Dynamic usage of transcription start sites within core promoters.

Hideya Kawaji; Martin C Frith; Shintaro Katayama; Albin Sandelin; Chikatoshi Kai; Jun Kawai; Piero Carninci; Yoshihide Hayashizaki

doi:10.1186/gb-2006-7-12-r118

Dynamic usage of transcription start sites within core promoters.

Hideya Kawaji, Martin C Frith, Shintaro Katayama, Albin Sandelin, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki

Functional Genomics

65 Citations (Scopus)

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. CONCLUSION: 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.
Udgivelsesdato: 2006-null

Original language	English
Journal	Genome Biology
Volume	7
Issue number	12
Pages (from-to)	R118
ISSN	1465-6906
DOIs	https://doi.org/10.1186/gb-2006-7-12-r118
Publication status	Published - 2006

Access to Document

10.1186/gb-2006-7-12-r118

Cite this

@article{482d9ad0de3a11dcbee902004c4f4f50,

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. CONCLUSION: 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. Udgivelsesdato: 2006-null",

author = "Hideya Kawaji and Frith, {Martin C} and Shintaro Katayama and Albin Sandelin and Chikatoshi Kai and Jun Kawai and Piero Carninci and Yoshihide Hayashizaki",

note = "Keywords: Animals; CpG Islands; DNA Methylation; Mice; Multigene Family; Promoter Regions (Genetics); Transcription, Genetic",

year = "2006",

doi = "10.1186/gb-2006-7-12-r118",

language = "English",

volume = "7",

pages = "R118",

journal = "Genome Biology (Online Edition)",

issn = "1474-7596",

publisher = "BioMed Central Ltd.",

number = "12",

}

TY - JOUR

T1 - Dynamic usage of transcription start sites within core promoters.

AU - Kawaji, Hideya

AU - Frith, Martin C

AU - Katayama, Shintaro

AU - Sandelin, Albin

AU - Kai, Chikatoshi

AU - Kawai, Jun

AU - Carninci, Piero

AU - Hayashizaki, Yoshihide

N1 - Keywords: Animals; CpG Islands; DNA Methylation; Mice; Multigene Family; Promoter Regions (Genetics); Transcription, Genetic

PY - 2006

Y1 - 2006

N2 - 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. CONCLUSION: 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. Udgivelsesdato: 2006-null

AB - 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. CONCLUSION: 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. Udgivelsesdato: 2006-null

U2 - 10.1186/gb-2006-7-12-r118

DO - 10.1186/gb-2006-7-12-r118

M3 - Journal article

C2 - 17156492

SN - 1474-7596

VL - 7

SP - R118

JO - Genome Biology (Online Edition)

JF - Genome Biology (Online Edition)

IS - 12

ER -