Naturally Occurring Deletions of Hunchback Binding Sites in the Even-Skipped Stripe 3+7 Enhancer

• Published in: PLoS ONE
• Main Authors: Wesolowska, Natalia, Reynisdóttir, Sigrún, Ludwig, Michael Z., Kreitman, Martin, Palsson, Arnar
• Other Authors: Líf- og umhverfisvísindadeild (HÍ), Faculty of Life and Environmental Sciences (UI), Verkfræði- og náttúruvísindasvið (HÍ), School of Engineering and Natural Sciences (UI), Háskóli Íslands, University of Iceland
• Format: Article in Journal/Newspaper
• Language: English
• Published: Public Library of Science (PLoS) 2014
• Subjects: Biochemistry; Genetics; Molecular Biology; Agricultural Sciences; Biological Sciences; Evolution; Development; Lífefnafræði; Erfðafræði; Sameindalíffræði; Þróun lífsins; Stripe; Iceland
• Online Access: https://hdl.handle.net/20.500.11815/176; https://doi.org/10.1371/journal.pone.0091924

Publisher's version 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. This project was funded by the National Institutes of Health (Grant R01 GM61001 to M.K. and M.Z.L.), Icelandic research fund (IRF 070260021 to A.P.), Marie Curie international reintegration grant (MIRG-CT-2007-046510 to A.P.) and the University of Iceland research fund to A.P. The funders had no role in study design, data collection and ...