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Dynamic usage of transcription start sites within core promoters

Hideya Kawaji1*, Martin C Frith23, Shintaro Katayama2*, Albin Sandelin24, Chikatoshi Kai2, Jun Kawai45, Piero Carninci45 and Yoshihide Hayashizaki25

Author Affiliations

1 NTT Software Corporation, 209 Yamashita-cho Nakak-ku, Yokohama, Kanagawa, 231-8551, Japan

2 Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan

3 Institute for Molecular Bioscience, University of Queensland, 306 Carmody Road, Brisbane, Queensland 4072, Australia

4 The Bioinformatics Centre, University of Copenhagen, Universitetsparken 15, DK-2100 København Ø, Denmark

5 Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan

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Genome Biology 2006, 7:R118  doi:10.1186/gb-2006-7-12-r118

Published: 12 December 2006



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.


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.


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.