Fig. 3: GMRN provides insights into the regulation of metabolites by transcription factors. | Nature Communications

Fig. 3: GMRN provides insights into the regulation of metabolites by transcription factors.

From: Multi-omics analyses reveal regulatory networks underpinning metabolite biosynthesis in Nicotiana tabacum

Fig. 3

a Genome-wide landscape of GMRN across 9 co-response clusters and 1 GINI-specific cluster (C0) (left panel) and mapping relationship of regulatory pairs between different clusters in GMRN (right panel). b, c Number of overlapping hub genes (b) and metabolites (c) between the GMRNs from different data sources. The orange bars represent the shared hub genes and metabolites across the four GMRNs. d, e GO (d) and KEGG (e) enrichment of hub genes in GMRNs. The P values were calculated using hypergeometric distribution (two-sided) and then adjusted using the FDR. BP, biological process; CC, cellular component; MF, molecular function. f The top 15 TF families with the highest total number of key regulators predicted by GMRN. g A sub-network centered on ERF genes. SG, structural genes. TF, transcription factors. ME, metabolites. h GMRN recovers targets of ERF1 and DREB3 associated with different metabolites. Green arrows represent the regulatory pairs used for validation. Dashed lines represent GINI coefficient relationships, while solid lines denote PCC (Pearson correlation coefficient) relationships. i Validation of the regulation to the targets of ERF1 and DREB3 (n = 5 biological replicates). ERF1 and DREB3 enhanced the transcription of BCCP1, POD1, HSFA2 and MST6 in a dual-luciferase reporter assay, respectively. The bottom panel show schematic diagrams of the effector and reporter plasmids. EV, empty vector. j A Sub-GMRN centered on WRKY genes. k GMRN recovers targets of WRKY11, WRKY22 and WRKY42 associated with different metabolites. Green arrows represent the regulatory pairs used for validation. l Validation of the regulation to the targets of WRKY11 and WRKY42 (n = 5 biological replicates). WRKY11 and WRKY42 enhanced the transcription of FLS, GATL9, Glu1 and LCYB in a dual-luciferase reporter assay, respectively. The bottom panels show schematic diagrams of the effector and reporter plasmids. In (i) and (l), error bars represent the means ± standard errors of five biological replicate. ***P < 0.001. A two-tailed Student’s t test was used to determine P values. Source data are provided as a Source Data file.

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