ArticleNucleic acids research2009
Identification of an inter-transcription factor regulatory network in human hepatoma cells by Matrix RNAi.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 36 citations in OpenAlex.
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- A computer-guided design tool to increase the efficiency of cellular conversions.Nature communications · 2021Article
- Peretinoin, an Acyclic Retinoid, for the Secondary Prevention of Hepatocellular Carcinoma.Molecules (Basel, Switzerland) · 2021Review
- Human Glial Progenitor Cells Effectively Remyelinate the Demyelinated Adult Brain.Cell reports · 2020Article
- Early Transcriptional Changes within Liver, Adrenal Gland, and Lymphoid Tissues Significantly Contribute to Ebola Virus Pathogenesis in Cynomolgus Macaques.Journal of virology · 2020Article
- The role of lineage specifiers in pancreatic ductal adenocarcinoma.Journal of gastrointestinal oncology · 2018Review
- The activity of the carbamoyl phosphate synthase 1 promoter in human liver-derived cells is dependent on hepatocyte nuclear factor 3-beta.Journal of cellular and molecular medicine · 2017Article
- DNA methylation alters transcriptional rates of differentially expressed genes and contributes to pathophysiology in mice fed a high fat diet.Molecular metabolism · 2017Article
- Integrative Analysis of Transcription Factor Combinatorial Interactions Using a Bayesian Tensor Factorization Approach.Frontiers in genetics · 2017Article
- Reconstruction of gene regulatory modules from RNA silencing of IFN-α modulators: experimental set-up and inference method.BMC genomics · 2016Article
- Telomerase reverse transcriptase regulates microRNAs.International journal of molecular sciences · 2015Article
- A transient disruption of fibroblastic transcriptional regulatory network facilitates trans-differentiation.Nucleic acids research · 2014Article
- ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs.Genome research · 2014Article
- A bayesian framework that integrates heterogeneous data for inferring gene regulatory networks.Frontiers in bioengineering and biotechnology · 2014Review
- Temporal dynamics and transcriptional control using single-cell gene expression analysis.Genome biology · 2013Article
- Deep resequencing of GWAS loci identifies rare variants in CARD9, IL23R and RNF186 that are associated with ulcerative colitis.PLoS genetics · 2013Article
- Reconstruction of monocyte transcriptional regulatory network accompanies monocytic functions in human fibroblasts.PloS one · 2012Article
- A comprehensive survey of 3' animal miRNA modification events and a possible role for 3' adenylation in modulating miRNA targeting effectiveness.Genome research · 2010Article
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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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