ArticlePLoS genetics2018
Spatially varying cis-regulatory divergence in Drosophila embryos elucidates cis-regulatory logic.
Article in PLoS genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
9 citing papers in PubMed, 23 citations in OpenAlex.
- SEESAW: detecting isoform-level allelic imbalance accounting for inferential uncertainty.Genome biology · 2023Article
- Existing methods are effective at measuring natural selection on gene expression.Nature ecology & evolution · 2022Article
- Airpart: interpretable statistical models for analyzing allelic imbalance in single-cell datasets.Bioinformatics (Oxford, England) · 2022Article
- Molecular Evolution across Mouse Spermatogenesis.Molecular biology and evolution · 2022Article
- Article
- Contributions of cis- and trans-Regulatory Evolution to Transcriptomic Divergence across Populations in the Drosophila mojavensis Larval Brain.Genome biology and evolution · 2020Article
- Evolution of larval segment position across 12 Drosophila species.Evolution; international journal of organic evolution · 2020Article
- Article
- Allele-specific expression elucidates cis-regulatory logic.PLoS genetics · 2018Article
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2 authors at 1 institution in 1 country.
Funding
Abstract
Spatial patterning of gene expression is a key process in development, yet how it evolves is still poorly understood. Both cis- and trans-acting changes could participate in complex interactions, so to isolate the cis-regulatory component of patterning evolution, we measured allele-specific spatial gene expression patterns in D. melanogaster × simulans hybrid embryos. RNA-seq of cryo-sectioned slices revealed 66 genes with strong spatially varying allele-specific expression. We found that hunchback, a major regulator of developmental patterning, had reduced expression of the D. simulans allele specifically in the anterior tip of hybrid embryos. Mathematical modeling of hunchback cis-regulation suggested a candidate transcription factor binding site variant, which we verified as causal using CRISPR-Cas9 genome editing. In sum, even comparing morphologically near-identical species we identified surprisingly extensive spatial variation in gene expression, suggesting not only that development is robust to many such changes, but also that natural selection may have ample raw material for evolving new body plans via changes in spatial patterning.
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Registered trials
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