System-wide analysis of the transcriptional network of human myelomonocytic leukemia cells predicts attractor structure and phorbol-ester-induced differentiation and dedifferentiation transitions

Katsumi Sakata; Hajime Ohyanagi; Shinji Sato; Hiroya Nobori; Akiko Hayashi; Hideshi Ishii; Carsten O. Daub; Jun Kawai; Harukazu Suzuki; Toshiyuki Saito

doi:10.1038/srep08283

System-wide analysis of the transcriptional network of human myelomonocytic leukemia cells predicts attractor structure and phorbol-ester-induced differentiation and dedifferentiation transitions

Katsumi Sakata^*, Hajime Ohyanagi, Shinji Sato, Hiroya Nobori, Akiko Hayashi, Hideshi Ishii, Carsten O. Daub, Jun Kawai, Harukazu Suzuki, Toshiyuki Saito

^*Corresponding author for this work

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3 Scopus citations

Abstract

We present a system-wide transcriptional network structure that controls cell types in the context of expression pattern transitions that correspond to cell type transitions. Co-expression based analyses uncovered a system-wide, ladder-like transcription factor cluster structure composed of nearly 1,600 transcription factors in a human transcriptional network. Computer simulations based on a transcriptional regulatory model deduced from the system-wide, ladder-like transcription factor cluster structure reproduced expression pattern transitions when human THP-1 myelomonocytic leukaemia cells cease proliferation and differentiate under phorbol myristate acetate stimulation. The behaviour of MYC, a reprogramming Yamanaka factor that was suggested to be essential for induced pluripotent stem cells during dedifferentiation, could be interpreted based on the transcriptional regulation predicted by the system-wide, ladder-like transcription factor cluster structure. This study introduces a novel system-wide structure to transcriptional networks that provides new insights into network topology.

Original language	English (US)
Article number	8283
Journal	Scientific Reports
Volume	5
DOIs	https://doi.org/10.1038/srep08283
State	Published - Feb 6 2015
Externally published	Yes

Bibliographical note

Funding Information:
The authors thank Prof. R. Albert for supplying the network analysis programs and Prof. K. Nakamura for valuable discussions. This study was partly supported by research grants from the Ministry of Education, Culture, Sports, Science and Technology, Japan for RIKEN OSC, CLST and PMI. This work was also supported by the Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research (Grant Number 26540157).

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Sakata, K., Ohyanagi, H., Sato, S., Nobori, H., Hayashi, A., Ishii, H., Daub, C. O., Kawai, J., Suzuki, H., & Saito, T. (2015). System-wide analysis of the transcriptional network of human myelomonocytic leukemia cells predicts attractor structure and phorbol-ester-induced differentiation and dedifferentiation transitions. Scientific Reports, 5, Article 8283. https://doi.org/10.1038/srep08283

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title = "System-wide analysis of the transcriptional network of human myelomonocytic leukemia cells predicts attractor structure and phorbol-ester-induced differentiation and dedifferentiation transitions",

abstract = "We present a system-wide transcriptional network structure that controls cell types in the context of expression pattern transitions that correspond to cell type transitions. Co-expression based analyses uncovered a system-wide, ladder-like transcription factor cluster structure composed of nearly 1,600 transcription factors in a human transcriptional network. Computer simulations based on a transcriptional regulatory model deduced from the system-wide, ladder-like transcription factor cluster structure reproduced expression pattern transitions when human THP-1 myelomonocytic leukaemia cells cease proliferation and differentiate under phorbol myristate acetate stimulation. The behaviour of MYC, a reprogramming Yamanaka factor that was suggested to be essential for induced pluripotent stem cells during dedifferentiation, could be interpreted based on the transcriptional regulation predicted by the system-wide, ladder-like transcription factor cluster structure. This study introduces a novel system-wide structure to transcriptional networks that provides new insights into network topology.",

author = "Katsumi Sakata and Hajime Ohyanagi and Shinji Sato and Hiroya Nobori and Akiko Hayashi and Hideshi Ishii and Daub, {Carsten O.} and Jun Kawai and Harukazu Suzuki and Toshiyuki Saito",

note = "Funding Information: The authors thank Prof. R. Albert for supplying the network analysis programs and Prof. K. Nakamura for valuable discussions. This study was partly supported by research grants from the Ministry of Education, Culture, Sports, Science and Technology, Japan for RIKEN OSC, CLST and PMI. This work was also supported by the Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research (Grant Number 26540157).",

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Sakata, K, Ohyanagi, H, Sato, S, Nobori, H, Hayashi, A, Ishii, H, Daub, CO, Kawai, J, Suzuki, H & Saito, T 2015, 'System-wide analysis of the transcriptional network of human myelomonocytic leukemia cells predicts attractor structure and phorbol-ester-induced differentiation and dedifferentiation transitions', Scientific Reports, vol. 5, 8283. https://doi.org/10.1038/srep08283

System-wide analysis of the transcriptional network of human myelomonocytic leukemia cells predicts attractor structure and phorbol-ester-induced differentiation and dedifferentiation transitions. / Sakata, Katsumi; Ohyanagi, Hajime; Sato, Shinji et al.
In: Scientific Reports, Vol. 5, 8283, 06.02.2015.

Research output: Contribution to journal › Article › peer-review

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AU - Sato, Shinji

AU - Nobori, Hiroya

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AU - Kawai, Jun

AU - Suzuki, Harukazu

AU - Saito, Toshiyuki

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AB - We present a system-wide transcriptional network structure that controls cell types in the context of expression pattern transitions that correspond to cell type transitions. Co-expression based analyses uncovered a system-wide, ladder-like transcription factor cluster structure composed of nearly 1,600 transcription factors in a human transcriptional network. Computer simulations based on a transcriptional regulatory model deduced from the system-wide, ladder-like transcription factor cluster structure reproduced expression pattern transitions when human THP-1 myelomonocytic leukaemia cells cease proliferation and differentiate under phorbol myristate acetate stimulation. The behaviour of MYC, a reprogramming Yamanaka factor that was suggested to be essential for induced pluripotent stem cells during dedifferentiation, could be interpreted based on the transcriptional regulation predicted by the system-wide, ladder-like transcription factor cluster structure. This study introduces a novel system-wide structure to transcriptional networks that provides new insights into network topology.

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System-wide analysis of the transcriptional network of human myelomonocytic leukemia cells predicts attractor structure and phorbol-ester-induced differentiation and dedifferentiation transitions

Abstract

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