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Identification of an inter-transcription factor regulatory network in human hepatoma cells by Matrix RNAi
Transcriptional regulation by transcriptional regulatory factors (TRFs) of their target TRF genes is central to the control of gene expression. To study a static multi-tiered inter-TRF regulatory network in the human hepatoma cells, we have applied a Matrix RNAi approach in which siRNA knockdown and...
Autores principales: | , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2009
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2651797/ https://www.ncbi.nlm.nih.gov/pubmed/19129217 http://dx.doi.org/10.1093/nar/gkn1028 |
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author | Tomaru, Yasuhiro Nakanishi, Misato Miura, Hisashi Kimura, Yasumasa Ohkawa, Hiroki Ohta, Yusuke Hayashizaki, Yoshihide Suzuki, Masanori |
author_facet | Tomaru, Yasuhiro Nakanishi, Misato Miura, Hisashi Kimura, Yasumasa Ohkawa, Hiroki Ohta, Yusuke Hayashizaki, Yoshihide Suzuki, Masanori |
author_sort | Tomaru, Yasuhiro |
collection | PubMed |
description | Transcriptional regulation by transcriptional regulatory factors (TRFs) of their target TRF genes is central to the control of gene expression. To study a static multi-tiered inter-TRF regulatory network in the human hepatoma cells, we have applied a Matrix RNAi approach in which siRNA knockdown and quantitative RT-PCR are used in combination on the same set of TRFs to determine their interdependencies. This approach focusing on several liver-enriched TRF families, each of which consists of structurally homologous members, revealed many significant regulatory relationships. These include the cross-talks between hepatocyte nuclear factors (HNFs) and the other TRF groups such as CCAAT/enhancer-binding proteins (CEBPs), retinoic acid receptors (RARs), retinoid receptors (RXRs) and RAR-related orphan receptors (RORs), which play key regulatory functions in human hepatocytes and liver. In addition, various multi-component regulatory motifs, which make up the complex inter-TRF regulatory network, were identified. A large part of the regulatory edges identified by the Matrix RNAi approach could be confirmed by chromatin immunoprecipitation. The resultant significant edges enabled us to depict the inter-TRF TRN forming an apparent regulatory hierarchy of (FOXA1, RXRA) → TCF1 → (HNF4A, ONECUT1) → (RORC, CEBPA) as the main streamline. |
format | Text |
id | pubmed-2651797 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-26517972009-03-13 Identification of an inter-transcription factor regulatory network in human hepatoma cells by Matrix RNAi Tomaru, Yasuhiro Nakanishi, Misato Miura, Hisashi Kimura, Yasumasa Ohkawa, Hiroki Ohta, Yusuke Hayashizaki, Yoshihide Suzuki, Masanori Nucleic Acids Res Gene regulation, Chromatin and Epigenetics Transcriptional regulation by transcriptional regulatory factors (TRFs) of their target TRF genes is central to the control of gene expression. To study a static multi-tiered inter-TRF regulatory network in the human hepatoma cells, we have applied a Matrix RNAi approach in which siRNA knockdown and quantitative RT-PCR are used in combination on the same set of TRFs to determine their interdependencies. This approach focusing on several liver-enriched TRF families, each of which consists of structurally homologous members, revealed many significant regulatory relationships. These include the cross-talks between hepatocyte nuclear factors (HNFs) and the other TRF groups such as CCAAT/enhancer-binding proteins (CEBPs), retinoic acid receptors (RARs), retinoid receptors (RXRs) and RAR-related orphan receptors (RORs), which play key regulatory functions in human hepatocytes and liver. In addition, various multi-component regulatory motifs, which make up the complex inter-TRF regulatory network, were identified. A large part of the regulatory edges identified by the Matrix RNAi approach could be confirmed by chromatin immunoprecipitation. The resultant significant edges enabled us to depict the inter-TRF TRN forming an apparent regulatory hierarchy of (FOXA1, RXRA) → TCF1 → (HNF4A, ONECUT1) → (RORC, CEBPA) as the main streamline. Oxford University Press 2009-03 2009-01-07 /pmc/articles/PMC2651797/ /pubmed/19129217 http://dx.doi.org/10.1093/nar/gkn1028 Text en © 2009 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Gene regulation, Chromatin and Epigenetics Tomaru, Yasuhiro Nakanishi, Misato Miura, Hisashi Kimura, Yasumasa Ohkawa, Hiroki Ohta, Yusuke Hayashizaki, Yoshihide Suzuki, Masanori Identification of an inter-transcription factor regulatory network in human hepatoma cells by Matrix RNAi |
title | Identification of an inter-transcription factor regulatory network in human hepatoma cells by Matrix RNAi |
title_full | Identification of an inter-transcription factor regulatory network in human hepatoma cells by Matrix RNAi |
title_fullStr | Identification of an inter-transcription factor regulatory network in human hepatoma cells by Matrix RNAi |
title_full_unstemmed | Identification of an inter-transcription factor regulatory network in human hepatoma cells by Matrix RNAi |
title_short | Identification of an inter-transcription factor regulatory network in human hepatoma cells by Matrix RNAi |
title_sort | identification of an inter-transcription factor regulatory network in human hepatoma cells by matrix rnai |
topic | Gene regulation, Chromatin and Epigenetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2651797/ https://www.ncbi.nlm.nih.gov/pubmed/19129217 http://dx.doi.org/10.1093/nar/gkn1028 |
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