The Functional Impact of the Noncoding SNP rs3741442 on Orofacial Clefting

Area of Science:

• Genetics
• Developmental Biology
• Congenital Anomalies

Background:

• Orofacial cleft (OFC) is a common congenital anomaly with varying prevalence across ethnic groups.
• Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) linked to nonsyndromic OFC (nsOFC), but underlying mechanisms are unclear.

Purpose of the Study:

• To investigate the biological mechanism of the intergenic SNP rs3741442 in nonsyndromic orofacial cleft (nsOFC).
• To explore the role of rs3741442 in gene expression modulation affecting palatogenesis.

Main Methods:

• Utilized expression quantitative trait locus (eQTL) analysis to assess SNP effects on gene expression.
• Employed epigenetic markers and in silico analysis to prioritize potential causal SNPs.
• Used CRISPR-edited cells to study the functional impact of rs3741442 risk allele on gene expression.
• Investigated transcription factor binding to different SNP alleles.

Main Results:

• The noncoding SNP rs3741442 exhibits cis-eQTL effects on epithelial genes involved in periderm differentiation.
• The risk allele of rs3741442, prevalent in East Asian populations, reduces expression of neighboring KRT18 and EIF4B.
• Transcription factor SP1 differentially binds to risk and non-risk alleles of rs3741442.
• rs3741442 also demonstrates a trans-eQTL effect on TP63, a gene linked to syndromic OFC and psoriasis.

Conclusions:

• The intergenic SNP rs3741442 may contribute to nsOFC by modulating epithelial gene expression during palatogenesis.
• Findings highlight a mechanism where noncoding genetic variations influence complex congenital anomalies through gene regulation.