Limits...
Coding limits on the number of transcription factors.

Itzkovitz S, Tlusty T, Alon U - BMC Genomics (2006)

Bottom Line: For example, the number of winged helix factors does not generally exceed 300, even in very large genomes.The magnitude of the maximal number of transcription factors from each super-family seems to correlate with the number of DNA bases effectively recognized by the binding mechanism of that super-family.This theory further predicts that factors with similar binding sequences should tend to have similar biological effect, so that errors based on mis-recognition are minimal.

View Article: PubMed Central - HTML - PubMed

Affiliation: Dept Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel. shalev.itzkovitz@weizmann.ac.il

ABSTRACT

Background: Transcription factor proteins bind specific DNA sequences to control the expression of genes. They contain DNA binding domains which belong to several super-families, each with a specific mechanism of DNA binding. The total number of transcription factors encoded in a genome increases with the number of genes in the genome. Here, we examined the number of transcription factors from each super-family in diverse organisms.

Results: We find that the number of transcription factors from most super-families appears to be bounded. For example, the number of winged helix factors does not generally exceed 300, even in very large genomes. The magnitude of the maximal number of transcription factors from each super-family seems to correlate with the number of DNA bases effectively recognized by the binding mechanism of that super-family. Coding theory predicts that such upper bounds on the number of transcription factors should exist, in order to minimize cross-binding errors between transcription factors. This theory further predicts that factors with similar binding sequences should tend to have similar biological effect, so that errors based on mis-recognition are minimal. We present evidence that transcription factors with similar binding sequences tend to regulate genes with similar biological functions, supporting this prediction.

Conclusion: The present study suggests limits on the transcription factor repertoire of cells, and suggests coding constraints that might apply more generally to the mapping between binding sites and biological function.

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Distribution of transcription factors for the 9 organisms in Table 1 among the different super-families. On the x axis are the 10 super-families of table 1, on the y axis their counts in each organism. The organisms are sorted according to increasing number of genes in the genome.  Note that the y-axis scale is different for different organisms.
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Figure 2: Distribution of transcription factors for the 9 organisms in Table 1 among the different super-families. On the x axis are the 10 super-families of table 1, on the y axis their counts in each organism. The organisms are sorted according to increasing number of genes in the genome. Note that the y-axis scale is different for different organisms.

Mentions: When examining the distribution of transcription factors among the different super-families for different organisms (Fig 2) one can observe a shift from the predominant use of super-families with less degrees of freedom and smaller maximal number of TFs to super-families with more degrees of freedom and higher maximal number of TFs. Organisms with a small number of genes predominantly use TF super-families such as Lambda-repressor like and C-terminal effectors, while as organisms with more genes shift to Zn2/Cys6 and Glucocorticoid receptor-like super-families, which have higher maximal numbers of TFs. Organisms with more genes, such as mouse and human, shift to the predominant use of C2H2 multi-domain zinc finger TFs, which have the highest maximal number.


Coding limits on the number of transcription factors.

Itzkovitz S, Tlusty T, Alon U - BMC Genomics (2006)

Distribution of transcription factors for the 9 organisms in Table 1 among the different super-families. On the x axis are the 10 super-families of table 1, on the y axis their counts in each organism. The organisms are sorted according to increasing number of genes in the genome.  Note that the y-axis scale is different for different organisms.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1590034&req=5

Figure 2: Distribution of transcription factors for the 9 organisms in Table 1 among the different super-families. On the x axis are the 10 super-families of table 1, on the y axis their counts in each organism. The organisms are sorted according to increasing number of genes in the genome. Note that the y-axis scale is different for different organisms.
Mentions: When examining the distribution of transcription factors among the different super-families for different organisms (Fig 2) one can observe a shift from the predominant use of super-families with less degrees of freedom and smaller maximal number of TFs to super-families with more degrees of freedom and higher maximal number of TFs. Organisms with a small number of genes predominantly use TF super-families such as Lambda-repressor like and C-terminal effectors, while as organisms with more genes shift to Zn2/Cys6 and Glucocorticoid receptor-like super-families, which have higher maximal numbers of TFs. Organisms with more genes, such as mouse and human, shift to the predominant use of C2H2 multi-domain zinc finger TFs, which have the highest maximal number.

Bottom Line: For example, the number of winged helix factors does not generally exceed 300, even in very large genomes.The magnitude of the maximal number of transcription factors from each super-family seems to correlate with the number of DNA bases effectively recognized by the binding mechanism of that super-family.This theory further predicts that factors with similar binding sequences should tend to have similar biological effect, so that errors based on mis-recognition are minimal.

View Article: PubMed Central - HTML - PubMed

Affiliation: Dept Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel. shalev.itzkovitz@weizmann.ac.il

ABSTRACT

Background: Transcription factor proteins bind specific DNA sequences to control the expression of genes. They contain DNA binding domains which belong to several super-families, each with a specific mechanism of DNA binding. The total number of transcription factors encoded in a genome increases with the number of genes in the genome. Here, we examined the number of transcription factors from each super-family in diverse organisms.

Results: We find that the number of transcription factors from most super-families appears to be bounded. For example, the number of winged helix factors does not generally exceed 300, even in very large genomes. The magnitude of the maximal number of transcription factors from each super-family seems to correlate with the number of DNA bases effectively recognized by the binding mechanism of that super-family. Coding theory predicts that such upper bounds on the number of transcription factors should exist, in order to minimize cross-binding errors between transcription factors. This theory further predicts that factors with similar binding sequences should tend to have similar biological effect, so that errors based on mis-recognition are minimal. We present evidence that transcription factors with similar binding sequences tend to regulate genes with similar biological functions, supporting this prediction.

Conclusion: The present study suggests limits on the transcription factor repertoire of cells, and suggests coding constraints that might apply more generally to the mapping between binding sites and biological function.

Show MeSH
Related in: MedlinePlus