Figure 6: Extensive neural reprogramming of the transcriptome in TTP-KO embryonic fibroblasts.

(a) Distributions of cerebral cortex ranks for all genes expressed in stimulated WT or/and TTP-KO MEFs (left) and for gene groups consistently up- (middle) and downregulated (right) in TTP-KO MEF samples. Note a significant right skew towards high cerebral cortical ranks in the upregulated (P=4.23 × 10⁻⁹; one-sided KS test) but not in the downregulated genes (P=0.976; one-sided KS test). (b) Distributions of 81 distinct tissue/cell type-specific ranks were plotted for genes upregulated in TTP-KO MEFs and significance of a right skew was estimated using the one-sided KS test introduced in a. The graph shows corresponding (−log₁₀)-transformed P values for each tissue/cell type. Note that the lowest P values are observed for neural tissues and non-neural parts of the eye. Overall, Wilcoxon rank-sum test (see inset) shows that neural P values are significantly smaller than non-neural ones. Red, neural tissues; blue, non-neural tissues/cells. (c) RT–qPCR analysis showing significantly elevated relative expression of TTP targets in untreated TTP KO MEFs compared with similarly prepared WT control. (d) RT–qPCR suggesting that the loss of TTP in the KO MEFs leads to accumulation of the long, ARE-containing form of the HuR mRNA. Data in c,d are averaged from three experiments±s.d. and compared by t-test. WT expression levels are set to 1 (see Fig. 1c for further details). (e) Immunoblot analysis showing drastic upregulation of TubβIII and HuB proteins in TTP KO MEFs.