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Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites.

Publication ,  Journal Article
Balhoff, JP; Wray, GA
Published in: Proceedings of the National Academy of Sciences of the United States of America
June 2005

The evolutionary mechanisms that operate on genetic variation within transcriptional regulatory sequences are not well understood. We present here an evolutionary analysis of an exceptionally well characterized cis-regulatory region, the endo16 promoter of the purple sea urchin. Segregating variation reveals striking differences in the intensity of negative selection among regulatory modules, reflecting their distinct functional roles. Surprisingly, transcription-factor-binding sites are as polymorphic and as likely to contain fixed differences as flanking nucleotides. Whereas nucleotides in protein-binding sites in the most proximal regulatory module exhibit reduced variation, those in other modules tend to be more polymorphic than putatively nonfunctional nucleotides. Two unrelated large insertions at the same position within the promoter are segregating at low frequencies; one is a strong ectodermal repressor that contains 16 verified transcription-factor-binding sites. These results demonstrate that a simple relationship between conservation and function does not exist within this cis-regulatory region and highlight significant population heterogeneity in the fine structure of a well understood promoter.

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Published In

Proceedings of the National Academy of Sciences of the United States of America

DOI

EISSN

1091-6490

ISSN

0027-8424

Publication Date

June 2005

Volume

102

Issue

24

Start / End Page

8591 / 8596

Related Subject Headings

  • Strongylocentrotus purpuratus
  • Species Specificity
  • Sequence Analysis, DNA
  • Selection, Genetic
  • Proteins
  • Promoter Regions, Genetic
  • Molecular Sequence Data
  • Genetic Variation
  • Evolution, Molecular
  • DNA Primers
 

Citation

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Balhoff, J. P., & Wray, G. A. (2005). Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites. Proceedings of the National Academy of Sciences of the United States of America, 102(24), 8591–8596. https://doi.org/10.1073/pnas.0409638102
Balhoff, James P., and Gregory A. Wray. “Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites.Proceedings of the National Academy of Sciences of the United States of America 102, no. 24 (June 2005): 8591–96. https://doi.org/10.1073/pnas.0409638102.
Balhoff JP, Wray GA. Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites. Proceedings of the National Academy of Sciences of the United States of America. 2005 Jun;102(24):8591–6.
Balhoff, James P., and Gregory A. Wray. “Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites.Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 24, June 2005, pp. 8591–96. Epmc, doi:10.1073/pnas.0409638102.
Balhoff JP, Wray GA. Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites. Proceedings of the National Academy of Sciences of the United States of America. 2005 Jun;102(24):8591–8596.
Journal cover image

Published In

Proceedings of the National Academy of Sciences of the United States of America

DOI

EISSN

1091-6490

ISSN

0027-8424

Publication Date

June 2005

Volume

102

Issue

24

Start / End Page

8591 / 8596

Related Subject Headings

  • Strongylocentrotus purpuratus
  • Species Specificity
  • Sequence Analysis, DNA
  • Selection, Genetic
  • Proteins
  • Promoter Regions, Genetic
  • Molecular Sequence Data
  • Genetic Variation
  • Evolution, Molecular
  • DNA Primers