Species-specific ER81 binding to the Th proximal promoter. A, location of consensus ER81 binding sites in the 9kb upstream regions of the rat and mouse Th genes. ER81 binding sites are indicated by “E” and conserved binding sites are indicated by shading between the two upstream regions. B, phylogenetic sequence comparison of equivalent Th proximal promoter regions from rats, mice, humans, cows and dogs. The ER81 consensus sequence (Brown and McKnight, 1992) is shaded in green, and the DA-motif position weight matrix (Flames and Hobert, 2009)is shaded in red. The core ETS DNA binding domain recognition sequence is boxed. Nucleotides that conform to both the DA-motif and ER81 consensus sequences are shaded yellow, whereas sequences that only conform to either the DA-motif or ER81 consensus sequence are shaded in red and green, respectively. Degenerate DNA code: R=A/G, S=C/G, M=A/C, W=A/T, Y=C/T. C, chromatin immunoprecipitation (ChIP) experiments with mouse OB tissue indicated that ER81 bound the mouse Th and Mmp-13 proximal promoters in vivo. By contrast, ChIP experiments with dog OB tissue indicated that ER81 bound only the Mmp-13, but not the Th, proximal promoters in vivo. The previously identified and conserved ER81 binding site in the Mmp-13 (Mmp-1/collagenase) proximal promoter was used as a positive control. D, electromobility shift assays (EMSA) revealed that bacterially expressed murine ER81 bound to the DA-motif/ER81 consensus binding site in the rodent proximal Th promoter, but not the equivalent site in the human Th proximal promoter. The human and mouse ER81 protein amino acid sequences are approximately 99% identical and the DNA binding domains of these proteins are 100% identical. Thus, the human and mouse ER81 proteins almost certainly have the same affinity for the binding sites in either the human or rodent Th promoters.