title: Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine.
abstract: In contrast to 5-methylcytosine (5-mC), which has been studied extensively, little is known about 5-hydroxymethylcytosine (5-hmC), a recently identified epigenetic modification present in substantial amounts in certain mammalian cell types. Here we present a method for determining the genome-wide distribution of 5-hmC. We use the T4 bacteriophage β-glucosyltransferase to transfer an engineered glucose moiety containing an azide group onto the hydroxyl group of 5-hmC. The azide group can be chemically modified with biotin for detection, affinity enrichment and sequencing of 5-hmC-containing DNA fragments in mammalian genomes. Using this method, we demonstrate that 5-hmC is present in human cell lines beyond those previously recognized. We also find a gene expression level-dependent enrichment of intragenic 5-hmC in mouse cerebellum and an age-dependent acquisition of this modification in specific gene bodies linked to neurodegenerative disorders.
authors.affiliation: Department of Chemistry and Institute for Biophysical Dynamics, the University of Chicago, Chicago, Illinois, USA.
authors.forename: Chun-Xiao
authors.initials: CX
authors.lastname: Song
authors.forename: Keith E
authors.initials: KE
authors.lastname: Szulwach
authors.forename: Ye
authors.initials: Y
authors.lastname: Fu
authors.forename: Qing
authors.initials: Q
authors.lastname: Dai
authors.forename: Chengqi
authors.initials: C
authors.lastname: Yi
authors.forename: Xuekun
authors.initials: X
authors.lastname: Li
authors.forename: Yujing
authors.initials: Y
authors.lastname: Li
authors.forename: Chih-Hsin
authors.initials: CH
authors.lastname: Chen
authors.forename: Wen
authors.initials: W
authors.lastname: Zhang
authors.forename: Xing
authors.initials: X
authors.lastname: Jian
authors.forename: Jing
authors.initials: J
authors.lastname: Wang
authors.forename: Li
authors.initials: L
authors.lastname: Zhang
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Looney
authors.forename: Baichen
authors.initials: B
authors.lastname: Zhang
authors.forename: Lucy A
authors.initials: LA
authors.lastname: Godley
authors.forename: Leslie M
authors.initials: LM
authors.lastname: Hicks
authors.forename: Bruce T
authors.initials: BT
authors.lastname: Lahn
authors.forename: Peng
authors.initials: P
authors.lastname: Jin
authors.forename: Chuan
authors.initials: C
authors.lastname: He
mesh_terms: D044503:5-Methylcytosine / Q000031:analogs & derivatives; D000818:Animals; D017122:Bacteriophage T4 / Q000201:enzymology; D001710:Biotin / Q000737:chemistry*; D002531:Cerebellum / Q000737:chemistry; D003596:Cytosine / Q000031:analogs & derivatives* / Q000032:analysis; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D016678:Genome; D015894:Genome, Human; D005964:Glucosyltransferases / Q000378:metabolism; D057809:HEK293 Cells; D006367:HeLa Cells; D006801:Humans; D051379:Mice; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA; D013194:Staining and Labeling / Q000379:methods*
chemical_list: C011865:5-hydroxymethylcytosine; D044503:5-Methylcytosine; D001710:Biotin; D003596:Cytosine; D004247:DNA; D005964:Glucosyltransferases