title: Dynamic usage of transcription start sites within core promoters.
abstract: BACKGROUND
  Mammalian promoters do not initiate transcription at single, well defined base pairs, but rather at multiple, alternative start sites spread across a region. We previously characterized the static structures of transcription start site usage within promoters at the base pair level, based on large-scale sequencing of transcript 5' ends.
  
  
  RESULTS
  In the present study we begin to explore the internal dynamics of mammalian promoters, and demonstrate that start site selection within many mouse core promoters varies among tissues. We also show that this dynamic usage of start sites is associated with CpG islands, broad and multimodal promoter structures, and imprinting.
  
  
  CONCLUSIONS
  Our results reveal a new level of biologic complexity within promoters--fine-scale regulation of transcription starting events at the base pair level. These events are likely to be related to epigenetic transcriptional regulation.
authors.affiliation: NTT Software Corporation, 209 Yamashita-cho Nakak-ku, Yokohama, Kanagawa, 231-8551, Japan. kawaji@po.ntts.co.jp
authors.forename: Hideya
authors.initials: H
authors.lastname: Kawaji
authors.forename: Martin C
authors.initials: MC
authors.lastname: Frith
authors.forename: Shintaro
authors.initials: S
authors.lastname: Katayama
authors.forename: Albin
authors.initials: A
authors.lastname: Sandelin
authors.forename: Chikatoshi
authors.initials: C
authors.lastname: Kai
authors.forename: Jun
authors.initials: J
authors.lastname: Kawai
authors.forename: Piero
authors.initials: P
authors.lastname: Carninci
authors.forename: Yoshihide
authors.initials: Y
authors.lastname: Hayashizaki
mesh_terms: D000818:Animals; D018899:CpG Islands; D019175:DNA Methylation; D051379:Mice; D005810:Multigene Family; D011401:Promoter Regions, Genetic; D014158:Transcription, Genetic