Identification of the early and late responder genes during the generation of induced pluripotent stem cells from mouse fibroblasts.
BACKGROUND
The generation of induced pluripotent stem cell (iPSC), a substitute for embryonic stem cell (ESC), requires the proper orchestration of a transcription program at the chromatin level. Our recent approach for the induction of pluripotent stem cells from fibroblasts using protein extracts from mouse ESCs could overcome the potential tumorigenicity risks associated with random retroviral integration. Here, we examine the epigenetic modifications and the transcriptome of two types of iPSC and of partially reprogrammed iPSCs (iPSCp) generated independently from adult cardiac and skin fibroblasts to assess any perturbations of the transcription program during reprogramming.


RESULTS
The comparative dissection of the transcription profiles and histone modification patterns at lysines 4 and 27 of histone H3 of the iPSC, iPSCp, ESC, and somatic cells revealed that the iPSC was almost completely comparable to the ESC, regardless of their origins, whereas the genes of the iPSCp were dysregulated to a larger extent. Regardless of the origins of the somatic cells, the fibroblasts induced using the ESC protein extracts appear to be completely reprogrammed into pluripotent cells, although they show unshared marginal differences in their gene expression programs, which may not affect the maintenance of stemness. A comparative investigation of the iPSCp generated by unwanted reprogramming showed that the two groups of genes on the pathway from somatic cells to iPSC might function as sequential reprogramming-competent early and late responders to the induction stimulus. Moreover, some of the divergent genes expressed only in the iPSCp were associated with many tumor-related pathways.


CONCLUSIONS
Faithful transcriptional reprogramming should follow epigenetic alterations to generate induced pluripotent stem cells from somatic cells. This genome-wide comparison enabled us to define the early and late responder genes during the cell reprogramming process to iPSC. Our results indicate that the cellular responsiveness to external stimuli should be pre-determined and sequentially orchestrated through the tight modulation of the chromatin environment during cell reprogramming to prevent unexpected reprogramming.
Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea.
Jihwan
J
Park
National Research Laboratory for Stem Cell Niche, Seoul National University College of Medicine, Seoul, Republic of Korea.|Innovative Research Institute for Cell Therapy and Cardiovascular Center & Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
Yoo-Wook
YW
Kwon
Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea.
Seokjin
S
Ham
Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea.
Chang-Pyo
CP
Hong
Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea.
Seonghye
S
Seo
Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea.
Moon Kyung
MK
Choe
Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea.
So-I
SI
Shin
National Research Laboratory for Stem Cell Niche, Seoul National University College of Medicine, Seoul, Republic of Korea.
Choon-Soo
CS
Lee
National Research Laboratory for Stem Cell Niche, Seoul National University College of Medicine, Seoul, Republic of Korea.|Innovative Research Institute for Cell Therapy and Cardiovascular Center & Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea.|Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Medicine or College of Pharmacy, Seoul National University, Seoul, Republic of Korea.
Hyo-Soo
HS
Kim
Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea.|Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea.
Tae-Young
http://orcid.org/0000-0001-5833-0844
TY
Roh
D000818:Animals; D002843:Chromatin / Q000378:metabolism; D044127:Epigenesis, Genetic / Q000235:genetics*; D005347:Fibroblasts / Q000378:metabolism*; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental / Q000235:genetics*; D015723:Gene Library; D005796:Genes / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D057026:Induced Pluripotent Stem Cells / Q000378:metabolism*; D051379:Mice; D008810:Mice, Inbred C57BL; D020411:Oligonucleotide Array Sequence Analysis; D014158:Transcription, Genetic
D002843:Chromatin