An Integrated Approach for the Identification of HNF4α-Centered Transcriptional Regulatory Networks During Early Liver Regeneration

Abstract

Background/Aims: Hepatocyte nuclear factor-4α (HNF4α), the liver enriched transcription factor (TF), is one of the major regulators of hepatocyte differentiation and proliferation. However, how HNF4α participate in liver regeneration after partial hepatectomy (PH) remains largely unknown. In order to identify the HNF4α-centered regulatory network, we applied an integrated analytic strategy, in which, TF array, mRNA microarray, bioinformatic analysis and ChIP-on-chip assays were integrated. Methods/Results: The TF signatures from MOUSE OATFA (TF-array) platform revealed that the activity of HNF4α was significantly reduced and 17 other TFs showed increased activity at 4 h post PH. Then the ChIP-on-chip analysis on HNF4α were combined with mRNA expression profiling to select the possible HNF4α target genes during early liver regeneration, which were then sub-grouped according to their signaling pathways. More specifically, the HNF4α target genes with the gene ontology (GO) terms of cytokine-cytokine receptor, Jak-STAT, MAPK, toll-like receptor and insulin signaling pathways were further analyzed with an advanced bioinformatics tool named oPOSSUM to identify TF binding sites occupancy and predict the co-regulatory relationship between TFs and targets. Furthermore, we identified that repressed HNF4α during the early phase of liver regeneration may contribute cooperatively to the induction of immediate early genes, such as, c-fos, c-jun and stat3. Conclusion: our data indicate that HNF4α may play an inhibitory role on the induction of specific promitogenic genes and liver regeneration initiation. The integrated approach of mRNA/OATFA/ChIP-DSL/oPOSSUM analysis may help us better characterize the target genes and co-regulatory network of HNF4α during the early stage of liver regeneration.