title: A study on promoter characteristics of head-to-head genes in Saccharomyces cerevisiae.
abstract: BACKGROUND
  Head-to-head (h2h) genes are prone to have association in expression and in functionality and have been shown conserved in evolution. Currently there are many studies on such h2h gene pairs. We found that the previous studies extremely focused on human genome. Furthermore, they only focused on analyses that require only gene or protein sequences but not conducted a systematic investigation on other promoter features such as the binding evidence of specific transcription factors (TFs). This is mainly because of the incomplete resources of higher organisms, though they are relatively of interest, than model organisms such as Saccharomyces cerevisiae. The authors of this study recently integrated nine promoter features of 6603 genes of S. cerevisiae from six databases and five papers. These resources are suitable to conduct a comprehensive analysis of h2h genes in S. cerevisiae.
  
  
  RESULTS
  This study analyzed various promoter features, including transcription boundaries (TSS, 5'UTR and 3'UTR), TATA box, TF binding evidence, TF regulation evidence, DNA bendability and nucleosome occupancy. The expression profiles and gene ontology (GO) annotations were used to measure if two genes are associated. Based on these promoter features, we found that i) the frequency of h2h genes was close to the expectation, namely they were not relatively frequent in genome; ii) the distance between the TSSs of most h2h genes fell into the range of 0-600 bps and was more centralized in 0-200 bps of the highly associated ones; iii) the number of TFs that regulate both h2h genes influenced the co-expression and co-function of the genes, while the number of TFs that bind both h2h genes influenced only the co-expression of the genes; iv) the association of two h2h genes was influenced by the existence of specific TFs such as STP2; v) the association of h2h genes whose bidirectional promoters have no TATA box was slightly higher than those who have TATA boxes; vi) the association of two h2h genes was not influenced by the DNA bendability and nucleosome occupancy.
  
  
  CONCLUSIONS
  This study analyzed h2h genes with various promoter features that have not been used in analyzing h2h genes. The results can be applied to other genomes to confirm if the observations of this study are limited to S. cerevisiae or universal in most organisms.
authors.affiliation: Department of Electrical Engineering, National Cheng Kung University, Tainan 70101, Taiwan. darby@mail.ncku.edu.tw
authors.forename: Darby Tien-Hao
authors.initials: DT
authors.lastname: Chang
authors.forename: Chi-Yeh
authors.initials: CY
authors.lastname: Wu
authors.forename: Chen-Yu
authors.initials: CY
authors.lastname: Fan
mesh_terms: D016681:Genome, Fungal / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics
chemical_list: D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors