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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

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...

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Autores principales: Sakata, Katsumi, Ohyanagi, Hajime, Sato, Shinji, Nobori, Hiroya, Hayashi, Akiko, Ishii, Hideshi, Daub, Carsten O., Kawai, Jun, Suzuki, Harukazu, Saito, Toshiyuki
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4319166/
https://www.ncbi.nlm.nih.gov/pubmed/25655563
http://dx.doi.org/10.1038/srep08283
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author Sakata, Katsumi
Ohyanagi, Hajime
Sato, Shinji
Nobori, Hiroya
Hayashi, Akiko
Ishii, Hideshi
Daub, Carsten O.
Kawai, Jun
Suzuki, Harukazu
Saito, Toshiyuki
author_facet Sakata, Katsumi
Ohyanagi, Hajime
Sato, Shinji
Nobori, Hiroya
Hayashi, Akiko
Ishii, Hideshi
Daub, Carsten O.
Kawai, Jun
Suzuki, Harukazu
Saito, Toshiyuki
author_sort Sakata, Katsumi
collection PubMed
description 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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spelling pubmed-43191662015-02-13 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 Nobori, Hiroya Hayashi, Akiko Ishii, Hideshi Daub, Carsten O. Kawai, Jun Suzuki, Harukazu Saito, Toshiyuki Sci Rep Article 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. Nature Publishing Group 2015-02-06 /pmc/articles/PMC4319166/ /pubmed/25655563 http://dx.doi.org/10.1038/srep08283 Text en Copyright © 2015, Macmillan Publishers Limited. All rights reserved http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder in order to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
Sakata, Katsumi
Ohyanagi, Hajime
Sato, Shinji
Nobori, Hiroya
Hayashi, Akiko
Ishii, Hideshi
Daub, Carsten O.
Kawai, Jun
Suzuki, Harukazu
Saito, Toshiyuki
System-wide analysis of the transcriptional network of human myelomonocytic leukemia cells predicts attractor structure and phorbol-ester-induced differentiation and dedifferentiation transitions
title System-wide analysis of the transcriptional network of human myelomonocytic leukemia cells predicts attractor structure and phorbol-ester-induced differentiation and dedifferentiation transitions
title_full System-wide analysis of the transcriptional network of human myelomonocytic leukemia cells predicts attractor structure and phorbol-ester-induced differentiation and dedifferentiation transitions
title_fullStr System-wide analysis of the transcriptional network of human myelomonocytic leukemia cells predicts attractor structure and phorbol-ester-induced differentiation and dedifferentiation transitions
title_full_unstemmed System-wide analysis of the transcriptional network of human myelomonocytic leukemia cells predicts attractor structure and phorbol-ester-induced differentiation and dedifferentiation transitions
title_short System-wide analysis of the transcriptional network of human myelomonocytic leukemia cells predicts attractor structure and phorbol-ester-induced differentiation and dedifferentiation transitions
title_sort system-wide analysis of the transcriptional network of human myelomonocytic leukemia cells predicts attractor structure and phorbol-ester-induced differentiation and dedifferentiation transitions
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4319166/
https://www.ncbi.nlm.nih.gov/pubmed/25655563
http://dx.doi.org/10.1038/srep08283
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