RNA interference-mediated inhibition of hepatocyte nuclear factor 1alpha identifies target genes.

Hepatocyte nuclear factor 1alpha (HNF1alpha) is a homeodomain transcription factor that is central to co-ordinated differentiation of a number of cell lineages, including hepatocytes in the liver and islet cells in the pancreas. HNF1alpha interacts directly with other transcription factors and co-factors and is involved in chromatin modification to alter gene expression. To further investigate the pivotal role of HNF1alpha in transcriptional control pathways we utilized RNA interference. An siRNA oligonucleotide specific for HNF1alpha reduced HNF1alpha protein levels by up to 70% in transient transfections of Caco2 cells. The same sequence incorporated into an shRNAi reduced protein levels by up to 90% in stable transfections. Microarray analysis of RNA from cell lines with stable RNAi-mediated down-regulation of HNF1alpha, identified genes known to be regulated by this transcription factor and also novel genes.