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Genomic repertoires of DNA-binding transcription factors across the tree of life

Sequence-specific transcription factors (TFs) are important to genetic regulation in all organisms because they recognize and directly bind to regulatory regions on DNA. Here, we survey and summarize the TF resources available. We outline the organisms for which TF annotation is provided, and discus...

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Autores principales: Charoensawan, Varodom, Wilson, Derek, Teichmann, Sarah A.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2995046/
https://www.ncbi.nlm.nih.gov/pubmed/20675356
http://dx.doi.org/10.1093/nar/gkq617
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author Charoensawan, Varodom
Wilson, Derek
Teichmann, Sarah A.
author_facet Charoensawan, Varodom
Wilson, Derek
Teichmann, Sarah A.
author_sort Charoensawan, Varodom
collection PubMed
description Sequence-specific transcription factors (TFs) are important to genetic regulation in all organisms because they recognize and directly bind to regulatory regions on DNA. Here, we survey and summarize the TF resources available. We outline the organisms for which TF annotation is provided, and discuss the criteria and methods used to annotate TFs by different databases. By using genomic TF repertoires from ∼700 genomes across the tree of life, covering Bacteria, Archaea and Eukaryota, we review TF abundance with respect to the number of genes, as well as their structural complexity in diverse lineages. While typical eukaryotic TFs are longer than the average eukaryotic proteins, the inverse is true for prokaryotes. Only in eukaryotes does the same family of DNA-binding domain (DBD) occur multiple times within one polypeptide chain. This potentially increases the length and diversity of DNA-recognition sequence by reusing DBDs from the same family. We examined the increase in TF abundance with the number of genes in genomes, using the largest set of prokaryotic and eukaryotic genomes to date. As pointed out before, prokaryotic TFs increase faster than linearly. We further observe a similar relationship in eukaryotic genomes with a slower increase in TFs.
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spelling pubmed-29950462010-12-01 Genomic repertoires of DNA-binding transcription factors across the tree of life Charoensawan, Varodom Wilson, Derek Teichmann, Sarah A. Nucleic Acids Res Survey and Summary Sequence-specific transcription factors (TFs) are important to genetic regulation in all organisms because they recognize and directly bind to regulatory regions on DNA. Here, we survey and summarize the TF resources available. We outline the organisms for which TF annotation is provided, and discuss the criteria and methods used to annotate TFs by different databases. By using genomic TF repertoires from ∼700 genomes across the tree of life, covering Bacteria, Archaea and Eukaryota, we review TF abundance with respect to the number of genes, as well as their structural complexity in diverse lineages. While typical eukaryotic TFs are longer than the average eukaryotic proteins, the inverse is true for prokaryotes. Only in eukaryotes does the same family of DNA-binding domain (DBD) occur multiple times within one polypeptide chain. This potentially increases the length and diversity of DNA-recognition sequence by reusing DBDs from the same family. We examined the increase in TF abundance with the number of genes in genomes, using the largest set of prokaryotic and eukaryotic genomes to date. As pointed out before, prokaryotic TFs increase faster than linearly. We further observe a similar relationship in eukaryotic genomes with a slower increase in TFs. Oxford University Press 2010-11 2010-07-30 /pmc/articles/PMC2995046/ /pubmed/20675356 http://dx.doi.org/10.1093/nar/gkq617 Text en © The Author(s) 2010. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Survey and Summary
Charoensawan, Varodom
Wilson, Derek
Teichmann, Sarah A.
Genomic repertoires of DNA-binding transcription factors across the tree of life
title Genomic repertoires of DNA-binding transcription factors across the tree of life
title_full Genomic repertoires of DNA-binding transcription factors across the tree of life
title_fullStr Genomic repertoires of DNA-binding transcription factors across the tree of life
title_full_unstemmed Genomic repertoires of DNA-binding transcription factors across the tree of life
title_short Genomic repertoires of DNA-binding transcription factors across the tree of life
title_sort genomic repertoires of dna-binding transcription factors across the tree of life
topic Survey and Summary
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2995046/
https://www.ncbi.nlm.nih.gov/pubmed/20675356
http://dx.doi.org/10.1093/nar/gkq617
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