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The effects of selection against spurious transcription factor binding sites.

Publication ,  Journal Article
Hahn, MW; Stajich, JE; Wray, GA
Published in: Molecular biology and evolution
June 2003

Most genomes contain nucleotide sequences with no known function; such sequences are assumed to be free of constraints, evolving only according to the vagaries of mutation. Here we show that selection acts to remove spurious transcription factor binding site motifs throughout 52 fully sequenced genomes of Eubacteria and Archaea. Examining the sequences necessary for polymerase binding, we find that spurious binding sites are underrepresented in both coding and noncoding regions. The average proportion of spurious binding sites found relative to the expected is 80% in eubacterial genomes and 89% in archaeal genomes. We also estimate the strength of selection against spurious binding sites in the face of the constant creation of new binding sites via mutation. Under conservative assumptions, we estimate that selection is weak, with the average efficacy of selection against spurious binding sites, Nes, of -0.12 for eubacterial genomes and -0.06 for archaeal genomes, similar to that of codon bias. Our results suggest that both coding and noncoding sequences are constrained by selection to avoid specific regions of sequence space.

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Published In

Molecular biology and evolution

DOI

EISSN

1537-1719

ISSN

0737-4038

Publication Date

June 2003

Volume

20

Issue

6

Start / End Page

901 / 906

Related Subject Headings

  • Transcription Factors
  • Selection, Genetic
  • Promoter Regions, Genetic
  • Evolutionary Biology
  • Binding Sites
  • Bacteria
  • Archaea
  • 3105 Genetics
  • 3104 Evolutionary biology
  • 3101 Biochemistry and cell biology
 

Citation

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Hahn, M. W., Stajich, J. E., & Wray, G. A. (2003). The effects of selection against spurious transcription factor binding sites. Molecular Biology and Evolution, 20(6), 901–906. https://doi.org/10.1093/molbev/msg096
Hahn, Matthew W., Jason E. Stajich, and Gregory A. Wray. “The effects of selection against spurious transcription factor binding sites.Molecular Biology and Evolution 20, no. 6 (June 2003): 901–6. https://doi.org/10.1093/molbev/msg096.
Hahn MW, Stajich JE, Wray GA. The effects of selection against spurious transcription factor binding sites. Molecular biology and evolution. 2003 Jun;20(6):901–6.
Hahn, Matthew W., et al. “The effects of selection against spurious transcription factor binding sites.Molecular Biology and Evolution, vol. 20, no. 6, June 2003, pp. 901–06. Epmc, doi:10.1093/molbev/msg096.
Hahn MW, Stajich JE, Wray GA. The effects of selection against spurious transcription factor binding sites. Molecular biology and evolution. 2003 Jun;20(6):901–906.
Journal cover image

Published In

Molecular biology and evolution

DOI

EISSN

1537-1719

ISSN

0737-4038

Publication Date

June 2003

Volume

20

Issue

6

Start / End Page

901 / 906

Related Subject Headings

  • Transcription Factors
  • Selection, Genetic
  • Promoter Regions, Genetic
  • Evolutionary Biology
  • Binding Sites
  • Bacteria
  • Archaea
  • 3105 Genetics
  • 3104 Evolutionary biology
  • 3101 Biochemistry and cell biology