Coding limits on the number of transcription factors.docVIP

BMC Genomics BioMedCentral Research article Open Access Coding limits on the number of transcription factors Shalev Itzkovitz1,2, Tsvi Tlusty2 and Uri Alon*1,2 Address: 1Dept. Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel and 2Dept. Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel Email: Shalev Itzkovitz - shalev.itzkovitz@weizmann.ac.il; Tsvi Tlusty - tsvi.tlusty@weizmann.ac.il; Uri Alon* - uri.alon@weizmann.ac.il * Corresponding author Published: 19 September 2006 Received: 25 May 2006 Accepted: 19 September 2006 BMC Genomics 2006, 7:239 doi:10.1186/1471-2164-7-239 This article is available from: /1471-2164/7/239 ? 2006 Itzkovitz et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 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