Single-cell transcriptome profiling reveals developmental trajectory and regulatory networks of mouse maxillary prominence [ATAC-seq]

The formation of maxillary prominence in vertebrates involves precisely coordinated migration and differentiation of neural crest cells. However, the regulatory factors and networks underpinning such an intricate process has not been fully elucidated. Here we combined bulk and single-cell RNA-Seq to comprehensively characterize the transcriptome dynamics during mouse maxillary development from embryonic day (E) 10.5 to 12.5, a critical period when a multitude of facial tissues start to emerge. We identified multiple cell populations that represent different developmental transition states and inferred the developmental trajectory of maxillary mesenchyme, revealing that a developmental bifurcation toward either an osteochondrogenic fate or a non-osteochondrogenic fate occurs at E11.5. We further deduced the core transcriptional regulators and gene regulatory networks associated with the maxillary cell fate transitions. Moreover, we revealed transcriptional regulators that are linked to dynamic changes in chromatin accessibility during maxillary development. Collectively, our study for the first time characterized the maxillary developmental process at single cell resolution, providing rich resources and important insights for achieving a systems level understanding of craniofacial morphogenesis and abnormality. ATAC-seq of E10.5, E11.5, E12.5 mouse embryonic maxillary process mesenchymal cells. Three biological replicates per group