Fig. 4

HMGA2 regulates MSI2 expression in NF1 MPNSTs (a) Heatmap showing differentially expressed genes in shHMGA2-transfected cells compared with genes in control cells. b KEGG analysis of HMGA2-regulated signalling pathways. c ChIP-Seq density heatmaps for HMGA2 within ±3 kb of the HMGA2 peak. d Gene ontology (GO) analysis of signalling pathways involving genes with potential HMGA2 binding. e Pie charts showing the distribution of HMGA2-binding sites in the genome. f Motif enrichment of the subgroup with shared increases in chromatin accessible regions. g Overlap of genes identified by ChIP-Seq and RNA-Seq and significantly differentially expressed genes in GSE66743. h Heatmap showing categories of differentially expressed genes targeted by HMGA2 in NF1 MPNST cells. i Verification of the expression levels of genes involved in neural development in five cell lines. j Correlation analysis between HMGA2 and MSI2 expression levels in GSE66743. k Immunofluorescence analysis of the co-localization and expression of MSI2 and HMGA2 in NF1 MPNST cells. l MSI2 promoter-containing luciferase reporter constructs (nucleotides − 2417 to − 2100) were transiently transfected into the indicated cells, and luciferase activity was analysed after 48 h. Data represent the mean ± SD of 3 separate determinations. *P < 0.05 by Student’s t-tests