Single-cell multi-omics decodes regulatory programs during development of mouse secondary palate II

Perturbations in gene regulation during palatogenesis can lead to cleft palate, which is among the most common congenital birth defects. However, currently there is no comprehensive multiomics map of the developing secondary palate. Here, we perform single-cell multiome sequencing and profile chromatin accessibility and gene expression simultaneously within the same cells (n = 36,154) isolated from mouse secondary palate across embryonic days (E) 12.5, E13.5, E14.0, and E14.5. We construct five trajectories representing continuous differentiation of cranial neural crest-derived multipotent cells into distinct lineages. By linking open chromatin signals to gene expression changes, we characterize the underlying lineage-determining transcription factors. In silico perturbation analysis identifies transcription factors SHOX2 and MEOX2 as important regulators of the development of the anterior and posterior palate, respectively. In conclusion, our study chart epigenetic and transcriptional dynamics in palatogenesis, serving as a valuable resource for further cleft palate research. The anterior (n=2) and posterior (n=2) 1/3 palatal shelves of E14.0 C57BL/6J mice were microdissected, isolated, and then subjected to ChIP-seq with either SHOX2 antibody (JK-6E) (sc-81955, Santa Cruz), MEOX2 Antibody (A-8) (Sc-376748, Santa Cruz), or normal rabbit IgG (2729, Cell Signaling Technology) as a negative control. The ChIP assays were performed according to the manufacture’s instruction using SimpleChIP® Enzymatic Chromatin IP Kit (Magnetic Beads) (9003, CST). Two independent ChIPs were conducted for library generation for each group.