Fig. 5

Loss of super enhancer element E_349 in melanoma unlocks tumor growth potential by modulating MEF2A expression. a Epigenetic and 3D genome profiles at the E_349-contained super enhancer and MEF2A locus (GRCh37/hg19 chr15: 99,800,000–100,400,000), including signals of A375 combined Hi-C, H3K27ac, H3K4me1, H3K4me3, ATAC-seq, and HiChIP loops. b Genomic profiles of recurrent DELs and CRISPRi enhancer screen results at the E_349 and MEF2A locus on 297 melanoma samples. c 4C assay result of interaction between the MEF2A promoter and E_349, light blue arrow refers to the 4C viewpoint (VP), and peak region highlighted by yellow arrow represents the chromosome region interacting with the VP. d Expression levels of MEF2A in tumor (T, n = 461 samples) and normal tissues (N, n = 558 samples) were analyzed using the TCGA-SKCM data. e Overall survival analysis of MEF2A in the low MEF2A expressed group and high MEF2A expressed group were compared using the TCGA-SKCM data. f, g The E_349 core sequence (GRCh37/hg19 chr15: 99,982,353–99,983,277) was cloned into pGL3-Promoter vector, and Luciferase assays were performed in 293T cells (f), and A375 cells (g). h, i Western blotting results of MEF2A protein expression in the E_349-inhibited A375-KRAB (h) and E_349-activated A375-VP64 (i) cells. j, k Cell apoptosis (j) and Plate clone formation (k) assay results of the E_349-inhibited A375-KRAB cells with 1 µM vemurafenib or without treatment (n = 3 samples). l, m The representative three-dimension (3D) modeling graphs and statistical results in calculating tumor volumes for E_349-inhibited A375-KRAB and control cells (l) at 2 or 3 weeks after subcutaneous injection in 5-week-old female nude mice, and then the tumors were weighed (m) after euthanasia of the mice (n = 7 mice). CI denotes CRISPR interference, and CA denotes CRISPR activation. Left graph is the representative result, and right graph is the statistical result. All the data are expressed as the means ± SD and analyzed by an unpaired two-tailed Student’s t test. Asterisks indicate significant differences between the indicated experimental groups: *, p < 0.05; **, p < 0.01; ***, p < 0.001; ****, p < 0.0001