Spatially varying cis-regulatory divergence in Drosophila embryos elucidates cis-regulatory logic

Abstract

Spatial patterning of gene expression is a key process in development--responsible for the incredible diversity of animal body plans--yet how it evolves is still poorly understood. Both cis- and trans-acting changes could accumulate and 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 x D. simulans hybrid embryos. RNA-seq of cryosectioned slices revealed 55 genes with strong spatially varying allele-specific expression, and several hundred more with weaker but significant spatial divergence. For example, we found that hunchback (hb), a major regulator of developmental patterning, had reduced expression specifically in the anterior tip of D. simulans embryos. Mathematical modeling of hb cis-regulation suggested that a mutation in a Bicoid binding site was responsible, which we verified using CRISPR-Cas9 genome editing. In sum, even comparing morphologically near-identical species we identified a substantial amount of spatial variation in gene expression, suggesting that development is robust to many such changes, but also that natural selection may have ample raw material for evolving new body plans via cis-regulatory divergence.