@article{106974928b3742a0a6c621d8d4ec80a8,
title = "Enhancer architecture and chromatin accessibility constrain phenotypic space during Drosophila development",
abstract = "Developmental enhancers bind transcription factors and dictate patterns of gene expression during development. Their molecular evolution can underlie phenotypical evolution, but the contributions of the evolutionary pathways involved remain little understood. Here, using mutation libraries in Drosophila melanogaster embryos, we observed that most point mutations in developmental enhancers led to changes in gene expression levels but rarely resulted in novel expression outside of the native pattern. In contrast, random sequences, often acting as developmental enhancers, drove expression across a range of cell types; random sequences including motifs for transcription factors with pioneer activity acted as enhancers even more frequently. Our findings suggest that the phenotypic landscapes of developmental enhancers are constrained by enhancer architecture and chromatin accessibility. We propose that the evolution of existing enhancers is limited in its capacity to generate novel phenotypes, whereas the activity of de novo elements is a primary source of phenotypic novelty.",
keywords = "Drosophila melanogaster, development, enhancers, evolution, gene regulation, novel expression patterns, phenotypical novelties, pioneer factors, random sequences, reporter assays",
author = "Rafael Galupa and Gilberto Alvarez-Canales and Borst, {Noa Ottilie} and Timothy Fuqua and Lautaro Gandara and Natalia Misunou and Kerstin Richter and Alves, {Mariana R.P.} and Esther Karumbi and Perkins, {Melinda Liu} and Tin Kocijan and Rushlow, {Christine A.} and Justin Crocker",
note = "Funding Information: We thank GenScript for gifting us the random DNA libraries, Hsiao-Yun Liu for making the protein for the Zelda antibody prep, Garth Ilsley for discussions about pattern quantifications, Claire Standley for title suggestions and Denis Krndija for critical feedback on the manuscript. We are grateful to other members of the Crocker lab for helpful suggestions and discussions during the course of the project, in particular Xueying Li. We also thank the ALMF imaging platform and Alessandra Reversi for some of the fly injections. Stocks obtained from the Bloomington Drosophila Stock Center ( NIH P40OD018537 ) were used in this study. R.G. and L.G. were supported by fellowships from the European Molecular Biology Laboratory Interdisciplinary Postdoc Programme (EIPOD) under Marie Sk{\l}odowska-Curie Actions COFUND ( 664726 and 847543 , respectively). Research in the Crocker lab is supported by the European Molecular Biology Laboratory (EMBL). Funding Information: We thank GenScript for gifting us the random DNA libraries, Hsiao-Yun Liu for making the protein for the Zelda antibody prep, Garth Ilsley for discussions about pattern quantifications, Claire Standley for title suggestions and Denis Krndija for critical feedback on the manuscript. We are grateful to other members of the Crocker lab for helpful suggestions and discussions during the course of the project, in particular Xueying Li. We also thank the ALMF imaging platform and Alessandra Reversi for some of the fly injections. Stocks obtained from the Bloomington Drosophila Stock Center (NIH P40OD018537) were used in this study. R.G. and L.G. were supported by fellowships from the European Molecular Biology Laboratory Interdisciplinary Postdoc Programme (EIPOD) under Marie Sk{\l}odowska-Curie Actions COFUND (664726 and 847543, respectively). Research in the Crocker lab is supported by the European Molecular Biology Laboratory (EMBL). Conceptualization: R.G. T.F. and J.C. Investigation: R.G. G.A.-C. M.R.P.A. N.O.B. T.F. L.G. N.M. K.R. E.K. T.K. C.A.R. and J.C. Methodology: R.G. G.A.-C. N.O.B. T.F. L.G. K.R. and J.C. Formal analysis: R.G. G.A.-C. N.O.B. T.F. L.G. N.M. and J.C. Data curation: R.G. N.M. and J.C. Visualization: R.G. T.F. K.R. N.M. and J.C. Software: G.A.-C. M.L.P. and J.C. Resources: C.A.R. Supervision: R.G. T.F. and J.C. Project administration: R.G. and J.C. Funding acquisition: J.C. Writing – original draft: R.G. and J.C. Writing – review & editing: R.G. G.A.-C. N.O.B. T.F. L.G. N.M. M.R.P.A. M.L.P. and J.C. The authors declare no competing interests. We support inclusive, diverse, and equitable conduct of research. Publisher Copyright: {\textcopyright} 2022 The Authors",
year = "2023",
month = jan,
day = "9",
doi = "10.1016/j.devcel.2022.12.003",
language = "English (US)",
volume = "58",
pages = "51--62.e4",
journal = "Developmental Cell",
issn = "1534-5807",
publisher = "Cell Press",
number = "1",
}