Perturbations in gene regulation during palatogenesis can lead to cleft palate, which is among the most common congenital birth defects. 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 charts epigenetic and transcriptional dynamics in palatogenesis, serving as a valuable resource for further cleft palate research.

腭形成过程中基因调控的扰动可导致腭裂，这是最常见的先天性出生缺陷之一。在这里，我们在胚胎期 （E） 12.5、E13.5、E14.0 和 E14.5 期间从小鼠次级上颚分离的相同细胞 （n = 36,154） 内同时进行单细胞多组测序并分析染色质可及性和基因表达。我们构建了五条轨迹，代表颅神经嵴衍生的多能细胞连续分化为不同的谱系。通过将开放染色质信号与基因表达变化联系起来，我们表征了潜在的谱系决定转录因子。计算机扰动分析确定转录因子 SHOX2 和 MEOX2 分别是前腭和后腭发育的重要调节因子。总之，我们的研究绘制了腭发生的表观遗传和转录动力学，为进一步的腭裂研究提供了宝贵的资源。