title: Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome.
abstract: The study of 5-hydroxylmethylcytosines (5hmC) has been hampered by the lack of a method to map it at single-base resolution on a genome-wide scale. Affinity purification-based methods cannot precisely locate 5hmC nor accurately determine its relative abundance at each modified site. We here present a genome-wide approach, Tet-assisted bisulfite sequencing (TAB-Seq), that when combined with traditional bisulfite sequencing can be used for mapping 5hmC at base resolution and quantifying the relative abundance of 5hmC as well as 5mC. Application of this method to embryonic stem cells not only confirms widespread distribution of 5hmC in the mammalian genome but also reveals sequence bias and strand asymmetry at 5hmC sites. We observe high levels of 5hmC and reciprocally low levels of 5mC near but not on transcription factor-binding sites. Additionally, the relative abundance of 5hmC varies significantly among distinct functional sequence elements, suggesting different mechanisms for 5hmC deposition and maintenance.
authors.affiliation: Department of Chemistry, Institute for Biophysical Dynamics, The University of Chicago, IL 60637, USA.
authors.forename: Miao
authors.initials: M
authors.lastname: Yu
authors.forename: Gary C
authors.initials: GC
authors.lastname: Hon
authors.forename: Keith E
authors.initials: KE
authors.lastname: Szulwach
authors.forename: Chun-Xiao
authors.initials: CX
authors.lastname: Song
authors.forename: Liang
authors.initials: L
authors.lastname: Zhang
authors.forename: Audrey
authors.initials: A
authors.lastname: Kim
authors.forename: Xuekun
authors.initials: X
authors.lastname: Li
authors.forename: Qing
authors.initials: Q
authors.lastname: Dai
authors.forename: Yin
authors.initials: Y
authors.lastname: Shen
authors.forename: Beomseok
authors.initials: B
authors.lastname: Park
authors.forename: Jung-Hyun
authors.initials: JH
authors.lastname: Min
authors.forename: Peng
authors.initials: P
authors.lastname: Jin
authors.forename: Bing
authors.initials: B
authors.lastname: Ren
authors.forename: Chuan
authors.initials: C
authors.lastname: He
mesh_terms: D044503:5-Methylcytosine / Q000032:analysis / Q000031:analogs & derivatives; D000818:Animals; D003596:Cytosine / Q000031:analogs & derivatives* / Q000032:analysis; D053595:Embryonic Stem Cells / Q000378:metabolism; D057890:Epigenomics; D005786:Gene Expression Regulation; D015894:Genome, Human; D055106:Genome-Wide Association Study; D006801:Humans; D051379:Mice; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: C011865:5-hydroxymethylcytosine; D044503:5-Methylcytosine; D003596:Cytosine