title: Tight associations between transcription promoter type and epigenetic variation in histone positioning and modification.
abstract: BACKGROUND
  Transcription promoters are fundamental genomic cis-elements controlling gene expression. They can be classified into two types by the degree of imprecision of their transcription start sites: peak promoters, which initiate transcription from a narrow genomic region; and broad promoters, which initiate transcription from a wide-ranging region. Eukaryotic transcription initiation is suggested to be associated with the genomic positions and modifications of nucleosomes. For instance, it has been recently shown that histone with H3K9 acetylation (H3K9ac) is more likely to be distributed around broad promoters rather than peak promoters; it can thus be inferred that there is an association between histone H3K9 and promoter architecture.
  
  
  RESULTS
  Here, we performed a systematic analysis of transcription promoters and gene expression, as well as of epigenetic histone behaviors, including genomic position, stability within the chromatin, and several modifications. We found that, in humans, broad promoters, but not peak promoters, generally had significant associations with nucleosome positioning and modification. Specifically, around broad promoters histones were highly distributed and aligned in an orderly fashion. This feature was more evident with histones that were methylated or acetylated; moreover, the nucleosome positions around the broad promoters were more stable than those around the peak ones. More strikingly, the overall expression levels of genes associated with broad promoters (but not peak promoters) with modified histones were significantly higher than the levels of genes associated with broad promoters with unmodified histones.
  
  
  CONCLUSIONS
  These results shed light on how epigenetic regulatory networks of histone modifications are associated with promoter architecture.
authors.affiliation: Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0017, Japan.
authors.forename: Tadasu
authors.initials: T
authors.lastname: Nozaki
authors.forename: Nozomu
authors.initials: N
authors.lastname: Yachie
authors.forename: Ryu
authors.initials: R
authors.lastname: Ogawa
authors.forename: Anton
authors.initials: A
authors.lastname: Kratz
authors.forename: Rintaro
authors.initials: R
authors.lastname: Saito
authors.forename: Masaru
authors.initials: M
authors.lastname: Tomita
mesh_terms: D042002:Chromatin Assembly and Disassembly / Q000235:genetics*; D044127:Epigenesis, Genetic / Q000235:genetics*; D005786:Gene Expression Regulation / Q000235:genetics; D042822:Genomic Instability; D006657:Histones / Q000235:genetics* / Q000378:metabolism*; D006801:Humans; D009707:Nucleosomes / Q000235:genetics / Q000378:metabolism; D011401:Promoter Regions, Genetic / Q000235:genetics*; D016329:Sp1 Transcription Factor / Q000378:metabolism; D024363:Transcription Initiation Site; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D006657:Histones; D009707:Nucleosomes; D016329:Sp1 Transcription Factor