90 Chapter 4 AP1 ETS SP1 TSS Exon1 Mo�f ID Mo�f Name Consensus Mo�f Enrichment Ra�o p-value q-value MA0099.2 AP1 TGACTCA 13 0 0.01 MA0079.5 SP1 GGGGCGGGG 1.08 0.76 0.76 a b c d ETS VGGAAS 6.5 0.2 0.3 MA0080.1 Figure 2. AP1 binding site in the TSPO promoter and LPS inducible TSPO expression is unique to the Muroidea superfamily of rodents. a Multiple sequence alignment of TSPO promoter region of 15 species from primate, rodent, non-primate mammals. AP1 (cyan) and an adjacent ETS (brown) site is present in only a sub-group of rodent family which includes mouse, rat and Chinese hamster. The ETS site which binds transcription factor PU.1 is present across species. SP1 (blue) site is found in the core promoter close to the TSS (green). For species where the TSS is not known Exon1 (pink) location is shown. Blue arrowhead indicates sequence without any motif hidden for visualization. b Phylogenetic tree is showing a clear branching of rat, mouse and Chinese hamster TSPO promoter from the rest of the species from rodents. Primates including marmoset forms a separate clade while sheep, cow and pig are part for the same branch. Green highlights represent species that contain the AP1 site in TSPO promoter. Phylogenetic tree was generated using the Maximum Parsimony method in MEGA11. The most parsimonious tree with length = 4279 is shown. The consistency index (CI) is 0.760458 (0.697014) and the retention index is 0.656386 (RI) (0.656386) for all sites and parsimony-informative sites (in parentheses). The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches. c Differential motif enrichment analysis between rodent vs non-rodent TSPO promoter region by SEA tools from MEME-suite confirms the significant enrichment of AP1 site in rodent promoter whereas SP1 site does not show any differential enrichment. TSS; Transcription start site. d TSPO gene expression in macrophages or microglia isolated frommultiple species after LPS stimulation. In line with the multiple sequence alignment of the TSPO promoter, species (mouse, rat) that contains an adjacent AP1 and ETS motif shows an upregulation of TSPO gene after LPS stimulation. Species lacking (human, pig, sheep, rabbit) those sites show a downregulation or no change in expression after stimulation. rat, mouse and chinese hamster from the other rodents and non-rodent mammals (Fig. 2b). Differential motif enrichment analysis of the TSPO promotor region between Muroidea vs non-Muroidea species confirmed a significant enrichment of the AP1 binding site in the
RkJQdWJsaXNoZXIy MTk4NDMw