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PMID: 16899657 Published · ppublish English Comparative Study Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Human embryonic stem cells have a unique epigenetic signature.

Genome research ·Vol. 16 ·No. 9 ·2006-09-00 ·Pages 1075-83

Bibikova M, Chudin E, Wu B, Zhou L, Garcia EW, Liu Y, Shin S, Plaia TW, Auerbach JM, Arking DE, Gonzalez R, Crook J, Davidson B, Schulz TC, Robins A, Khanna A, Sartipy P, Hyllner J, Vanguri P, Savant-Bhonsale S, Smith AK, Chakravarti A, Maitra A, Rao M, Barker DL, Loring JF, Fan JB

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.

MeSH Terms
Cell Differentiation Cell Line Cell Line, Tumor Cell Lineage Cluster Analysis DNA Methylation Embryo, Mammalian/cytology Epigenesis, Genetic Female Humans Male Pluripotent Stem Cells/cytology,metabolism Stem Cells/cytology,metabolism
Authors & Affiliations
27 authors, click to expand affiliations / ORCID
Bibikova Marina
Illumina, Inc., San Diego, California 92121, USA.
Chudin Eugene
Wu Bonnie
Zhou Lixin
Garcia Eliza Wickham
Liu Ying
Shin Soojung
Plaia Todd W
Auerbach Jonathan M
Arking Dan E
Gonzalez Rodolfo
Crook Jeremy
Davidson Bruce
Schulz Thomas C
Robins Allan
Khanna Aparna
Sartipy Peter
Hyllner Johan
Vanguri Padmavathy
Savant-Bhonsale Smita
Smith Alan K
Chakravarti Aravinda
Maitra Anirban
Rao Mahendra
Barker David L
Loring Jeanne F
Fan Jian-Bing
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Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1088-9051
DOI
10.1101/gr.5319906
Published
2006-09-00
Epub
2006-00-09
Pages
1075-83
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC1557765
Subset
IM
Grants
NCI NIH HHS · R44 CA097851 · United States
NCI NIH HHS · R44-CA097851 · United States
External Links
PubMed source DOI: 10.1101/gr.5319906 PMC Full Text View journal details
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