Naturally occurring deletions of hunchback binding sites in the even-skipped stripe 3+7 enhancer.
Changes in regulatory DNA contribute to phenotypic differences within and between taxa. Comparative studies show that many transcription factor binding sites (TFBS) are conserved between species whereas functional studies reveal that some mutations segregating within species alter TFBS function. Consistently, in this analysis of 13 regulatory elements in Drosophila melanogaster populations, single base and insertion/deletion polymorphism are rare in characterized regulatory elements. Experimentally defined TFBS are nearly devoid of segregating mutations and, as has been shown before, are quite conserved. For instance 8 of 11 Hunchback binding sites in the stripe 3+7 enhancer of even-skipped are conserved between D. melanogaster and Drosophila virilis. Oddly, we found a 72 bp deletion that removes one of these binding sites (Hb8), segregating within D. melanogaster. Furthermore, a 45 bp deletion polymorphism in the spacer between the stripe 3+7 and stripe 2 enhancers, removes another predicted Hunchback site. These two deletions are separated by ∼250 bp, sit on distinct haplotypes, and segregate at appreciable frequency. The Hb8Δ is at 5 to 35% frequency in the new world, but also shows cosmopolitan distribution. There is depletion of sequence variation on the Hb8Δ-carrying haplotype. Quantitative genetic tests indicate that Hb8Δ affects developmental time, but not viability of offspring. The Eve expression pattern differs between inbred lines, but the stripe 3 and 7 boundaries seem unaffected by Hb8Δ. The data reveal segregating variation in regulatory elements, which may reflect evolutionary turnover of characterized TFBS due to drift or co-evolution.
Faculty of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland; Institute of Biology, University of Iceland, Reykjavik, Iceland; Biomedical Center, University of Iceland, Reykjavik, Iceland; Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America.
Arnar
A
Palsson
Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
Natalia
N
Wesolowska
Faculty of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland; Institute of Biology, University of Iceland, Reykjavik, Iceland.
Sigrún
S
Reynisdóttir
Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America.
Michael Z
MZ
Ludwig
Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America.
Martin
M
Kreitman
D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D017124:Conserved Sequence; D004268:DNA-Binding Proteins / Q000378:metabolism*; D004175:Diptera / Q000235:genetics* / Q000378:metabolism*; D004742:Enhancer Elements, Genetic; D023061:Gene Order; D006239:Haplotypes; D018398:Homeodomain Proteins / Q000235:genetics* / Q000378:metabolism; D054643:INDEL Mutation; D008969:Molecular Sequence Data; D010802:Phylogeny; D011110:Polymorphism, Genetic; D016415:Sequence Alignment; D017384:Sequence Deletion; D014157:Transcription Factors / Q000378:metabolism*
D004268:DNA-Binding Proteins; D018398:Homeodomain Proteins; D014157:Transcription Factors