ArticleDevelopmental cell2023
Enhancer architecture and chromatin accessibility constrain phenotypic space during Drosophila development.
Article in Developmental cell, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 50 citations in OpenAlex.
- Mechanisms of Phenotypic Evolution from Molecules to Organisms: Integrating Evolutionary Biochemistry and Evolutionary Developmental Biology.Annual review of ecology, evolution, and systematics · 2026Article
- Review
- Predictive design of tissue-specific mammalian enhancers that function in the mouse embryo.Nature genetics · 2026Article
- Genomic language model for predicting enhancers and their allele-specific activity in the human genome.Bioinformatics (Oxford, England) · 2026Article
- Emergence Biases in Molecular Evolution.Genome biology and evolution · 2026Review
- Genome architecture shapes the evolutionary origins of redundant enhancers in fly and mouse.bioRxiv : the preprint server for biology · 2026Article
- Histone mark remodeling in cancer: an enhancer-centered perspective.Genes & genomics · 2026Review
- Cis-regulatory architecture downstream of FLOWERING LOCUS T underlies quantitative control of flowering in Arabidopsis thaliana.Genome biology · 2026Article
- Review
- A novel Hox gene promoter fuels the evolution of adaptive phenotypic plasticity in wing eyespots of satyrid butterflies.Nature ecology & evolution · 2025Article
- The structure of an ancient genotype-phenotype map shaped the functional evolution of a protein family.Nature ecology & evolution · 2025Article
- Gene regulatory networks and essential transcription factors for de novo-originated genes.Nature ecology & evolution · 2025Article
- Article
- Article
- Conservation of regulatory elements with highly diverged sequences across large evolutionary distances.Nature genetics · 2025Article
- The structure of an ancient genotype-phenotype map shaped the functional evolution of a protein family.bioRxiv : the preprint server for biology · 2025Article
- AntagonizingProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Novelty versus innovation of gene regulatory elements in human evolution and disease.Current opinion in genetics & development · 2025Review
- Chromatin enables precise and scalable gene regulation with factors of limited specificity.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Spherical harmonics texture extraction for versatile analysis of biological objects.PLoS computational biology · 2025Article
Corrections and comments
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Authors and funding
13 authors at 3 institutions in 2 countries.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.