title: Human embryonic stem cells have a unique epigenetic signature.
abstract: Human embryonic stem (hES) cells originate during an embryonic period of active epigenetic remodeling. DNA methylation patterns are likely to be critical for their self-renewal and pluripotence. We compared the DNA methylation status of 1536 CpG sites (from 371 genes) in 14 independently isolated hES cell lines with five other cell types: 24 cancer cell lines, four adult stem cell populations, four lymphoblastoid cell lines, five normal human tissues, and an embryonal carcinoma cell line. We found that the DNA methylation profile clearly distinguished the hES cells from all of the other cell types. A subset of 49 CpG sites from 40 genes contributed most to the differences among cell types. Another set of 25 sites from 23 genes distinguished hES cells from normal differentiated cells and can be used as biomarkers to monitor differentiation. Our results indicate that hES cells have a unique epigenetic signature that may contribute to their developmental potential.
authors.affiliation: Illumina, Inc., San Diego, California 92121, USA.
authors.forename: Marina
authors.initials: M
authors.lastname: Bibikova
authors.forename: Eugene
authors.initials: E
authors.lastname: Chudin
authors.forename: Bonnie
authors.initials: B
authors.lastname: Wu
authors.forename: Lixin
authors.initials: L
authors.lastname: Zhou
authors.forename: Eliza Wickham
authors.initials: EW
authors.lastname: Garcia
authors.forename: Ying
authors.initials: Y
authors.lastname: Liu
authors.forename: Soojung
authors.initials: S
authors.lastname: Shin
authors.forename: Todd W
authors.initials: TW
authors.lastname: Plaia
authors.forename: Jonathan M
authors.initials: JM
authors.lastname: Auerbach
authors.forename: Dan E
authors.initials: DE
authors.lastname: Arking
authors.forename: Rodolfo
authors.initials: R
authors.lastname: Gonzalez
authors.forename: Jeremy
authors.initials: J
authors.lastname: Crook
authors.forename: Bruce
authors.initials: B
authors.lastname: Davidson
authors.forename: Thomas C
authors.initials: TC
authors.lastname: Schulz
authors.forename: Allan
authors.initials: A
authors.lastname: Robins
authors.forename: Aparna
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authors.lastname: Khanna
authors.forename: Peter
authors.initials: P
authors.lastname: Sartipy
authors.forename: Johan
authors.initials: J
authors.lastname: Hyllner
authors.forename: Padmavathy
authors.initials: P
authors.lastname: Vanguri
authors.forename: Smita
authors.initials: S
authors.lastname: Savant-Bhonsale
authors.forename: Alan K
authors.initials: AK
authors.lastname: Smith
authors.forename: Aravinda
authors.initials: A
authors.lastname: Chakravarti
authors.forename: Anirban
authors.initials: A
authors.lastname: Maitra
authors.forename: Mahendra
authors.initials: M
authors.lastname: Rao
authors.forename: David L
authors.initials: DL
authors.lastname: Barker
authors.forename: Jeanne F
authors.initials: JF
authors.lastname: Loring
authors.forename: Jian-Bing
authors.initials: JB
authors.lastname: Fan
mesh_terms: D002454:Cell Differentiation; D002460:Cell Line; D045744:Cell Line, Tumor; D019070:Cell Lineage; D016000:Cluster Analysis; D019175:DNA Methylation; D004622:Embryo, Mammalian / Q000166:cytology*; D044127:Epigenesis, Genetic; D005260:Female; D006801:Humans; D008297:Male; D039904:Pluripotent Stem Cells / Q000166:cytology / Q000378:metabolism; D013234:Stem Cells / Q000166:cytology / Q000378:metabolism*