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 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.

Cleft Lip and Palate in Four Full-Sib Puppies from a Single Litter of Staffordshire Bull Terrier Dogs: An Anatomical and Genetic Study

“…Although cleft palate is one of dogs' most common congenital malformations, detailed morphological evaluation of the head by computed tomography has been rare and limited to selected breeds [17]. A CP can range from a simple fissure involving only a small portion of the caudal soft palate to complex defects involving the soft palate, the hard palate caudal to the palatine fissures, and the vomer in the nasal cavity [18,19]. CP has been recognized as a factor that can lead to death within the first three days of life of puppies belonging to large dog breeds.…”

JAG‐1/Notch signaling axis in the spinal cord contributes to bone cancer pain in rats

“…The interaction between DNA and protein was studied using chromatin immunoprecipitation (CHIP) experiments as described previously (Qin et al, 2022; Xiao et al, 2022). Briefly, PC12 cells were cross‐linked with 1% formaldehyde for 15 min at room temperature.…”

JAG-1/Notch signaling axis contributes to the maintenance of bone cancer pain in female rats via spinal astrocyte-neuron crosstalk

“…The interaction between DNA and protein was studied using chromatin immunoprecipitation (CHIP) experiments as described previously [35,36]. Brie y, PC12 cells were cross-linked with 1% formaldehyde for 15 min at room temperature.…”