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PMID: 15937122 Published · ppublish English Comparative Study Journal Article Research Support, U.S. Gov't, Non-P.H.S.

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 ·2005-06-14 ·Pages 8591-6

Balhoff JP, Wray GA

Abstract

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.

Keywords

NASA Discipline Evolutionary Biology Non-NASA Center

MeSH Terms

Animals Base Sequence Binding Sites/genetics Cell Adhesion Molecules/genetics Cloning, Molecular DNA Primers Evolution, Molecular Genetic Variation Molecular Sequence Data Promoter Regions, Genetic/genetics Proteins/genetics Selection, Genetic Sequence Analysis, DNA Species Specificity Strongylocentrotus purpuratus/genetics

Chemicals

Cell Adhesion Molecules DNA Primers Proteins endo16 protein, sea urchin

Authors & Affiliations

2 authors, click to expand affiliations / ORCID

Balhoff James P

Department of Biology, Duke University, Durham, NC 27708, USA.

Wray Gregory A

Investigators

1 investigators, click to expand

Wray G A

Duke U, Durham, NC

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Article Info

Journal

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

Abbr.

Proc Natl Acad Sci U S A

ISSN

0027-8424

DOI

10.1073/pnas.0409638102

Published

2005-06-14

Epub

2005-00-03

Pages

8591-6

Language

English

Region

United States

NLM ID

7505876

PMCID

PMC1150811

Subset

Databases

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External Links

PubMed source DOI: 10.1073/pnas.0409638102 PMC Full Text View journal details

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

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