Chromatin conformation of human oral epithelium can identify orofacial cleft missing functional variants

作     者：Yao Xiao Shengbo Jiao Miao He Da Lin Huanyan Zuo Jiahao Han Yonghua Sun Gang Cao Zhi Chen Huan Liu Yao Xiao;Shengbo Jiao;Miao He;Da Lin;Huanyan Zuo;Jiahao Han;Yonghua Sun;Gang Cao;Zhi Chen;Huan Liu

作者机构：The State Key Laboratory Breeding Base of Basic Science of Stomatology&Key Laboratory for Oral Biomedicine of Ministry of EducationSchool and Hospital of StomatologyWuhan University237 Luoyu RoadWuhanChina Department of StomatologyNanfang HospitalSouthern Medical UniversityGuangzhouChina State Key Laboratory of Freshwater Ecology and BiotechnologyHubei Hongshan LaboratoryInstitute of HydrobiologyInnovation Academy for Seed DesignChinese Academy of SciencesWuhanChina College of Advanced Agricultural SciencesUniversity of Chinese Academy of SciencesBeijingChina State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural UniversityWuhanChina Taikang Center for Life and Medical SciencesWuhan UniversityWuhanChina 

出 版 物：《International Journal of Oral Science》 (国际口腔科学杂志（英文版）)

年 卷 期：2022年第14卷第4期

页      面：497-508页

核心收录：

学科分类：1003[医学-口腔医学] 10[医学] 

基　　金：supported by the National Natural Science Foundation of China(grant numbers:82071077,81771057,and 81400477 to H.L 82181340279,82071110,and 81771066 to Z.C.) “the Fundamental Research Funds for the Central Universities”(no.2042021kf0197) “The Young Top-notch Talent Cultivation Program of Hubei Province”to H.L 

主　　题：epithelium functional variants 

摘      要：Genome-wide association studies(GWASs) are the most widely used method to identify genetic risk loci associated with orofacial clefts(OFC). However, despite the increasing size of cohort, GWASs are still insufficient to detect all the heritability,suggesting there are more associations under the current stringent statistical threshold. In this study, we obtained an integrated epigenomic dataset based on the chromatin conformation of a human oral epithelial cell line(HIOEC) using RNA-seq, ATAC-seq,H3K27ac Ch IP-seq, and DLO Hi-C. Presumably, this epigenomic dataset could reveal the missing functional variants located in the oral epithelial cell active enhancers/promoters along with their risk target genes, despite relatively less-stringent statistical association with OFC. Taken a non-syndromic cleft palate only(NSCPO) GWAS data of the Chinese Han population as an example, 3664 SNPs that cannot reach the strict significance threshold were subjected to this functional identification *** total, 254 potential risk SNPs residing in active cis-regulatory elements interacting with 1 718 promoters of oral epitheliumexpressed genes were screened. Gapped k-mer machine learning based on enhancers interacting with epithelium-expressed genes along with in vivo and in vitro reporter assays were employed as functional validation. Among all the potential SNPs, we chose and confirmed that the risk alleles of rs560789 and rs174570 reduced the epithelial-specific enhancer activity by preventing the binding of transcription factors related to epithelial development. In summary, we established chromatin conformation datasets of human oral epithelial cells and provided a framework for testing and understanding how regulatory variants impart risk for clefts.