title: Integrated detection of both 5-mC and 5-hmC by high-throughput tag sequencing technology highlights methylation reprogramming of bivalent genes during cellular differentiation.
abstract: 5-methylcytosine (5-mC) can be oxidized to 5-hydroxymethylcytosine (5-hmC). Genome-wide profiling of 5-hmC thus far indicates 5-hmC may not only be an intermediate form of DNA demethylation but could also constitute an epigenetic mark per se. Here we describe a cost-effective and selective method to detect both the hydroxymethylation and methylation status of cytosines in a subset of cytosines in the human genome. This method involves the selective glucosylation of 5-hmC residues, short-Sequence tag generation and high-throughput sequencing. We tested this method by screening H9 human embryonic stem cells and their differentiated embroid body cells, and found that differential hydroxymethylation preferentially occurs in bivalent genes during cellular differentiation. Especially, our results support hydroxymethylation can regulate key transcription regulators with bivalent marks through demethylation and affect cellular decision on choosing active or inactive state of these genes upon cellular differentiation. Future application of this technology would enable us to uncover the status of methylation and hydroxymethylation in dynamic biological processes and disease development in multiple biological samples.
authors.affiliation: Science & Technology Department; BGI-Shenzhen; Shenzhen, China.
authors.forename: Fei
authors.initials: F
authors.lastname: Gao
authors.affiliation: Science & Technology Department; BGI-Shenzhen; Shenzhen, China.
authors.forename: Yudong
authors.initials: Y
authors.lastname: Xia
authors.affiliation: Science & Technology Department; BGI-Shenzhen; Shenzhen, China.
authors.forename: Junwen
authors.initials: J
authors.lastname: Wang
authors.affiliation: Science & Technology Department; BGI-Shenzhen; Shenzhen, China.
authors.forename: Huijuan
authors.initials: H
authors.lastname: Luo
authors.affiliation: Science & Technology Department; BGI-Shenzhen; Shenzhen, China.
authors.forename: Zhaowei
authors.initials: Z
authors.lastname: Gao
authors.affiliation: Science & Technology Department; BGI-Shenzhen; Shenzhen, China.
authors.forename: Xu
authors.initials: X
authors.lastname: Han
authors.affiliation: Science & Technology Department; BGI-Shenzhen; Shenzhen, China.
authors.forename: Juyong
authors.initials: J
authors.lastname: Zhang
authors.affiliation: College of Life Sciences; Wuhan University; Wuhan, China.
authors.forename: Xiaojun
authors.initials: X
authors.lastname: Huang
authors.affiliation: Science & Technology Department; BGI-Shenzhen; Shenzhen, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Yao
authors.affiliation: Science & Technology Department; BGI-Shenzhen; Shenzhen, China.
authors.forename: Hanlin
authors.initials: H
authors.lastname: Lu
authors.affiliation: Science & Technology Department; BGI-Shenzhen; Shenzhen, China.
authors.forename: Na
authors.initials: N
authors.lastname: Yi
authors.affiliation: Science & Technology Department; BGI-Shenzhen; Shenzhen, China.
authors.forename: Baojin
authors.initials: B
authors.lastname: Zhou
authors.affiliation: Science & Technology Department; BGI-Shenzhen; Shenzhen, China.
authors.forename: Zhilong
authors.initials: Z
authors.lastname: Lin
authors.affiliation: Science & Technology Department; BGI-Shenzhen; Shenzhen, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Wen
authors.affiliation: Science & Technology Department; BGI-Shenzhen; Shenzhen, China.
authors.forename: Xiuqing
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Science & Technology Department; BGI-Shenzhen; Shenzhen, China.
authors.forename: Huanming
authors.initials: H
authors.lastname: Yang
authors.affiliation: Science & Technology Department; BGI-Shenzhen; Shenzhen, China; Department of Biology; University of Copenhagen; Copenhagen, Denmark; King Abdulaziz University; Jeddah, Saudi Arabia; The Novo Nordisk Foundation Center for Basic Metabolic Research; University of Copenhagen; Copenhagen, Denmark.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
mesh_terms: D044503:5-Methylcytosine / Q000378:metabolism* / Q000031:analogs & derivatives; D000818:Animals; D002454:Cell Differentiation / Q000235:genetics*; D002478:Cells, Cultured; D003596:Cytosine / Q000031:analogs & derivatives* / Q000378:metabolism; D019175:DNA Methylation / Q000502:physiology*; D058732:Embryoid Bodies / Q000166:cytology; D053595:Embryonic Stem Cells / Q000166:cytology* / Q000378:metabolism; D057166:High-Throughput Screening Assays / Q000379:methods*; D006801:Humans; D051379:Mice; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: C011865:5-hydroxymethylcytosine; D044503:5-Methylcytosine; D003596:Cytosine
keywords: HMST-Seq; differentiation; embryonic stem cells; hydroxymethylation; methylation