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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
Analysis of the expression level in the indicated gene sets.A. The median, 25% and 75% quartiles of tissue average expression for each gene sets. B. The gene sets were divided into short (intron <8000 nt, white box) or long genes (intron >8000 nt, grey box), and the median, 25% and 75% quartile of the avarage expression for each gene set is shown. C. 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 3: Analysis of the expression level in the indicated gene sets.A. The median, 25% and 75% quartiles of tissue average expression for each gene sets. B. The gene sets were divided into short (intron <8000 nt, white box) or long genes (intron >8000 nt, grey box), and the median, 25% and 75% quartile of the avarage expression for each gene set is shown. C. 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 first determined the average expression of each gene in all tissues, setting a threshold value of 200, a value that is above background. Then we determined the 25%, median and 75% quartile of the average expression for each group (Fig. 3A). Since a significant fraction of genes in the different sets shows tissue specific patterns of expression (expressed in some but not all tissues) we were concerned that the average expression from all tissues would result in a bias towards ubiquitously expressed genes rather than providing information regarding each gene's potential strength of expression. Therefore we also determined the median of the highest expression value of each gene, representing the maximal expression potential using the same threshold value of 200. The results revealed that the relative expression levels in the different groups are very similar in the two types of analysis. The data of the average expression levels is shown in Fig. 3 and that of the maximal expression is shown in Additional file 1.


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)

Analysis of the expression level in the indicated gene sets.A. The median, 25% and 75% quartiles of tissue average expression for each gene sets. B. The gene sets were divided into short (intron <8000 nt, white box) or long genes (intron >8000 nt, grey box), and the median, 25% and 75% quartile of the avarage expression for each gene set is shown. C. 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 3: Analysis of the expression level in the indicated gene sets.A. The median, 25% and 75% quartiles of tissue average expression for each gene sets. B. The gene sets were divided into short (intron <8000 nt, white box) or long genes (intron >8000 nt, grey box), and the median, 25% and 75% quartile of the avarage expression for each gene set is shown. C. 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 first determined the average expression of each gene in all tissues, setting a threshold value of 200, a value that is above background. Then we determined the 25%, median and 75% quartile of the average expression for each group (Fig. 3A). Since a significant fraction of genes in the different sets shows tissue specific patterns of expression (expressed in some but not all tissues) we were concerned that the average expression from all tissues would result in a bias towards ubiquitously expressed genes rather than providing information regarding each gene's potential strength of expression. Therefore we also determined the median of the highest expression value of each gene, representing the maximal expression potential using the same threshold value of 200. The results revealed that the relative expression levels in the different groups are very similar in the two types of analysis. The data of the average expression levels is shown in Fig. 3 and that of the maximal expression is shown in Additional file 1.

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