Explaining the correlations among properties of mammalian promoters

Frith, Martin C. and The FANTOM Consortium (2014) Explaining the correlations among properties of mammalian promoters. Nucleic Acids Research, 42 8: 4823-4832. doi:10.1093/nar/gku115

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Author Frith, Martin C.
The FANTOM Consortium
Title Explaining the correlations among properties of mammalian promoters
Journal name Nucleic Acids Research   Check publisher's open access policy
ISSN 0305-1048
1362-4962
1362-4954
Publication date 2014-04-01
Sub-type Article (original research)
DOI 10.1093/nar/gku115
Open Access Status DOI
Volume 42
Issue 8
Start page 4823
End page 4832
Total pages 10
Place of publication Oxford, United Kingdom
Publisher Oxford University Press
Language eng
Formatted abstract
Proximal promoters are fundamental genomic elements for gene expression. They vary in terms of GC percentage, CpG abundance, presence of TATA signal, evolutionary conservation, chromosomal spread of transcription start sites and breadth of expression across cell types. These properties are correlated, and it has been suggested that there are two classes of promoters: one class with high CpG, widely spread transcription start sites and broad expression, and another with TATA signals, narrow spread and restricted expression. However, it has been unclear why these properties are correlated in this way. We reexamined these features using the deep FANTOM5 CAGE data from hundreds of cell types. First, we point out subtle but important biases in previous definitions of promoters and of expression breadth. Second, we show that most promoters are rather nonspecifically expressed across many cell types. Third, promoters’ expression breadth is independent of maximum expression level, and therefore correlates with average expression level. Fourth, the data show a more complex picture than two classes, with a network of direct and indirect correlations among promoter properties. By tentatively distinguishing the direct from the indirect correlations, we reveal simple explanations for them.
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Non HERDC
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Citation counts: TR Web of Science Citation Count  Cited 3 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 4 times in Scopus Article | Citations
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Created: Thu, 26 Jun 2014, 22:12:41 EST by Cathy Fouhy on behalf of Aust Institute for Bioengineering & Nanotechnology