NF-Y activates genes of metabolic pathways altered in cancer cells

Abstract

The trimeric transcription factor NF-Y binds to the CCAAT box, an element enriched in promoters of genes overexpressed in tumors. Previous studies on the NF-Y regulome identified the general term metabolism as significantly enriched. We dissect here in detail the targeting of metabolic genes by integrating analysis of NF-Y genomic binding and profilings after inactivation of NF-Y subunits in different cell types. NF-Y controls de novo biosynthetic pathways of lipids, teaming up with the master SREBPs regulators. It activates glycolytic genes, but, surprisingly, is neutral or represses mitochondrial respiratory genes. NF-Y targets the SOCG (Serine, One Carbon, Glycine) and Glutamine pathways, as well as genes involved in the biosynthesis of polyamines and purines. Specific cancer-driving nodes are generally under NF-Y control. Altogether, these data delineate a coherent strategy to promote expression of metabolic genes fuelling anaerobic energy production and other anabolic pathways commonly altered in cancer cells.

Keywords: NF-Y; SOCG pathway; cancer metabolism; glycolysis; transcription.

Figure 1. NF-Y targets in metabolic pathways

Global map of metabolic pathways targeted by NF-YA. A. Metabolic genes upregulated (in green) and downregulated (in red) after silencing of NF-YA in HeLa cells [11]. B. Metabolic genes with core promoters bound by NF-YA are indicated in blue according to ENCODE ChIP-Seq data. The maps are constructed with the KEGG Mapper v 2.5 tool.

Figure 2. NF-Y activates genes of lipid metabolism

A. Genes involved in cholesterol and fatty acids metabolisms are shown. The heatmap represents the log2 fold change of relative expression derived from profiling analysis (See colour scale) in the indicated cell lines after inactivation of NF-Y subunits: H322 (This manuscript, Fig. S2), HCT116 (This manuscript, Fig. S2), HeLaS3 [11] and mESC [12]. The presence of NF-Y binding in ENCODE datasets is indicated with P (core promoter binding), E (external enhancer), Ei (enhancer in gene body) or R (repetitive sequence within 5 kb from the TSS). In vivo binding of SREB-1/2 according to ChIP-Seq experiments is indicated by a grey background. B. Analyses of over-represented motifs in SREBPs peaks in HepG2 ChIP-Seq data analyzed by ENCODE. The matrices were derived with Pscan-ChIP (Left panel) and MEME (Right panel), and the relative p-values are shown.

Figure 3. NF-Y and expression of respiratory genes

A. Genes of oxidative phosphorylation chain complexes are shown with the relative expression levels after inactivation of NF-Y in different cell lines, and the relative presence of NF-Y binding in P (promoter), E (external enhancer), Ei (enhancer in gene body) or R (repetitive sequence within 5 kb from TSS). B. qRT-PCR evaluation of expression levels of respiratory genes after inactivation of NF-YB in Hela cells. The average −/+ SD of three biological replicates is represented. (*p<0.05).

Figure 4. Glycolytic enzymes are regulated by NF-Y

A. Genes encoding for glycolytic enzymes are shown with their expression levels after inactivation of NF-Y in different cell lines, and the presence of NF-Y binding is indicated as in Fig. 3. B. qRT-PCR evaluation of expression levels of selected genes after inactivation of NF-YB in Hela cells. The average −/+ SD of three biological replicates is represented. (*p<0.05). C. Western blot analysis of protein levels of NF-Y targets in Hela cells inactivated of NF-YA (Left panel), or NF-YB (Right panel).

Figure 5. Activation of SOCG genes by NF-Y

A. Genes of the SOCG (Serine, One Carbon, Glycine) pathway are shown with the expression levels after inactivation of NF-Y, and the presence of NF-Y binding as in Fig. 3. B. qRT-PCR evaluation of expression levels of PHGDH, PSAT1, PSPH, SHMT1 after inactivation of NF-YB in Hela cells. The average −/+ SD of three biological replicates is represented (*p<0.05).

Figure 6. Activation of genes of the polyamine metabolism by NF-Y

Genes of the polyamine pathway are shown with the expression levels after inactivation of NF-Y, and the presence of in vivo NF-Y binding as in Figs. 3-5.

Figure 7. Schematic representation of metabolic pathways regulated by NF-Y