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Redundant and cryptic enhancer activities of the Drosophila yellow gene

Gizem Kalay, Jennifer Lachowiec, Ulises Rosas, Mackenzie R. Dome, Patricia Wittkopp
doi: https://doi.org/10.1101/419226
Gizem Kalay
1Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
4Present address: Department of Evolution and Ecology, University of California, Davis, Davis, CA 95616
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Jennifer Lachowiec
1Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
5Present address: Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717
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Ulises Rosas
3Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, 04510, CDMX, Mexico.
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Mackenzie R. Dome
1Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
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Patricia Wittkopp
1Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
2Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109
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Abstract

cis-regulatory sequences known as enhancers play a key role in regulating gene expression. Evolutionary changes in these DNA sequences contribute to phenotypic evolution. The Drosophila yellow gene, which is required for pigmentation, has emerged as a model system for understanding how cis-regulatory sequences evolve, providing some of the most detailed insights available into how activities of orthologous enhancers have diverged between species. Here, we examine the evolution of yellow cis-regulatory sequences on a broader scale by comparing the distribution and function of yellow enhancer activities throughout the 5’ intergenic and intronic sequences of Drosophila melanogaster, Drosophila pseudoobscura, and Drosophila willistoni. We find that cis-regulatory sequences driving expression in a particular tissue are not as modular as previously described, but rather have many redundant and cryptic enhancer activities distributed throughout the regions surveyed. Interestingly, cryptic enhancer activities of sequences from one species often drove patterns of expression observed in other species, suggesting that the frequent evolutionary changes in yellow expression observed among Drosophila species may be facilitated by gaining and losing repression of pre-existing cis-regulatory sequences.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted September 27, 2018.
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Redundant and cryptic enhancer activities of the Drosophila yellow gene
Gizem Kalay, Jennifer Lachowiec, Ulises Rosas, Mackenzie R. Dome, Patricia Wittkopp
bioRxiv 419226; doi: https://doi.org/10.1101/419226
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Redundant and cryptic enhancer activities of the Drosophila yellow gene
Gizem Kalay, Jennifer Lachowiec, Ulises Rosas, Mackenzie R. Dome, Patricia Wittkopp
bioRxiv 419226; doi: https://doi.org/10.1101/419226

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