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Links between core promoter and basic gene features influence gene expression.

Moshonov S, Elfakess R, Golan-Mashiach M, Sinvani H, Dikstein R - BMC Genomics (2008)

Bottom Line: 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.Our results suggest that interplay between core promoter type and gene size can generate significant diversity in gene expression.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel. sandra.moshonov@weizmann.ac.il

ABSTRACT

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.

Show MeSH
Relationship between core promoter type and gene length.A-C. Gene sets which differ in their core promoter, as described in the text, were analyzed for the length of their genes (A), mRNA (B) and introns (C). The boxplots present the median, 25% and 75% quartile values that were calculated from 527 TATA, 694 TATA-1, 3916 TATA-2 and 9491 TATA-less genes. D. The p-values of the differences in the median value between each two gene sets as indicated. NS is non-significant difference (p > 0.05).
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Figure 1: Relationship between core promoter type and gene length.A-C. Gene sets which differ in their core promoter, as described in the text, were analyzed for the length of their genes (A), mRNA (B) and introns (C). The boxplots present the median, 25% and 75% quartile values that were calculated from 527 TATA, 694 TATA-1, 3916 TATA-2 and 9491 TATA-less genes. D. The p-values of the differences in the median value between each two gene sets as indicated. NS is non-significant difference (p > 0.05).

Mentions: We used the UCSC Genome Browser to retrieve structural data of genes in the different groups. We determined the median, 25% and 75% quartile gene lengths for each group and the p-values of the differences between the median values and the results are presented in boxplots (Fig. 1). Remarkably, we found that in the TATA containing groups (TATA, TATA-1 and TATA-2) gene size is inversely correlated with the compatibility to the TATA consensus, where even one nucleotide variation in the TATA box sequence results in a dramatic increase (2.1 fold p = 2 × 10-16) of median gene length (Fig. 1A and 1D). Likewise genes with two substitutions in their TATA or TATA-less genes are 3 fold longer than canonical TATA genes (p = 4.6 × 10-51 and 2.43 × 10-62 respectively) (Fig. 1A and 1D). Thus gene length is tightly associated with core promoter type.


Links between core promoter and basic gene features influence gene expression.

Moshonov S, Elfakess R, Golan-Mashiach M, Sinvani H, Dikstein R - BMC Genomics (2008)

Relationship between core promoter type and gene length.A-C. Gene sets which differ in their core promoter, as described in the text, were analyzed for the length of their genes (A), mRNA (B) and introns (C). The boxplots present the median, 25% and 75% quartile values that were calculated from 527 TATA, 694 TATA-1, 3916 TATA-2 and 9491 TATA-less genes. D. The p-values of the differences in the median value between each two gene sets as indicated. NS is non-significant difference (p > 0.05).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2279122&req=5

Figure 1: Relationship between core promoter type and gene length.A-C. Gene sets which differ in their core promoter, as described in the text, were analyzed for the length of their genes (A), mRNA (B) and introns (C). The boxplots present the median, 25% and 75% quartile values that were calculated from 527 TATA, 694 TATA-1, 3916 TATA-2 and 9491 TATA-less genes. D. The p-values of the differences in the median value between each two gene sets as indicated. NS is non-significant difference (p > 0.05).
Mentions: We used the UCSC Genome Browser to retrieve structural data of genes in the different groups. We determined the median, 25% and 75% quartile gene lengths for each group and the p-values of the differences between the median values and the results are presented in boxplots (Fig. 1). Remarkably, we found that in the TATA containing groups (TATA, TATA-1 and TATA-2) gene size is inversely correlated with the compatibility to the TATA consensus, where even one nucleotide variation in the TATA box sequence results in a dramatic increase (2.1 fold p = 2 × 10-16) of median gene length (Fig. 1A and 1D). Likewise genes with two substitutions in their TATA or TATA-less genes are 3 fold longer than canonical TATA genes (p = 4.6 × 10-51 and 2.43 × 10-62 respectively) (Fig. 1A and 1D). Thus gene length is tightly associated with core promoter type.

Bottom Line: 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.Our results suggest that interplay between core promoter type and gene size can generate significant diversity in gene expression.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel. sandra.moshonov@weizmann.ac.il

ABSTRACT

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.

Show MeSH