Evolutionary turnover of mammalian transcription start sites

Frith, Martin C., Ponjavic, Jasmina, Fredman, David, Kai, Chikatoshi, Kawai, Jun, Carninci, Piero, Hayshizaki, Yoshihide and Sandelin, Albin (2006) Evolutionary turnover of mammalian transcription start sites. Genome Research, 16 6: 713-722. doi:10.1101/gr.5031006

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Author Frith, Martin C.
Ponjavic, Jasmina
Fredman, David
Kai, Chikatoshi
Kawai, Jun
Carninci, Piero
Hayshizaki, Yoshihide
Sandelin, Albin
Title Evolutionary turnover of mammalian transcription start sites
Journal name Genome Research   Check publisher's open access policy
ISSN 1088-9051
Publication date 2006
Sub-type Article (original research)
DOI 10.1101/gr.5031006
Open Access Status File (Publisher version)
Volume 16
Issue 6
Start page 713
End page 722
Total pages 10
Place of publication Cold Spring Harbor, NY, United States
Publisher Cold Spring Harbor Lab Press, Publications Dept
Collection year 2006
Language eng
Abstract Alignments of homologous genomic sequences are widely used to identify functional genetic elements and study their evolution. Most studies tacitly equate homology of functional elements with sequence homology. This assumption is violated by the phenomenon of turnover, in which functionally equivalent elements reside at locations that are nonorthologous at the sequence level. Turnover has been demonstrated previously for transcription-factor-binding sites. Here, we show that transcription start sites of equivalent genes do not always reside at equivalent locations in the human and mouse genomes. We also identify two types of partial turnover, illustrating evolutionary pathways that could lead to complete turnover. These findings suggest that the signals encoding transcription start sites are highly flexible and evolvable, and have cautionary implications for the use of sequence-level conservation to detect gene regulatory elements.
Keyword Biochemistry & Molecular Biology
Biotechnology & Applied Microbiology
Genetics & Heredity
Cis-regulatory Sequences
Factor-binding Sites
Cpg Islands
Alternative Promoters
Vertebrate Genomes
Rapid Evolution
Cap Analysis
Q-Index Code C1
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: 2007 Higher Education Research Data Collection
Institute for Molecular Bioscience - Publications
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Citation counts: TR Web of Science Citation Count  Cited 57 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 59 times in Scopus Article | Citations
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Created: Wed, 15 Aug 2007, 08:44:14 EST