title: Identification of a binding motif specific to HNF4 by comparative analysis of multiple nuclear receptors.
abstract: Nuclear receptors (NRs) regulate gene expression by binding specific DNA sequences consisting of AG[G/T]TCA or AGAACA half site motifs in a variety of configurations. However, those motifs/configurations alone do not adequately explain the diversity of NR function in vivo. Here, a systematic examination of DNA binding specificity by protein-binding microarrays (PBMs) of three closely related human NRs--HNF4α, retinoid X receptor alpha (RXRα) and COUPTF2--reveals an HNF4-specific binding motif (H4-SBM), xxxxCAAAGTCCA, as well as a previously unrecognized polarity in the classical DR1 motif (AGGTCAxAGGTCA) for HNF4α, RXRα and COUPTF2 homodimers. ChIP-seq data indicate that the H4-SBM is uniquely bound by HNF4α but not 10 other NRs in vivo, while NRs PXR, FXRα, Rev-Erbα appear to bind adjacent to H4-SBMs. HNF4-specific DNA recognition and transactivation are mediated by residues Asp69 and Arg76 in the DNA-binding domain; this combination of amino acids is unique to HNF4 among all human NRs. Expression profiling and ChIP data predict ≈ 100 new human HNF4α target genes with an H4-SBM site, including several Co-enzyme A-related genes and genes with links to disease. These results provide important new insights into NR DNA binding.
authors.affiliation: Department of Cell Biology and Neuroscience, University of California Riverside, Riverside, CA 92521, USA.
authors.forename: Bin
authors.initials: B
authors.lastname: Fang
authors.forename: Daniel
authors.initials: D
authors.lastname: Mane-Padros
authors.forename: Eugene
authors.initials: E
authors.lastname: Bolotin
authors.forename: Tao
authors.initials: T
authors.lastname: Jiang
authors.forename: Frances M
authors.initials: FM
authors.lastname: Sladek
mesh_terms: D001120:Arginine / Q000737:chemistry; D001224:Aspartic Acid / Q000737:chemistry; D001665:Binding Sites; D051837:COUP Transcription Factor II / Q000378:metabolism; D051557:Hepatocyte Nuclear Factor 4 / Q000737:chemistry / Q000378:metabolism*; D006801:Humans; D059372:Nucleotide Motifs; D040081:Protein Array Analysis; D011485:Protein Binding; D050436:Regulatory Elements, Transcriptional; D047490:Retinoid X Receptor alpha / Q000378:metabolism; D015533:Transcriptional Activation
chemical_list: D051837:COUP Transcription Factor II; C496592:HNF4A protein, human; D051557:Hepatocyte Nuclear Factor 4; D047490:Retinoid X Receptor alpha; D001224:Aspartic Acid; D001120:Arginine