title: Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape.
abstract: DNA sequence is a major determinant of the binding specificity of transcription factors (TFs) for their genomic targets. However, eukaryotic cells often express, at the same time, TFs with highly similar DNA binding motifs but distinct in vivo targets. Currently, it is not well understood how TFs with seemingly identical DNA motifs achieve unique specificities in vivo. Here, we used custom protein-binding microarrays to analyze TF specificity for putative binding sites in their genomic sequence context. Using yeast TFs Cbf1 and Tye7 as our case studies, we found that binding sites of these bHLH TFs (i.e., E-boxes) are bound differently in vitro and in vivo, depending on their genomic context. Computational analyses suggest that nucleotides outside E-box binding sites contribute to specificity by influencing the three-dimensional structure of DNA binding sites. Thus, the local shape of target sites might play a widespread role in achieving regulatory specificity within TF families.
authors.affiliation: Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Raluca
authors.initials: R
authors.lastname: Gordân
authors.forename: Ning
authors.initials: N
authors.lastname: Shen
authors.forename: Iris
authors.initials: I
authors.lastname: Dror
authors.forename: Tianyin
authors.initials: T
authors.lastname: Zhou
authors.forename: John
authors.initials: J
authors.lastname: Horton
authors.forename: Remo
authors.initials: R
authors.lastname: Rohs
authors.forename: Martha L
authors.initials: ML
authors.lastname: Bulyk
mesh_terms: D000595:Amino Acid Sequence; D051778:Basic Helix-Loop-Helix Leucine Zipper Transcription Factors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D001665:Binding Sites; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D024721:E-Box Elements; D016681:Genome, Fungal; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs; D011485:Protein Binding; D017433:Protein Structure, Secondary; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D015534:Trans-Activators / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
chemical_list: D051778:Basic Helix-Loop-Helix Leucine Zipper Transcription Factors; C064042:CBF1 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; C092673:TYE7 protein, S cerevisiae; D015534:Trans-Activators; D004247:DNA
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