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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
Statistical analysis of several properties of the TATA, TATA-1, TATA-2 and TATA-less gene sets.A. The median, 25% and 75% quartile number of exons. B. The median, 25% and 75% quartile length of a single intron. C. The fraction of intron-less genes in the different gene sets. The number of genes in each set is as in Fig. 1. D. The p-values of the differences in the median values (A-C) and intron-less probability (D) were calculated using the Kruskal-Wallis test with Bonferroni correction and chi-square distribution respectively. NS is a non-significant difference (p > 0.05).
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Figure 2: Statistical analysis of several properties of the TATA, TATA-1, TATA-2 and TATA-less gene sets.A. The median, 25% and 75% quartile number of exons. B. The median, 25% and 75% quartile length of a single intron. C. The fraction of intron-less genes in the different gene sets. The number of genes in each set is as in Fig. 1. D. The p-values of the differences in the median values (A-C) and intron-less probability (D) were calculated using the Kruskal-Wallis test with Bonferroni correction and chi-square distribution respectively. NS is a non-significant difference (p > 0.05).

Mentions: We next determined the number of exons in the different groups and here again we found the exon number is inversely correlated with the strength of the TATA box (Fig. 2A and 2D). In all gene groups the length of an exon is very close (data not shown) whereas the length of an intron in the canonical TATA containing genes is significantly shorter than in non-canonical TATA or TATA-less sets (Fig. 2B and 2D). Another differential feature that we found relates to the percentage of intron-less genes which is relatively high in the TATA set and gradually declines in the TATA-1 and TATA-2 and the TATA-less groups (Fig. 2C and 2D).


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)

Statistical analysis of several properties of the TATA, TATA-1, TATA-2 and TATA-less gene sets.A. The median, 25% and 75% quartile number of exons. B. The median, 25% and 75% quartile length of a single intron. C. The fraction of intron-less genes in the different gene sets. The number of genes in each set is as in Fig. 1. D. The p-values of the differences in the median values (A-C) and intron-less probability (D) were calculated using the Kruskal-Wallis test with Bonferroni correction and chi-square distribution respectively. NS is a 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 2: Statistical analysis of several properties of the TATA, TATA-1, TATA-2 and TATA-less gene sets.A. The median, 25% and 75% quartile number of exons. B. The median, 25% and 75% quartile length of a single intron. C. The fraction of intron-less genes in the different gene sets. The number of genes in each set is as in Fig. 1. D. The p-values of the differences in the median values (A-C) and intron-less probability (D) were calculated using the Kruskal-Wallis test with Bonferroni correction and chi-square distribution respectively. NS is a non-significant difference (p > 0.05).
Mentions: We next determined the number of exons in the different groups and here again we found the exon number is inversely correlated with the strength of the TATA box (Fig. 2A and 2D). In all gene groups the length of an exon is very close (data not shown) whereas the length of an intron in the canonical TATA containing genes is significantly shorter than in non-canonical TATA or TATA-less sets (Fig. 2B and 2D). Another differential feature that we found relates to the percentage of intron-less genes which is relatively high in the TATA set and gradually declines in the TATA-1 and TATA-2 and the TATA-less groups (Fig. 2C and 2D).

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