Transcriptome profiling of human and murine ESCs identifies divergent paths required to maintain the stem cell state.
Human embryonic stem cells (hESCs) are an important source of stem cells in regenerative medicine, and much remains unknown about their molecular characteristics. To develop a detailed genomic profile of ESC lines in two different species, we compared transcriptomes of one murine and two different hESC lines by massively parallel signature sequencing (MPSS). Over 2 million signature tags from each line and their differentiating embryoid bodies were sequenced. Major differences and conserved similarities between species identified by MPSS were validated by reverse transcription polymerase chain reaction (RT-PCR) and microarray. The two hESC lines were similar overall, with differences that are attributable to alleles and propagation. Human-mouse comparisons, however, identified only a small (core) set of conserved genes that included genes known to be important in ESC biology, as well as additional novel genes. Identified were major differences in leukemia inhibitory factor, transforming growth factor-beta, and Wnt and fibroblast growth factor signaling pathways, as well as the expression of genes encoding metabolic, cytoskeletal, and matrix proteins, many of which were verified by RT-PCR or by comparing them with published databases. The study reported here underscores the importance of cross-species comparisons and the versatility and sensitivity of MPSS as a powerful complement to current array technology.
Wei
Chia Lin
CL
Genome Institute of Singapore, 60 Biopolis Street, Genome#02-01, Singapore 138672.
Miura
Takumi
T
Robson
Paul
P
Lim
Sai-Kiang
SK
Xu
Xiu-Qin
XQ
Lee
Mathia Yu-Chuan
MY
Gupta
Sanjay
S
Stanton
Lawrence
L
Luo
Yongquan
Y
Schmitt
Jacqui
J
Thies
Scott
S
Wang
Wei
W
Khrebtukova
Irina
I
Zhou
Daixing
D
Liu
Edison T
ET
Ruan
Yi Jun
YJ
Rao
Mahendra
M
Lim
Bing
B
D000818:Animals; D002460:Cell Line; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000235:genetics / Q000502:physiology*; D006801:Humans; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis; D012333:RNA, Messenger / Q000096:biosynthesis* / Q000235:genetics; D039901:Totipotent Stem Cells / Q000502:physiology*; D014158:Transcription, Genetic / Q000235:genetics / Q000502:physiology*
D012333:RNA, Messenger