Fig. 7: NF1 exon23a splicing in pHGG is regulated downstream from REST.
From: Splicing is an alternate oncogenic pathway activation mechanism in glioma
a Enrichment of transcription factor binding sites in NF1 exon23a splice regulators were calculated by Enrichr using ENCODE ChIP-Seq data. All significant results (FDR < 0.05, red) are highlighted red and the dataset labeled. b ChIP was carried out using REST or IgG antibodies with chromatin from primary DIPG cell lines and analyzed as percent input at the indicated loci (n = 3). Bars show mean ± standard deviation. c REST expression in pHGG (n = 64) and normal brain (n = 20). Bars show mean ± standard deviation. d Gene set enrichment analysis of REST signature genes with a REST-bound RE1 motif. NES normalized enrichment score, FDR false discovery rate. e Pearson correlation of REST expression and expression of NF1 exon23a splice regulators (CELF1, P = 0.01; CELF3; P = 10−5, CELF4, P = 10−4, CELF5, P = 10−6, CELF6, P = 0.01; ELAVL2, P = 0.01; ELAVL3, P = 10−5, ELAVL4, P = 0.04). Genes bound by REST across ENCODE ChIP-Seq datasets are shaded in solid color, genes not bound by REST are empty. f qRT-PCR in SU-DIPG-VII and SU-DIPG-XIII cell lines transfected with control or REST-specific siRNA. Bars show mean ± standard deviation (n = 3) relative to 18S housekeeping, normalized to siCTR expression for each gene. g qRT-PCR in SU-DIPG-VII and SU-DIPG-XIII cell lines transfected with control or REST-specific siRNA. Bars show mean ± standard deviation (n = 3) relative to 18S housekeeping, normalized to siCTR expression for each gene. h Scatter plot of REST expression and NF1 exon23a inclusion in pHGG. r: Pearson correlation. i Scatter plot of REST expression and RAS pathway activity (ssGSEA ES) in pHGG. r: Pearson correlation. Statistical tests: t (all; multiple t tests with two-stage linear step-up procedure of Benjamini, Krieger, and Yekutieli (f, g)). *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001. Source data are provided as a Source Data file.
