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Although it is generally accepted that the condition arises from failed fusion between the upper lip and primary palate, the precise mechanism underlying this fusion process remains enigmatic. In this study, we utilized transposase\u2010accessible chromatin sequencing (scATAC\u2010seq) and single\u2010cell RNA sequencing (scRNA\u2010seq) to interrogate lambdoidal junction tissue derived from C57BL\/6J mouse embryos at critical stages of embryogenesis (10.5, 11.5 and 12.5 embryonic days). We successfully identified distinct subgroups of mesenchymal and ectodermal cells involved in the fusion process and characterized their unique transcriptional profiles. Furthermore, we conducted cell differentiation trajectory analysis, revealing a dynamic repertoire of genes that are sequentially activated or repressed during pseudotime, facilitating the transition of relevant cell types. Additionally, we employed scATAC data to identify key genes associated with the fusion process and demonstrated differential chromatin accessibility across major cell types. Finally, we constructed a dynamic intercellular communication network and predicted upstream transcriptional regulators of critical genes involved in important signalling pathways. Our findings provide a valuable resource for future studies on upper lip and primary palate development, as well as congenital defects.<\/jats:p>","DOI":"10.1111\/jcmm.70128","type":"journal-article","created":{"date-parts":[[2024,10,11]],"date-time":"2024-10-11T11:04:30Z","timestamp":1728644670000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Single\u2010cell transcriptome and chromatin accessibility mapping of upper lip and primary palate fusion"],"prefix":"10.1111","volume":"28","author":[{"given":"Sini","family":"Cai","sequence":"first","affiliation":[{"name":"The Department of Cleft Lip and Palate of Plastic Surgery Hospital Chinese Academy of Medical Sciences and Peking Union Medical College  Beijing China"},{"name":"Medical Cosmetic Center of Dermatology Hospital of Southern Medical University Guangdong Provincial Dermatology Hospital  Guangzhou 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