Human core promoter motifs discovered by XXmotif. (A) List of motifs up to an E-value of 0.1 in a set of 1871 human core promoter regions (−300 bp to +100 bp around TSS) from the eukaryotic promoter database (EPD) (Schmid et al. 2006). For 20 of the 39 predicted motifs, similar literature motifs were assigned by TOMTOM (Gupta et al. 2007) or us (last two columns). The motif at position 18, which was originally named Initiator (Xi et al. 2007), is actually the reverse complement of YY1. Eight novel, highly significant motifs, designated XX1 to XX6, XX1(rev), and XX3(rev), show positional distribution peaks near the TSS. XX6 is the canonical Initiator motif similar to elements found in D. melanogaster and S. cerevisiae. Ten motifs with a broad positional distribution are not shown. The positional distributions of the PWMs were obtained by scanning the PWMs over a larger region (−1000 bp to +500 bp) around the TSS. (B) Top eight motifs obtained with the core promoter sequences of the 65 genes annotated as coding for ribosomal proteins in EPD (Xi et al. 2007; FitzGerald et al. 2006; Parry et al. 2010).
