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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.
Arnone,
The hardwiring of development: organization and function of genomic regulatory systems.
1997, Pubmed,
Echinobase
Arnone,
The hardwiring of development: organization and function of genomic regulatory systems.
1997,
Pubmed
,
Echinobase Britten,
The single-copy DNA sequence polymorphism of the sea urchin Strongylocentrotus purpuratus.
1978,
Pubmed
,
Echinobase Britten,
Majority of divergence between closely related DNA samples is due to indels.
2003,
Pubmed
,
Echinobase Carroll,
Endless forms: the evolution of gene regulation and morphological diversity.
2000,
Pubmed Charlesworth,
The effect of deleterious mutations on neutral molecular variation.
1993,
Pubmed Cliften,
Finding functional features in Saccharomyces genomes by phylogenetic footprinting.
2003,
Pubmed Dayal,
Creation of cis-regulatory elements during sea urchin evolution by co-option and optimization of a repetitive sequence adjacent to the spec2a gene.
2004,
Pubmed
,
Echinobase Kidwell,
Transposable elements as sources of variation in animals and plants.
1997,
Pubmed Ludwig,
Evidence for stabilizing selection in a eukaryotic enhancer element.
2000,
Pubmed Ludwig,
Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change.
1998,
Pubmed Macdonald,
Identifying signatures of selection at the enhancer of split neurogenic gene complex in Drosophila.
2005,
Pubmed McDonald,
Adaptive protein evolution at the Adh locus in Drosophila.
1991,
Pubmed Phinchongsakuldit,
Evolution of developmental genes: molecular microevolution of enhancer sequences at the Ubx locus in Drosophila and its impact on developmental phenotypes.
2004,
Pubmed Ransick,
Whole mount in situ hybridization shows Endo 16 to be a marker for the vegetal plate territory in sea urchin embryos.
1993,
Pubmed
,
Echinobase Romano,
Conservation of Endo16 expression in sea urchins despite evolutionary divergence in both cis and trans-acting components of transcriptional regulation.
2003,
Pubmed
,
Echinobase Rozas,
DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis.
1999,
Pubmed Stormo,
DNA binding sites: representation and discovery.
2000,
Pubmed Tajima,
Evolutionary relationship of DNA sequences in finite populations.
1983,
Pubmed Thompson,
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
1997,
Pubmed Watterson,
On the number of segregating sites in genetical models without recombination.
1975,
Pubmed Wray,
The evolution of transcriptional regulation in eukaryotes.
2003,
Pubmed Yuh,
Modular cis-regulatory organization of Endo16, a gut-specific gene of the sea urchin embryo.
1996,
Pubmed
,
Echinobase Yuh,
Cis-regulatory logic in the endo16 gene: switching from a specification to a differentiation mode of control.
2001,
Pubmed
,
Echinobase Yuh,
Complexity and organization of DNA-protein interactions in the 5'-regulatory region of an endoderm-specific marker gene in the sea urchin embryo.
1994,
Pubmed
,
Echinobase Yuh,
Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene.
1998,
Pubmed
,
Echinobase Zeller,
A multimerizing transcription factor of sea urchin embryos capable of looping DNA.
1995,
Pubmed
,
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