FIGURE 6.

Particular multi-motif combinations enhance PTB binding. PTB contains four RRMs that have been shown to interact with RNA semi-independently. (A) Motif finding was repeated allowing up to four binding models. The resulting motifs (A–D) were used to annotate the pool. The average number of annotated sites was used to calculate the over- or under-representation of motifs in the top and bottom 1% of oligonucleotides ranked by enrichment (histogram bars over each motif). (B) Co-occurrences of motifs were analyzed in the top 1% of oligonucleotides ranked by enrichment. The number of pairs that occur in the specified order were counted in the top 1% of the data. The value in parentheses represents the number of co-occurrences expected in the top 1% under a null model of no motif enrichment. (C) Oligonucleotides containing motif combinations were selected from the top one percentile for validation. UV-cross-linking was performed as before using radiolabeled S¹¹ as a probe in the presence of increasing amounts (0-, 5-, or 50-fold molar excess) of unlabeled competitors as indicated.