Figure 3.

TRα knockout drastically reduces T3 regulation of TR-bound genes. Heatmap showing the fold changes by T3 treatment in the expression of TR-bound genes detected by ChIP-seq in only the wild-type hind limb (left), both wild type and TRα (-/-) hind limb (middle), or only TRα (-/-) hind limb (right). RNA samples were isolated from wild type and TRα (-/-) hind limb with and without 18 h T3 treatment and subjected to RNA-seq analyses. Note that a much higher fraction of the genes in each of the three classes of TR-bound genes were upregulated (red) or downregulated (blue) by T3 in the wild-type animal hind limb. In addition, TRα knockout reduced the magnitudes of T3-regulation, i.e., leading to lighter red or blue, for individual genes in the knockout hind limb, suggesting that TRα (-/-) is important for gene regulation by T3. Note that the blank regions between the red and blue areas were genes whose expression has no or little change after T3 treatment of wild type or TRα knockout animals. The color range shows fold changes, with the darkest red or blue colors showing 4-fold changes or more for the individual genes.