Links between core promoter and basic gene features influence gene expression

Sandra Moshonov, Rofa Elfakess, Michal Golan-Mashiach, Hadar Sinvani, Rivka Dikstein

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29 Scopus citations


Background: Diversity in rates of gene expression is essential for basic cell functions and is controlled by a variety of intricate mechanisms. Revealing general mechanisms that control gene expression is important for understanding normal and pathological cell functions and for improving the design of expression systems. Here we analyzed the relationship between general features of genes and their contribution to expression levels. Results: Genes were divided into four groups according to their core promoter type and their characteristics analyzed statistically. Surprisingly we found that small variations in the TATA box are linked to large differences in gene length. Genes containing canonical TATA are generally short whereas long genes are associated with either non-canonical TATA or TATA-less promoters. These differences in gene length are primarily determined by the size and number of introns. Generally, gene expression was found to be tightly correlated with the strength of the TATA-box. However significant reduction in gene expression levels were linked with long TATA-containing genes (canonical and non-canonical) whereas intron length hardly affected the expression of TATA-less genes. Interestingly, features associated with high translation are prevalent in TATA-containing genes suggesting that their protein production is also more efficient. Conclusion: Our results suggest that interplay between core promoter type and gene size can generate significant diversity in gene expression.

Original languageEnglish
Article number92
JournalBMC Genomics
StatePublished - 25 Feb 2008
Externally publishedYes

Bibliographical note

Funding Information:
We thank Dr. Hillary Voet (Hebrew University, Israel) for her advice and assistance in the statistical analyses, Dr. Shalev Itzkovitz (Weizmann Institute of Science, Israel) for his guidance in use of the MATLAB program, Ofer Rahat (Weizmann Institute of Science, Israel) and Eliezer Dikstein for assistance in programming. This work was supported by a grant from the Israel Science Foundation.


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