Chromatin conformation of human oral epithelium can identify orofacial cleft missing functional variants
Abstract 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 u...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Publishing Group
2022-08-01
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| Series: | International Journal of Oral Science |
| Online Access: | https://doi.org/10.1038/s41368-022-00194-0 |
| _version_ | 1811285861823676416 |
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| author | Yao Xiao Shengbo Jiao Miao He Da Lin Huanyan Zuo Jiahao Han Yonghua Sun Gang Cao Zhi Chen Huan Liu |
| author_facet | Yao Xiao Shengbo Jiao Miao He Da Lin Huanyan Zuo Jiahao Han Yonghua Sun Gang Cao Zhi Chen Huan Liu |
| author_sort | Yao Xiao |
| collection | DOAJ |
| description | Abstract 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 ChIP-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 pipeline. In total, 254 potential risk SNPs residing in active cis-regulatory elements interacting with 1 718 promoters of oral epithelium-expressed 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. |
| first_indexed | 2024-04-13T02:51:13Z |
| format | Article |
| id | doaj.art-55e7ce681fac4bdf868bfbe37daf8017 |
| institution | Directory Open Access Journal |
| issn | 1674-2818 2049-3169 |
| language | English |
| last_indexed | 2024-04-13T02:51:13Z |
| publishDate | 2022-08-01 |
| publisher | Nature Publishing Group |
| record_format | Article |
| series | International Journal of Oral Science |
| spelling | doaj.art-55e7ce681fac4bdf868bfbe37daf80172022-12-22T03:05:50ZengNature Publishing GroupInternational Journal of Oral Science1674-28182049-31692022-08-0114111210.1038/s41368-022-00194-0Chromatin conformation of human oral epithelium can identify orofacial cleft missing functional variantsYao Xiao0Shengbo Jiao1Miao He2Da Lin3Huanyan Zuo4Jiahao Han5Yonghua Sun6Gang Cao7Zhi Chen8Huan Liu9The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan UniversityState Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of SciencesThe State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan UniversityState Key Laboratory of Agricultural Microbiology, Huazhong Agricultural UniversityThe State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan UniversityThe State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan UniversityState Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of SciencesState Key Laboratory of Agricultural Microbiology, Huazhong Agricultural UniversityThe State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan UniversityThe State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan UniversityAbstract 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 ChIP-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 pipeline. In total, 254 potential risk SNPs residing in active cis-regulatory elements interacting with 1 718 promoters of oral epithelium-expressed 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.https://doi.org/10.1038/s41368-022-00194-0 |
| spellingShingle | Yao Xiao Shengbo Jiao Miao He Da Lin Huanyan Zuo Jiahao Han Yonghua Sun Gang Cao Zhi Chen Huan Liu Chromatin conformation of human oral epithelium can identify orofacial cleft missing functional variants International Journal of Oral Science |
| title | Chromatin conformation of human oral epithelium can identify orofacial cleft missing functional variants |
| title_full | Chromatin conformation of human oral epithelium can identify orofacial cleft missing functional variants |
| title_fullStr | Chromatin conformation of human oral epithelium can identify orofacial cleft missing functional variants |
| title_full_unstemmed | Chromatin conformation of human oral epithelium can identify orofacial cleft missing functional variants |
| title_short | Chromatin conformation of human oral epithelium can identify orofacial cleft missing functional variants |
| title_sort | chromatin conformation of human oral epithelium can identify orofacial cleft missing functional variants |
| url | https://doi.org/10.1038/s41368-022-00194-0 |
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