DNA sequence perplexity analysis of TATA and no-motif promoters reveal conserved informational architectures in eukaryotic genomes

Promoters are the genetic elements that govern the transcription of all coding and non-coding genes. The TATA box is the most conserved promoter element across genomes, encompassing from single-celled yeasts to complex mammals. Previous studies revealed that TATA box-containing promoter regions vary in their GC composition, CpG island content, and DNA structural features in various lineages. In our recent study, we showed that sequence perplexity is a unique and novel feature of functional regions of genomes that is conserved across cellular life. In this study, we examined the promoter architecture of TATA-containing and no-motif (NM) promoter no promoter elements genes using sequence perplexity to evaluate the similarities and differences in 15 genomes. Further, we attempted to compare the perplexity distribution with free energy to reveal their conserveness. The results indicated that the core promoter regions in both TATA and motif-less classes indicate lower perplexity compared to the upstream and downstream regions. Irrespective of TATA box presence, genome GC content, or phylogenetic group the perplexity is less invariant. We further confirmed the trends with statistical analysis and difference sequence logo analysis. These findings establish perplexity as a robust, motif-independent marker of promoter identity conserved across eukaryotic life and position free energy and perplexity as complementary rather than redundant descriptors of promoter organization.