Integrated Approach for the Identification of Human Hepatocyte Nuclear Factor 4α Target Genes Using Protein Binding Microarrays

• DOI: 10.1002/hep.23357
• Publication Date: 2009-10-05T22:38:49Z
• Authors: Eugene Bolotin; Hailing Liao; Tuong Chi Ta; Chuhu Yang; Wendy Hwang-Verslues; Jane R. Evans; Tao Jiang; Frances M. Sladek
• Keywords: Identification

Hepatocyte nuclear factor 4 alpha (HNF4α), a member of the receptor superfamily, is essential for liver function and linked to several diseases including diabetes, hemophilia, atherosclerosis, hepatitis. Although many DNA response elements target genes have been identified HNF4α, complete repertoire binding sites in human genome unknown. Here, we adapt protein microarrays (PBMs) examine DNA-binding characteristics two HNF4α species (rat human) isoforms (HNF4α2 HNF4α8) high-throughput fashion. We ˜1400 new sequences used this dataset successfully train Support Vector Machine (SVM) model that predicts an additional ˜10,000 unique HNF4α-binding sequences; also identify rules binding. performed expression profiling RNA interference knockdown HepG2 cells compared results search promoters all with PBM SVM models, as well published genome-wide location analysis. Using integrated approach, ˜240 direct genes, functional categories not typically associated such cell cycle, immune function, apoptosis, stress response, other cancer-related genes. Conclusion: report first use PBMs full-length liver-enriched transcription greatly expand thereby identifying functions HNF4α. establish web-based tool, HNF4 Motif Finder, can be potential any sequence. (Hepatology 2009.)