title: Genome-wide analysis of transcription factor binding sites and their characteristic DNA structures.
abstract: BACKGROUND
  Transcription factors (TF) regulate gene expression by binding DNA regulatory regions. Transcription factor binding sites (TFBSs) are conserved not only in primary DNA sequences but also in DNA structures. However, the global relationship between TFs and their preferred DNA structures remains to be elucidated.
  
  
  RESULTS
  In this paper, we have developed a computational method to generate a genome-wide landscape of TFs and their characteristic binding DNA structures in Saccharomyces cerevisiae. We revealed DNA structural features for different TFs. The structural conservation shows positional preference in TFBSs. Structural levels of DNA sequences are correlated with TF-DNA binding affinities.
  
  
  CONCLUSIONS
  We provided the genome-wide correspondences of TFs to DNA structures. Our findings will have implications in understanding TF regulatory mechanisms.
authors.forename: Zhiming
authors.initials: Z
authors.lastname: Dai
authors.forename: Dongliang
authors.initials: D
authors.lastname: Guo
authors.forename: Xianhua
authors.initials: X
authors.lastname: Dai
authors.forename: Yuanyan
authors.initials: Y
authors.lastname: Xiong
mesh_terms: D001665:Binding Sites; D019295:Computational Biology; D016681:Genome, Fungal; D020218:Response Elements; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D014157:Transcription Factors