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Identification of an inter-transcription factor regulatory network in human hepatoma cells by Matrix RNAi.

Tomaru Y, Nakanishi M, Miura H, Kimura Y, Ohkawa H, Ohta Y, Hayashizaki Y, Suzuki M - Nucleic Acids Res. (2009)

Bottom Line: This approach focusing on several liver-enriched TRF families, each of which consists of structurally homologous members, revealed many significant regulatory relationships.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.

View Article: PubMed Central - PubMed

Affiliation: OMICS Sciences Center (OSC), RIKEN Yokohama Institute 1-7-22 Suehiro-Cho, Japan.

ABSTRACT
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.

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Perturbation network among HNFs. For depiction of the putative network, only significant edges (>2 SD and P < 0.05) among HNFs (TCF1, TCF2, FOXA1, FOXA2, FOXA3, HNF4A, HNF4G and ONECUT1) were extracted on the basis of Matrix RNAi data (Table 1). The network graph was drawn by Cytoscape (50). In this graph, TRFs and TRF genes regulated by them are not distinguished from each other, but the nodes emitting and accepting an arrow represent the putative regulators and regulated genes, respectively.
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Figure 5: Perturbation network among HNFs. For depiction of the putative network, only significant edges (>2 SD and P < 0.05) among HNFs (TCF1, TCF2, FOXA1, FOXA2, FOXA3, HNF4A, HNF4G and ONECUT1) were extracted on the basis of Matrix RNAi data (Table 1). The network graph was drawn by Cytoscape (50). In this graph, TRFs and TRF genes regulated by them are not distinguished from each other, but the nodes emitting and accepting an arrow represent the putative regulators and regulated genes, respectively.

Mentions: Perturbation network depicted based on the Matrix RNAi data (Figure 5 for inter-HNFs and Supplementary Figure 1 for the entire perturbation matrices, respectively) showed TCF1, ONECUT1, HNF4A and RXRA represent key hubs to emit multiple outputting regulatory signals and accept multiple inputting ones in the static HepG2 TRN. RXRA predominantly functions as a multiple outputting node and conversely RORC, CEBPA and HNF4G receive regulatory information from a lot of TRFs. Besides RORC, CEBPA and HNF4G, two PPARs (PPARG and PPARD) appear to be peripherally located because these TRF genes exclusively function as acceptors and, by contrast, PPARA primarily functions as an outputting node and thus appears to be epistatic in this perturbation network. PPAR and RAR families seem less related to other TRF families as compared with inter HNFs, RXR and ROR families, significantly connected to each other.Figure 5.


Identification of an inter-transcription factor regulatory network in human hepatoma cells by Matrix RNAi.

Tomaru Y, Nakanishi M, Miura H, Kimura Y, Ohkawa H, Ohta Y, Hayashizaki Y, Suzuki M - Nucleic Acids Res. (2009)

Perturbation network among HNFs. For depiction of the putative network, only significant edges (>2 SD and P < 0.05) among HNFs (TCF1, TCF2, FOXA1, FOXA2, FOXA3, HNF4A, HNF4G and ONECUT1) were extracted on the basis of Matrix RNAi data (Table 1). The network graph was drawn by Cytoscape (50). In this graph, TRFs and TRF genes regulated by them are not distinguished from each other, but the nodes emitting and accepting an arrow represent the putative regulators and regulated genes, respectively.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2651797&req=5

Figure 5: Perturbation network among HNFs. For depiction of the putative network, only significant edges (>2 SD and P < 0.05) among HNFs (TCF1, TCF2, FOXA1, FOXA2, FOXA3, HNF4A, HNF4G and ONECUT1) were extracted on the basis of Matrix RNAi data (Table 1). The network graph was drawn by Cytoscape (50). In this graph, TRFs and TRF genes regulated by them are not distinguished from each other, but the nodes emitting and accepting an arrow represent the putative regulators and regulated genes, respectively.
Mentions: Perturbation network depicted based on the Matrix RNAi data (Figure 5 for inter-HNFs and Supplementary Figure 1 for the entire perturbation matrices, respectively) showed TCF1, ONECUT1, HNF4A and RXRA represent key hubs to emit multiple outputting regulatory signals and accept multiple inputting ones in the static HepG2 TRN. RXRA predominantly functions as a multiple outputting node and conversely RORC, CEBPA and HNF4G receive regulatory information from a lot of TRFs. Besides RORC, CEBPA and HNF4G, two PPARs (PPARG and PPARD) appear to be peripherally located because these TRF genes exclusively function as acceptors and, by contrast, PPARA primarily functions as an outputting node and thus appears to be epistatic in this perturbation network. PPAR and RAR families seem less related to other TRF families as compared with inter HNFs, RXR and ROR families, significantly connected to each other.Figure 5.

Bottom Line: This approach focusing on several liver-enriched TRF families, each of which consists of structurally homologous members, revealed many significant regulatory relationships.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.

View Article: PubMed Central - PubMed

Affiliation: OMICS Sciences Center (OSC), RIKEN Yokohama Institute 1-7-22 Suehiro-Cho, Japan.

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus