNA modifications in peripheral blood by liquid chromatography-tandem mass spectrometry analysis

Chen, Mengyuan; Gui, Zhu; Chen, Keke; Ding, Jiang-Hui; He, Jin-Gang; Xiong, Jun; Li, Jiale; Wang, Jie; Yuan, Bi-Feng; Feng, Yun

doi:10.1016/j.cclet.2021.08.094

Cited by 45 publications

(20 citation statements)

References 45 publications

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“…12–14 Some methods have been developed to detect 5hmC in genomic DNA, including thin layer chromatography detection, 3,4 liquid chromatography or capillary electrophoresis with mass spectrometry (LC-MS or CE-MS) analysis. 15–25 In these methods, genomic DNA is normally digested to nucleosides or nucleotides followed by analysis with different platforms, which mainly provides the qualitative and quantitative detection of 5hmC.…”

Section: Introductionmentioning

confidence: 99%

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

Xie

Wang

et al. 2022

Chem. Sci.

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Section: Introductionmentioning

confidence: 99%

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

Xie

Wang

et al. 2022

Chem. Sci.

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“…Enzymatic digestion of DNA was carried out according to a previously described method. 43,44 The detailed procedure can be found in the ESI †…”

Section: Methodsmentioning

confidence: 99%

Genome-wide mapping of N⁴-methylcytosine at single-base resolution by APOBEC3A-mediated deamination sequencing

et al. 2022

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“…The enzymatic digestion of DNA was carried out under neutral conditions according to the previous report. − The analysis of nucleosides was performed on an LC–ESI–MS/MS system consisting of a Shimadzu 8045 mass spectrometer (Kyoto, Japan) with an ESI source (Turbo Ionspray) coupled with a Shimadzu LC-30AD UPLC system . The detailed procedure for enzymatic digestion of DNA and LC–ESI–MS/MS analysis can be found in the Supporting Information.…”

Section: Methodsmentioning

confidence: 99%

Engineered APOBEC3C Sequencing Enables Bisulfite-Free and Direct Detection of DNA Methylation at a Single-Base Resolution

et al. 2022

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DNA methylation (5-methylcytosine, 5mC) is the most important epigenetic modification in mammals. Deciphering the roles of 5mC relies on the quantitative detection of 5mC at the single-base resolution. Bisulfite sequencing (BS-seq) is the most often employed technique for mapping 5mC in DNA. However, bisulfite treatment may cause serious degradation of input DNA due to the harsh reaction conditions. Here, we engineered the human apolipoprotein B mRNA-editing catalytic polypeptide-like 3C (A3C) protein to endow the engineered A3C (eA3C) protein with differential deamination activity toward cytosine and 5mC. By the virtue of the unique property of eA3C, we proposed an engineered A3C sequencing (EAC-seq) method for the bisulfitefree and quantitative mapping of 5mC in DNA at the single-base resolution. In EAC-seq, the eA3C protein can deaminate C but not 5mC, which is employed to differentiate C and 5mC in sequencing. Using the EAC-seq method, we quantitatively detected 5mC in genomic DNA of lung cancer tissue. In contrast to the harsh reaction conditions of BS-seq, which could lead to significant degradation of DNA, the whole procedure of EAC-seq is carried out under mild conditions, thereby preventing DNA damage. Taken together, the EAC-seq approach is bisulfite-free and straightforward, making it an invaluable tool for the quantitative detection of 5mC in limited DNA at the single-base resolution.

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Adolescent alcohol exposure alters DNA and RNA modifications in peripheral blood by liquid chromatography-tandem mass spectrometry analysis

Cited by 45 publications

References 45 publications

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

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

Genome-wide mapping of N⁴-methylcytosine at single-base resolution by APOBEC3A-mediated deamination sequencing

Engineered APOBEC3C Sequencing Enables Bisulfite-Free and Direct Detection of DNA Methylation at a Single-Base Resolution

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Adolescent alcohol exposure alters DNA and RNA modifications in peripheral blood by liquid chromatography-tandem mass spectrometry analysis

Cited by 45 publications

References 45 publications

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

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

Genome-wide mapping of N4-methylcytosine at single-base resolution by APOBEC3A-mediated deamination sequencing

Engineered APOBEC3C Sequencing Enables Bisulfite-Free and Direct Detection of DNA Methylation at a Single-Base Resolution

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Genome-wide mapping of N⁴-methylcytosine at single-base resolution by APOBEC3A-mediated deamination sequencing