Cis-regulatory landscapes of the fat-tailed dunnart and mouse provide insights into the drivers of craniofacial heterochrony

Marsupials display accelerated development of the craniofacial region relative to the neurocranium when compared to placental mammals. This is thought to facilitate suckling by the highly altricial neonate after making the journey into the pouch. While cis-regulatory regions are considered to play a significant role in morphological evolution the face, the genetic mechanisms involved in craniofacial heterochrony among the major mammal lineages remain unclear. Here, we compared the cis-regulatory landscapes of the fat-tailed dunnart (Sminthopsis crassicaudata; Dasyuridae), a small marsupial amenable to laboratory husbandry, and mouse to gain insights into the basis of heterochrony. We compared patterns of the chromatin modifications, H3K4me3 and H3K27ac, between the dunnart and mouse during developmental stages when homologous craniofacial structures form each in species. We found that dunnart promoter- and enhancer- associated peaks at the time of birth in the dunnart broadly overlapped with all the stages of embryonic craniofacial development assessed in the mouse. However, dunnart-specific peaks were significantly enriched around genes whose mouse orthologs exhibit increased expression in the face over time. Moreover, genes displaying this temporal expression pattern were enriched for Gene Ontology terms related to ossification and skeletal development, processes that underlie development of the cranial muscles and bones of the face. This suggests a greater similarity between immediate postnatal chromatin landscape in the dunnart and late embryonic craniofacial development in the mouse. Using mouse-dunnart comparisons, we also discovered evidence of dunnart-specific peaks active near genes involved in the development of mechanosensory structures that may relate to the distinctive postnatal journey marsupial young take to the reach the pouch. This study characterised cis-regulatory elements driving craniofacial development in marsupials and their potential role in craniofacial heterochrony.