Fig. 3

Genome-wide transcription target analysis of the Slug-PRMT5-LSD1 complex. (A) Public ChIP-seq datasets (GSE55421, GSE130194 and GSE101150) were extracted from Gene Expression Omnibus (GEO) database for genome-wide identification of the Slug, PRMT5 and LSD1 binding sites. The percentages of binding sites mapped to seven different genomic regions are shown in the periphery of the pie chart. (B) Venn diagram of overlapping promoters bound by Slug, PRMT5 and LSD1. The number of genes targeted by themselves is indicated. (C) Gene ontology (GO) analysis of the 87 overlapped target genes is shown. Based on the different functions of these genes, the GO function network was built (Left). Barplots represent top20 GO Biological Processes, ranked by − log10 (p.value) (Right) (D) Visualized binding peaks of Slug, PRMT5 and LSD1 at representative target genes (CDH1 and VIM) loci using a genome browser (IGV). (E) The binding motifs for Slug, PRMT5 and LSD1 were analyzed by MEME suite. (F) Verification of the ChIP-seq results by qChIP analysis of the indicated genes in MDA-MB-231 cells. The occupation of Slug, PRMT5 and LSD1 at the indicated promoters in MDA-MB-231 cells was analyzed with the qChIP assay. (G) The level of H4R3me2s, H3R2me2s, H3K9me2 and H3K4me2 at the indicated promoters in MDA-MB-231 cells was analyzed with the qChIP assay. For E and F, results are represented as the fold-change compared to the control IgG. Error bars represent the mean ± SD from three independent experiments (**p < 0.01, ***p < 0.001, and two-tailed unpaired t-test)