title: Promoter modeling: the case study of mammalian histone promoters.
abstract: BACKGROUND
  Histone proteins play important roles in chromosomal functions. They are significantly evolutionarily conserved across species, which suggests similarity in their transcription regulation. The abundance of experimental data on histone promoters provides an excellent background for the evaluation of computational methods. Our study addresses the issue of how well computational analysis can contribute to unveiling the biologically relevant content of promoter regions for a large number of mammalian histone genes taken across several species, and suggests the consensus promoter models of different histone groups.
  
  
  RESULTS
  This is the first study to unveil the detailed promoter structures of all five mammalian histone groups and their subgroups. This is also the most comprehensive computational analysis of histone promoters performed to date. The most exciting fact is that the results correlate very well with the biologically known facts and experimental data. Our analysis convincingly demonstrates that computational approach can significantly contribute to elucidation of promoter content (identification of biologically relevant signals) complementing tedious wet-lab experiments. We believe that this type of analysis can be easily applied to other functional gene classes, thus providing a general framework for modelling promoter groups. These results also provide the basis to hunt for genes co-regulated with histone genes across mammalian genomes.
authors.affiliation: Knowledge Extraction Lab, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613.
authors.forename: Rajesh
authors.initials: R
authors.lastname: Chowdhary
authors.forename: R Ayesha
authors.initials: RA
authors.lastname: Ali
authors.forename: Werner
authors.initials: W
authors.lastname: Albig
authors.forename: Detlef
authors.initials: D
authors.lastname: Doenecke
authors.forename: Vladimir B
authors.initials: VB
authors.lastname: Bajic
mesh_terms: D000465:Algorithms; D000818:Animals; D017124:Conserved Sequence; D019143:Evolution, Molecular; D006657:Histones / Q000235:genetics*; D006801:Humans; D051379:Mice; D008957:Models, Genetic; D010802:Phylogeny; D011401:Promoter Regions, Genetic / Q000235:genetics*; D051381:Rats; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity
chemical_list: D006657:Histones