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Proc Natl Acad Sci U S A 2005 Jun 14;10224:8591-6. doi: 10.1073/pnas.0409638102.
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Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites.

Balhoff JP , Wray GA .

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.

PubMed ID: 15937122
PMC ID: PMC1150811
Article link: Proc Natl Acad Sci U S A

Genes referenced: endo16 LOC100887844 LOC115925415 LOC115926321

References [+] :
Arnone, The hardwiring of development: organization and function of genomic regulatory systems. 1997, Pubmed, Echinobase