Fig. 3

Enhancers regulate the expression of SERPINH1 through the three-dimensional structure of chromatin. a Heatmap of contact domains around SERPINH1 based on hg38. The left shows the difference in chromatin interactions between HEEC (top) and KYSE150 (bottom) cells at 25 kb resolution (red: interactions with high frequency; blue: interactions with low frequency). The contact domain is marked by a blue rectangle. The right panel shows a magnified view of the domains around SERPINH1, with differences in the interactions highlighted in green circles. b Integrated Genomics Viewer (IGV) visualization of the differences in chromatin accessibility, histone modifications and RNA expression between normal and tumor cells and tissues. The promoter of SERPINH1 and possible enhancers are highlighted by red rectangles. c Significant intrachromosomal loops around SERPINH1. Only loops at 10 kb resolution with contact counts greater than 10 are shown. The vertical coordinates represent the interaction frequency, which varies greatly between tumor and normal cell lines. d Real-time qPCR quantification of SERPINH1 Enhancer 2 abundance in bulk ATAC libraries from the KYSE150, KYSE510 and KYSE180 cell lines (n = 3). e Real-time qPCR quantification of the SERPINH1 Enhancer 2 abundance in bulk ATAC libraries generated from ESCC samples at early (stages I and II) and advanced (stages III and IV) stages (n = 6). f, g GSEA showing the enrichment of EMT-related gene sets. h Transwell migration assays were used to assess the effect of SERPINH1 overexpression in KYSE150 cells (OE-SERPINH1) compared with control cells (Vector). i GSVA of RNA-seq data from the KYSE150 and KYSE30 cell lines, with OE and WT representing overexpression and control cells, respectively, and KD and NC representing the knockdown and negative control groups, respectively