Fig. 5: Promoter G4 landscape changes are related to stem cell identity.
From: G-quadruplex DNA structures in human stem cells and differentiation
a–d Top 20 significant (FDR < 0.05) biological processes obtained from Gene Ontology enrichment analysis (GO:BP) performed with g:Profiler84 for genes showing increased expression in a CNCCs vs hESCs (FDR < 0.05, Log2FC > 1) that gain a promoter G4 (G4E– G4D+; n = 136 genes) and c in NSCs vs hESCs (FDR < 0.05, Log2FC > 1) that gain a promoter G4 (G4D– G4D+; n = 37 genes). Number of genes in intersection for each term shown in brackets. See Supplementary Data 2 and 3 for full list of GO and KEGG terms. Genome browser view for representative gene promoters demonstrating G4E– G4D+ promoter status after hESC differentiation into b CNCCs or c NSCs. Yellow shading highlights location of cell-specific G4 across open chromatin sites (ATAC) and OQs13. Grey shading highlights G4s common to both CNCCs and NSCs. Heatmap showing median gene expression (Log10(TPM + 0.01)) is shown for the indicated genes. N = 5, 3 and 4 biologically independent samples for hESCs, CNCCs and NSCs, respectively. e, f Top 10 KEGG terms for genes with increased expression (FDR < 0.05, Log2FC > 1) in hESCs compared to CNCCs (n = 1,128 genes) or NSCs (n = 1175 genes) which lose a promoter G4 (G4E+ G4D−) (e). Genes in bold represent those in common in NSC and CNCC differentiation. f Genome browser view for representative gene promoters demonstrating G4E+ G4D− promoter status after hESC differentiation.
