Cleft palate is a common congenital maxillofacial malformation in newborns. All-trans retinoic acid (atRA) is an ideal exogenous stimulus to construct a mouse cleft palate model. However, the precise pathogenic mechanism remains to be elucidated. In our study, to explore the toxicity of atRA on palatal shelves during different stages of palate development, a total of 100 mg/kg atRA was administered to C57BL/6 mice at embryonic day 10.5 (E10.5). Mouse embryonic palatal shelves at E13.5, E14.5, E15.5, and E16.5 were collected for RNA extraction and histological treatment. Changes in gene expression were tested through RNA-seq. Selected differentially expressed genes (DEGs) related to metabolic pathways, such as Ptgds, Ttr, Cyp2g1, Ugt2a1 and Mgst3, were validated and analyzed by Quantitative real-time PCR (qRT-PCR). In addition, Gene Oncology analysis showed that transcriptional changes of genes from extracellular matrix (ECM) components, such as Spp1, and crystallin family might play important role in palatal shelves elevation (E13.5-E14.5). Therefore, the protein expression level of Ttr and Spp1 from E13.5 to E16.5 were tested by immunohistochemistry (IHC). Besides, the mRNA level of Spp1, were down-regulated at E16.5 and the protein were down-regulated at E15.5 and E16.5 in all-trans retinoic acid group, suggesting that atRA may involve in palatal bone formation by regulating Spp1. Overall, gene transcriptional profiles were obviously different at each time point of palate development. Thus, this study summarized some pathways and genes that may be related to palatogenesis and cleft palate through RNA-seq, to provide a direction for subsequent studies on the mechanism and targeted therapy of cleft palate.

late裂是新生儿常见的先天性颌面部畸形。全反式维甲酸（atRA）是构建小鼠mouse裂模型的理想外源刺激。但是，确切的致病机制尚待阐明。在我们的研究中，为探讨atRA在pa发育不同阶段对shelves架的毒性，在胚胎第10.5天（E10.5）向C57BL / 6小鼠总共施用了100 mg / kg atRA。收集E13.5，E14.5，E15.5和E16.5的小鼠胚胎pa架进行RNA提取和组织学处理。通过RNA-seq测试基因表达的变化。与代谢途径相关的选定差异表达基因（DEG），例如Ptgds，Ttr，Cyp2g1，Ugt2a1和Mgst3，通过实时定量PCR（qRT-PCR）进行了验证和分析。此外，基因肿瘤学分析表明，来自细胞外基质（ECM）组件（例如Spp1和晶体蛋白家族）的基因的转录变化可能在pa架升高（E13.5-E14.5）中起重要作用。因此，通过免疫组织化学（IHC）检测了从E13.5到E16.5的Ttr和Spp1的蛋白表达水平。此外，全反式维甲酸组的Spp1 mRNA水平下调至E16.5，蛋白水平下调至E15.5和E16.5，提示atRA可能通过调节其参与pa骨的形成。Spp1。总体而言，在上颚发育的每个时间点，基因转录谱均明显不同。因此，本研究总结了可能通过RNA-seq与to裂和and裂相关的一些途径和基因，为后续研究subsequent裂的机理和靶向治疗提供了方向。