ArticleBMC genomics2006
Coding limits on the number of transcription factors.
Article in BMC genomics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 96 citations in OpenAlex.
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- Partitioning of a 2-bit hash function across 66 communicating cells.Nature chemical biology · 2025Article
- Marginal specificity in protein interactions constrains evolution of a paralogous family.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Ligand-receptor promiscuity enables cellular addressing.Cell systems · 2022Article
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- The relation between crosstalk and gene regulation form revisited.PLoS computational biology · 2020Article
- Evolution of protein kinase substrate recognition at the active site.PLoS biology · 2019Article
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- Modelling the evolution of transcription factor binding preferences in complex eukaryotes.Scientific reports · 2017Article
- Intrinsic limits to gene regulation by global crosstalk.Nature communications · 2016Article
- Mechanisms of transcription factor evolution in Metazoa.Nucleic acids research · 2016Article
- Information capacity of specific interactions.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
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- Information Limited Oligonucleotide Amplification Assay for Affinity-Based, Parallel Detection Studies.PloS one · 2016Article
- Reliable scaling of position weight matrices for binding strength comparisons between transcription factors.BMC bioinformatics · 2015Article
- Evolution of context dependent regulation by expansion of feast/famine regulatory proteins.BMC systems biology · 2014Article
- In silico identification of transcription factors in Medicago sativa using available transcriptomic resources.Molecular genetics and genomics : MGG · 2014Article
- Genomic mining of prokaryotic repressors for orthogonal logic gates.Nature chemical biology · 2014Article
- Early evolution of the T-box transcription factor family.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Indirect and suboptimal control of gene expression is widespread in bacteria.Molecular systems biology · 2013Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTranscription 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.
resultsWe 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.
conclusionThe 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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