Human embryonic stem cells have a unique epigenetic signature.
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.
Bibikova
Marina
M
Illumina, Inc., San Diego, California 92121, USA.
Chudin
Eugene
E
Wu
Bonnie
B
Zhou
Lixin
L
Garcia
Eliza Wickham
EW
Liu
Ying
Y
Shin
Soojung
S
Plaia
Todd W
TW
Auerbach
Jonathan M
JM
Arking
Dan E
DE
Gonzalez
Rodolfo
R
Crook
Jeremy
J
Davidson
Bruce
B
Schulz
Thomas C
TC
Robins
Allan
A
Khanna
Aparna
A
Sartipy
Peter
P
Hyllner
Johan
J
Vanguri
Padmavathy
P
Savant-Bhonsale
Smita
S
Smith
Alan K
AK
Chakravarti
Aravinda
A
Maitra
Anirban
A
Rao
Mahendra
M
Barker
David L
DL
Loring
Jeanne F
JF
Fan
Jian-Bing
JB
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*