Direct enzymatic sequencing of 5-methylcytosine at single-base resolution.
Journal
Nature chemical biology
ISSN: 1552-4469
Titre abrégé: Nat Chem Biol
Pays: United States
ID NLM: 101231976
Informations de publication
Date de publication:
08 2023
08 2023
Historique:
received:
07
06
2022
accepted:
17
03
2023
medline:
31
7
2023
pubmed:
16
6
2023
entrez:
15
6
2023
Statut:
ppublish
Résumé
5-methylcytosine (5mC) is the most important DNA modification in mammalian genomes. The ideal method for 5mC localization would be both nondestructive of DNA and direct, without requiring inference based on detection of unmodified cytosines. Here we present direct methylation sequencing (DM-Seq), a bisulfite-free method for profiling 5mC at single-base resolution using nanogram quantities of DNA. DM-Seq employs two key DNA-modifying enzymes: a neomorphic DNA methyltransferase and a DNA deaminase capable of precise discrimination between cytosine modification states. Coupling these activities with deaminase-resistant adapters enables accurate detection of only 5mC via a C-to-T transition in sequencing. By comparison, we uncover a PCR-related underdetection bias with the hybrid enzymatic-chemical TET-assisted pyridine borane sequencing approach. Importantly, we show that DM-Seq, unlike bisulfite sequencing, unmasks prognostically important CpGs in a clinical tumor sample by not confounding 5mC with 5-hydroxymethylcytosine. DM-Seq thus offers an all-enzymatic, nondestructive, faithful and direct method for the reading of 5mC alone.
Identifiants
pubmed: 37322153
doi: 10.1038/s41589-023-01318-1
pii: 10.1038/s41589-023-01318-1
doi:
Substances chimiques
5-Methylcytosine
6R795CQT4H
Cytosine
8J337D1HZY
DNA
9007-49-2
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
1004-1012Subventions
Organisme : NHGRI NIH HHS
ID : F31 HG012892
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01-HG10646
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG010646
Pays : United States
Organisme : NHGRI NIH HHS
ID : HG-012892
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32-GM07729
Pays : United States
Commentaires et corrections
Type : CommentIn
Informations de copyright
© 2023. The Author(s), under exclusive licence to Springer Nature America, Inc.
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