A comparative analysis is presented, based on sequences from the Eukaryotic promoter database EPD and covering four metazoan phyla: Cnidarians, Nematodes, Arthropods and Chordates. Eukaryotic promoters contain sequence motifs that are over-represented at specific distances from the transcription start site (TSS). Two types are distinguished: (i) core promoter elements (CPEs) occurring at fixed locations, and upstream elements (UPEs), spread over a larger upstream region. CPEs interact with basal transcription factors (TFs), while UPEs interact with regulatory TFs found at enhancers as well. This study focuses on UPEs. The CCAAT- and GC-boxes were the first UPEs identified in humans and were later found to be recognized by NFY and SP1 proteins. Additional vertebrate UPEs include ETS, NRF-1, and bZIP binding motifs. When Drosophila promoters were systematically analyzed, it came as a surprise that none of the vertebrate UPEs were found. Instead, two new motifs popped up, later assigned to proteins M1BP and BEAF-32. This suggested that UPEs, unlike CPEs, are not conserved across distant metazoan phyla. The results presented here suggest otherwise. Surprisingly, honeybee shows strong over-representation of vertebrate UPEs, including NFY and NFR-1, but none or only marginal over-representation of Drosophila motifs. Perhaps even more surprisingly, the starlet sea anemone, the most primordial species analyzed, featured all vertebrate UPEs except SP1. These findings point to the existence of an ancestral metazoan UPE inventory, which has been conserved in many branches of the animal tree but lost and replaced in others, including flies and nematodes.

Co-authors: None