Fig. 5

Confirmation of the regulatory effect of rs3862386. a, b The SNP rs3862386 disrupts CTCF and REST binding. c The SNP rs3862386 is located in a genomic region with DNase-Seq, ChIP-Seq, and histone modification signals, indicating that it is located in a genomic region with active transcription in neuronal cells. d Reporter gene assays showed that the G allele of rs3862386 produced significantly higher luciferase activity than the C allele in all three tested cell lines. e–g The expression of PACS1 and YIF1A was significantly altered by CTCF knockdown. h–j A 331-bp genomic sequence containing rs3862386 was deleted by CRISPR/Cas9-mediated genome editing. Deletion of rs3862386 resulted in altered expression of PACS1 and YIF1A. h Genomic PCR/electrophoresis results showed deletion of the genomic region containing rs3862386. WT, genomic DNA containing rs3862386 in wild-type cells (882 bp). KO, genomic DNA containing rs3862386 in edited cells (311 bp). N = 8 per group for HEK293T cells, n = 8 for the control group, n = 16 per experimental group for SH-SY5Y and U251 cells, n = 3 per group in (e–h) and (j–l). Two-tailed Student’s t test. *P < 0.05, **P < 0.01, ***P < 0.001