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Liver regeneration after partial hepatectomy (PH) is a synchronized process that is precisely controlled by system-wide transcriptional regulatory networks.To clarify the transcriptional changes and regulatory networks involving transcription factors (TFs) and their target genes during the priming phase, an advanced mouse oligonucleotide array-based transcription factor assay (MOUSE OATFA), mRNA microarray analysis, bioinformatic analysis and ChIP-on-chip experiments were used.A total of 774 genes were upregulated or downregulated in PH liver samples compared with the sham operation (SH) group.Seventeen TFs showed significant changes in activity in regenerating livers, some which were not described in previous reports, including upstream stimulatory transcription factor1 (USF1).The TF signatures from MOUSE OATFA were combined with mRNA expression profiles and ChiP-on-chip analyses to construct experimental transcriptional regulatory networks in regenerating livers.USF1-centered regulatory networks were further confirmed by ChIP assays, revealing some of its target genes and comprehensieve coregulatory networks.The combination of MOUSE OATFA with transcriptome profiling and bioinformatics analysis represents an integrated paradigm for the comprehensive prediction of transcriptional networks in the early phase of liver regeneration.