Epigenetic program leading to vessel differentiation
Identification of histone and transcriptional regulation in vessel differentiationClarification of how human blood vessels are constructed is desperately needed to advance regenerative medicine. A collaborative research group from Kumamoto University, Kyoto University, and the University of Tokyo in Japan investigated the changes in gene functions that occur when stem cells become vascular cells. They found that the histone code, which alters the transcriptional state of the gene, changes over time as stem cells differentiate into blood vessels in response to a stimulus. Furthermore, they found that a transcription factor group essential for blood vessel differentiation (ETS/GATA/SOX) has a previously unknown role.
Regenerative medicine has made remarkable progress due to research with embryonic stem (ES) cells and induced pluripotent stem (iPS) cells. However, the mechanism of how blood vessels are constructed from these undifferentiated cells has not yet been clarified. During the creation of new blood vessels, the vascular endothelial growth factor (VEGF) protein differentiates stem cells into vascular endothelial cells and stimulates them to create new blood vessels. Researchers at Kumamoto University added VEGF to undifferentiated ES cells and tracked the behavior of the entire genome and epigenome changes over time in vitro.
Using ES cells developed at Kyoto University's Institute for Frontier Medical Sciences, the research group collected RNA and histones of each cell immediately after VEGF stimulation (0 h), before differentiation (6 h), during differentiation (12 - 24 h), and after differentiation (48 h). They then comprehensively analyzed the changes in the whole genome and epigenome using next generation deep sequencing.
In the process of blood vessel differentiation, the function of the protein ETS variant 2 (ETV2), which determines the differentiation into vascular endothelium, was first induced within 6 hours of differentiation stimulation. The protein GATA2, which binds to ETV2 and supports vascular endothelial differentiation, was induced immediately thereafter. Transcription factors SOX and FLI1, both important for endothelial differentiation, were induced between 12 and 24 hours. At 48 hours, after differentiation into vascular endothelium was determined, a system of transcription was established in which genes unique to vascular endothelial differentiation were induced.
Furthermore, an examination of the histone code revealed that the regulatory genomic region of the transcription factors (ETS/GATA/SOX) was found to have gradually switched from a "brake histone mark," which suppresses transcription, to an "accelerator histone mark," which activates transcription, while in the process of differentiating into the vascular endothelium. Previously, in the region that controls the function of the transcription factor that promotes differentiation from ES cells to a specific cell type, bivalent modifications of histones such as the accelerator and brake histone marks for transcription were thought to have coexisted.
In addition, when these transcription factors lose their function, terminal differentiation into the vascular endothelium (completion of differentiation) is completely suppressed, and genes that are key to differentiation into vascular endothelial cells as well as transcription factors that maintain the undifferentiated state are adversely induced. Collectively, the transcription factors (ETS/GATA/SOX) not only induce vascular endothelial differentiation, but also suppress regression to an undifferentiated state and differentiation into other ectodermal- or endoderm-derived cells.
It is expected that the knowledge of the functions of these transcription factors, when combined with gene editing techniques, will allow for the efficient regeneration of blood vessels.
This finding was first reported in "Nucleic Acid Research" on March 17th, 2017.
[Citation]
Y. Kanki, R. Nakaki, T. Shimamura, T. Matsunaga, K. Yamamizu, S. Katayama, J. Suehiro, T. Osawa, H. Aburatani, T. Kodama, et al., “Dynamically and epigenetically coordinated gata/ets/sox transcription factor expression is indispensable for endothelial cell differentiation.,” Nucleic acids research, Mar. 2017. DOI: 10.1093/nar/gkx159
[Paper Info]
TITLE:
Dynamically and epigenetically coordinated GATA/ETS/SOX transcription factor expression is indispensable for endothelial cell differentiation
AUTHORS:
Yasuharu Kanki1,2,3,*,†, Ryo Nakaki4,†, Teppei Shimamura5,†, Taichi Matsunaga6,7, Kohei Yamamizu6,7, Shiori Katayama6,7, Jun-ichi Suehiro2,8, Tsuyoshi Osawa2,3, Hiroyuki Aburatani4, Tatsuhiko Kodama1,3, Youichiro Wada1, Jun K. Yamashita6,7 and Takashi Minami2,9,*
1 Isotope Science Center, The University of Tokyo
2 Division of Vascular Biology, RCAST, The University of Tokyo
3 Division of Systems Biology, RCAST, The University of Tokyo
4 Division of Genome Sciences, RCAST, The University of Tokyo
5 Department of Systems Biology, Graduate School of Medicine, Nagoya University
6 Department of Stem Cell Differentiation, Institute for Frontier Medical Sciences
7 Deparment of Cell Growth and Differentiation, CiRA, Kyoto University
8 Department of Pharmacology and Toxicology, Kyorin University School of Medicine
9 Division of Molecular and Vascular Biology, IRDA, Kumamoto University
* Corresponding author
†Contributed equally to the paper as first authors
JOURNAL:
Nucleic acids research
DOI:
https://doi.org/10.1093/nar/gkx159
URL:
https://academic.oup.com/nar/article/3064173/Dynamically-and-epigenetically-coordinated-GATA?searchresult=1
[Funds]
Grant-in-Aid for Young Scientists (B), Japan Society for the Promotion of Science
[24710227 to Y.K.];
NOVARTIS Foundation (Japan) for the Promotion of Science (to Y.K.);
Uehara Memorial Foundation (to Y.K.);
Cooperative Research Program of the Institute for Frontier Medical Sciences, Kyoto University, Japan (in part) (to Y.K.);
Leading-edge Research Promotion Fund from the Japan Society for the Promotion of Science
[LS038 to T. M.];
Life Science promotion Fund (Daiichi-Sankyo) (to T.M.).
Funding for open access charge: Grant-in-Aid, Japan Society for the Promotion of Science
[15H01348 to T.M.]
[Image]
Blood vessel differentiation through vascular endothelial growth factor
CAPTION:
(A) An epigenetic landscape was observed in the EC generation stage. Methylation state on the histone tail on the chromatin, histone code, in endothelial cells was read via hi-speed deep sequencer. (B) Histone marking on the regulatory region of EC master transcription factors was switched following the order, ① release the brake mark and then ② enter the acceleration mark. (C) A new concept proposal for the EC differentiation switch. Dynamic epigenetic analysis revealed that differentiated ECs were tightly regulated via histone modification switch, which looks like a baton pass, rather than bivalent histone modifications.
Adapted from: Y. Kanki, R. Nakaki, T. Shimamura, T. Matsunaga, K. Yamamizu, S. Katayama, J. Suehiro, T. Osawa, H. Aburatani, T. Kodama, et al., “Dynamically and epigenetically coordinated gata/ets/sox transcription factor expression is indispensable for endothelial cell differentiation.,” Nucleic acids research, Mar. 2017. DOI: 10.1093/nar/gkx159
[Image2]
Regulatory gene circuit of the master transcription factors for EC differentiation
CAPTION:
Schematic representation of the genetic regulatory network linking four transcription factors and EC differentiation. TFs: transcription factors, SMC: smooth muscle cells, HPC: hematopoietic stem cells, Epi: epithelial cells, CM: cardiomyocytes. Representative activated (red) or repressed (blue) genes by each transcription factor are shown in the box.
Adapted from: Y. Kanki, R. Nakaki, T. Shimamura, T. Matsunaga, K. Yamamizu, S. Katayama, J. Suehiro, T. Osawa, H. Aburatani, T. Kodama, et al., “Dynamically and epigenetically coordinated gata/ets/sox transcription factor expression is indispensable for endothelial cell differentiation.,” Nucleic acids research, Mar. 2017. DOI: 10.1093/nar/gkx159
CREDIT: Professor Takashi Minami
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