Fig. 3

Transcriptome sequencing reveals distinct changes in gene signatures associated with REST. A RNA-seq analyses showing gene upregulation and downregulation (highlighted in red, log₂FC cutoff = 0.58, padj < 0.05) in REST KO cells compared to corresponding control (T98G—left, HEK293—right). Representative volcano plots were built using “Enhanced Volcano” Bioconductor package. B Venn diagrams of deregulated genes shared between three “slow” T98G REST-KO clones (C10, F7, and G2): upregulated genes are shown on the left, downregulated genes are shown on the right. C GO (gene ontology) categories enriched among upregulated genes (top) and downregulated genes (bottom) in T98G REST-KO vs control. D Overlap of upregulated genes in glioblastoma (left, shared between three “slow” clones, in green) and HEK293 (right, shared between two clones, in green) and a published subset of genes with REST binding sites in human embryonic stem cells (in yellow) [29]. E A list of representative REST-target genes (n = 6) based on Tag-Seq and TCGA-GBM data analysis (shown are correlation coefficients of gene expression with REST mRNA). F Validation of REST-target genes by qPCR assay in REST-KO cells. Shown are fold changes (FC) vs T98G control cells derived from three independent biological replicates. Gene expression was measured using ddCt method and normalized by ACTB expression. Comparison vs control was performed using one-tailed t-tests. Dashed line indicates FC = 1.5. Individual data values are provided in Additional File 10G