Fig. 3

The Tug1 locus harbors a cis-repressive DNA regulatory element. a Differential expression of genes in the local region (± 1 Mb) of Tug1 for each indicated mouse tissue, depicted as fold change (FC) between Tug1^−/− (KO) and wild-type (WT). Significantly differentially expressed genes are marked and labeled in red. b Plot of the number of tissues where genes downstream of Tug1 TSS are found significantly dysregulated. c Strategy for allele-specific RNA sequencing (RNA-seq). Tug1^+/− C57BL/6J females were crossed with wild-type Cast/EiJ males, and the testes from the F1 hybrid progeny were harvested for RNA-seq. Single nucleotide polymorphisms (SNPs) allowed for the differentiation between the C57BL/6J and the Cast/EiJ allele. d Allele-specific expression of local genes surrounding Tug1 in the testes from F1 hybrid C57BL/6J::Cast/EiJ wild-type (Tug1^{BL6-WT/Cast-WT}) and heterozygous Tug1-knockout (Tug1^{BL6-KO/Cast-WT}) mice containing a deletion on the C57BL/6J allele. Upper panel: expression levels of neighboring genes from the C57BL/6J allele. Lower panel: expression levels of neighboring genes from the Cast/EiJ allele. Boxes are centered at the mean, extend one standard deviation, and the bottom and top notches are the minimum and maximum samples, respectively. The genomic locus encompassing the local genes around Tug1 is depicted. Asterisks indicate significant Bayesian posterior probability (PP > 0.95) differential expression between hybrid wild-type and Tug1^BL6-KO testes. Horizontal dotted line indicates expression levels below 0.1 TPM