title: Chemical modification-assisted bisulfite sequencing (CAB-Seq) for 5-carboxylcytosine detection in DNA.
abstract: 5-Methylcytosine (5mC) in DNA can be oxidized stepwise to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) by the TET family proteins. Thymine DNA glycosylase can further remove 5fC and 5caC, connecting 5mC oxidation with active DNA demethylation. Here, we present a chemical modification-assisted bisulfite sequencing (CAB-Seq) that can detect 5caC with single-base resolution in DNA. We optimized 1-ethyl-3-[3-dimethylaminopropyl]carbodiimide hydrochloride (EDC)-catalyzed amide bond formation between the carboxyl group of 5caC and a primary amine group. We found that the modified 5caC can survive the bisulfite treatment without deamination. Therefore, this chemical labeling coupled with bisulfite treatment provides a base-resolution detection and sequencing method for 5caC.
authors.affiliation: Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States.
authors.forename: Xingyu
authors.initials: X
authors.lastname: Lu
authors.forename: Chun-Xiao
authors.initials: CX
authors.lastname: Song
authors.forename: Keith
authors.initials: K
authors.lastname: Szulwach
authors.forename: Zhipeng
authors.initials: Z
authors.lastname: Wang
authors.forename: Payton
authors.initials: P
authors.lastname: Weidenbacher
authors.forename: Peng
authors.initials: P
authors.lastname: Jin
authors.forename: Chuan
authors.initials: C
authors.lastname: He
mesh_terms: D000577:Amides / Q000737:chemistry; D002384:Catalysis; D003596:Cytosine / Q000031:analogs & derivatives* / Q000032:analysis; D004247:DNA / Q000737:chemistry*; D005022:Ethyldimethylaminopropyl Carbodiimide / Q000737:chemistry; D015394:Molecular Structure; D013447:Sulfites / Q000737:chemistry*
chemical_list: C560974:5-carboxylcytosine; D000577:Amides; D013447:Sulfites; D003596:Cytosine; D004247:DNA; C042345:hydrogen sulfite; D005022:Ethyldimethylaminopropyl Carbodiimide