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Fig. 4 | Genome Biology

Fig. 4

From: The Tug1 lncRNA locus is essential for male fertility

Fig. 4

Tug1 lncRNA regulates gene expression in trans. a Adult tissue types and mouse embryonic fibroblasts (MEFs) used for RNA sequencing of wild-type (WT) and Tug1−/− (KO) mice. For each tissue, the number of biological replicates per genotype and the number of upregulated and downregulated genes (FDR < 0.05) are shown from KO to WT comparisons. b The number of perturbed genes (y-axis) in KO animals according to the number of tissues in which the gene was found to be dysregulated (x-axis). c Gene set enrichment analysis (GSEA) of differentially expressed genes found in wild-type versus Tug1−/− murine tissues and MEFs. Red shading indicates tissue in which gene set is perturbed; gray shading indicates tissue in which gene set is not different between WT and KO. d Schematic showing the experimental design to identify genes reciprocally regulated by Tug1 RNA. (I) Testing the impact of the Tug1 transgene expression on gene expression in vivo. (II) Schematic of the Tug1 transgene (tg(Tug1)) and systemic induction by mating to CAG-rtTA3 mice in the presence of doxycycline (dox). (III) Schematic of matings to generate Tug1rescue mice (Tug1−/−; tg(Tug1); rtTA), enabling dox-inducible Tug1 expression in a Tug1-knockout background. (IV) Collection of testes from WT (Tug1+/+) (n = 4), KO (Tug1−/−) (n = 4), and Tug1rescue (n = 3) mice for RNA sequencing. e Tug1 gene expression level (log2TPM+1) in the testes of wild-type (gray), KO (red), and doxycycline-induced Tug1rescue (blue) mice. Error bars represent the standard error of the mean. f Expression levels (log2TPM+1) for Tug1 neighboring genes in WT (gray), KO (red), and Tug1rescue (blue) mice. g Heatmap of fold changes of gene expression (TPM) for the reciprocally regulated genes in the comparisons of KO/WT and rescue/KO. h Examples of differentially expressed genes in the testes showing significant reciprocal regulation in WT (gray), KO (red), and Tug1rescue (blue) mice

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