Differential Gene Expression following DHX36/ G4R1 Knockout Is Associated with G-Quadruplex Content and Cancer

Abstract

G-quadruplexes (G4s) are secondary DNA and RNA structures stabilized by positive cations in a central channel formed by stacked tetrads of Hoogsteen base-paired guanines. G4s form from G-rich sequences across the genome, whose biased distribution in regulatory regions points towards a gene-regulatory role. G4s can themselves be regulated by helicases, such as DHX36 (aliases: G4R1 and RHAU), which possess the necessary activity to resolve these stable structures. G4s have been shown to both positively and negatively regulate gene expression when stabilized by ligands, or through the loss of helicase activity. Using DHX36 knockout Jurkat cell lines, we identified widespread, although often subtle, effects on gene expression that are associated with the presence or number of observed G-quadruplexes in promoters or gene regions. Genes that significantly change their expression, particularly those that show a significant increase in RNA abundance under DHX36 knockout, are associated with a range of cellular functions and processes, including numerous transcription factors and oncogenes, and are linked to several cancers. Our work highlights the direct and indirect role of DHX36 in the transcriptome of T-lymphocyte leukemia cells and the potential for DHX36 dysregulation in cancer.

Keywords: DHX36; G-quadruplex; G4R1; Jurkat cells; RHAU; helicase; leukemia.

Figure 1

Distributions of effect sizes for genomic features that are upregulated (A) or downregulated (B) in DHX36 knockout cell lines relative to control.

Figure 2

Top 10 most significantly enriched (by adjusted p-value) GO terms among three categories for genes upregulated in DHX36 knockout cell lines. BP = biological process; MF = molecular function; CC = cellular component.

Figure 3

Significantly enriched KEGG categories for genes upregulated in knockout versus control cells. Gene Ratio = fraction of differentially expressed genes matching KEGG description. padj = Benjamini–Hochberg-adjusted p-value.

Figure 4

Significantly enriched disease ontology (DO) categories for genes upregulated in knockout versus control cells. Gene Ratio = fraction of differentially expressed genes matching disease ontology description. padj = Benjamini–Hochberg-adjusted p-value.

Figure 5

Differentially expressed promoters and genes following DHX36 KO are more likely to contain OQs compared to the genomic background. (A) Percentage of gene promoters with OQ. (B) Percentage of gene regions with OQs.

Figure 6

Differentially expressed promoters and genes following DHX36 KO have significantly more OQs per region than non-differentially expressed genes. (A) Mean number of G4s per promoter for differentially and non-differentially expressed genes. (B) Mean number of G4s per gene, for differentially and non-differentially expressed genes.