Extended Data Fig. 3: The enhancer E4 interacts with the promoter of MFSD12 and affects the expression of MFSD12.
(a, b) Chromatin interactions near MFSD12 identified by Hi-C and H3K27ac HiChIP with Hae3 digestion. The upper matrix is from MNT-1 Hi-C data, and the lower matrix is from MNT-1 H3K27ac HiChIP data. TADs were called by onTAD100 and colored by nested TAD levels. The solid arch was a loop defined using FitHiChIP29 software, the dashed arch was a potential loop based on the observed interaction matrix. The interaction matrix between MFSD12 and HMG20B was highlighted with orange angles. The DNase track of melanocytes was downloaded from ENCODE68. rs6510760 and rs657246261 in E4 were colored in red. The plotted region is chr19:3519998-3589998 (hg19). (c) Schematic showing the location of the two sgRNAs targeting the enhancer E4 of MFSD12. (d) PCR results showing efficient knockout of the enhancer by the two sgRNAs. Three independent experiments. (e) qPCR showed that CRISPRi of E4 reduces the gene expression of MFSD12 and HMG20B in MNT-1 cells. Two-sided Dunnett’s test with adjustments for multiple comparisons (n = 3). (f) CRISPRi of E4 slightly increases melanin levels in MNT-1 cells. Two-tailed unpaired t-tests (n = 19). (g) qPCR showed that CRISPR knockout of E4 decreases the gene expression of MFSD12 and HMG20B in MNT-1 cells. Two-tailed unpaired t-tests without multiple testing adjustments (n = 6). Data are presented as mean ± SEM.
