Conserved sequence motifs upstream of TSSs. (A) List of known motifs identified for outron- and exon-TSSs, and a list of novel motifs. (B) Frequency distribution of motif occurrences and their conservation around representative TSSs. (The upper histogram) The frequency distribution of motifs around outron-TSSs with downstream SL1 sites; (the lower histogram) the motif distribution around exon-TSSs without SL1 sites. The conservation rate of a motif occurrence is the average conservation rate of all positions in a given instance, where the conservation rate in the worm genome was calculated using six allied species (see Methods). Conservation rates ranging from 0 to 1 were divided into five levels. Darker colors indicate higher conservation rate; for example, the darkest color denotes a range from 0.8 to 1. In the figure, an SP1 motif (Xi et al. 2007) was observed around outron-TSSs and exon-TSSs. The SP1 motif was significantly conserved around a strong peak ∼50 bp upstream of the TSS, and P-values were calculated for representative TSSs from the Wilcoxon rank-sum test (Methods). (C) The SP1 motif is orientation independent in the sense that its reverse complement was observed and conserved around outron/exon-TSSs. Motifs were examined upstream of TSSs collected from two samples, embryos and adults. The distributions from the two samples tend to be similar; thus, the graphs for embryos are displayed exclusively hereafter unless significant differences were observed between the distributions of the two samples. (D) Distribution of TATAA-box occurrences around representative TSSs. TATAA-box occurrences were enriched significantly upstream of both types of TSSs according to the rank-sum test (Methods). (E) Distribution of TATAA-box around Gaussian TSSs. (F) A TATAA-box occurs upstream of the representative outron-TSS for NM_058327 (taf-4) that is encoded in the plus strand. The outron is displayed as a yellow box. The information is available at http://wormtss.utgenome.org/ by making a query of taf-4.
