Nucleotide composition of preferred A3 protein binding sites.

(A) The 100 PARalyzer-generated clusters in mRNAs with the greatest number of total associated reads in A3 CLIP experiments were inspected and the fraction the sequence composed of each of the four nucleotides was plotted (top). PARalyzer-generated clusters were filtered according to size (<50 nucleotides) and the clusters with the greatest number of total associated reads in A3 CLIP experiments were inspected and the fraction the sequence composed of each of the four nucleotides was plotted (bottom). (B) Deoxyribonucleotide sequence motifs identified by cERMIT in CLIP-seq cDNA libraries as most frequently present in A3-bound RNA in uninfected cells, infected cells and in immature and mature purified virions. Cumulative percentages of clusters containing the motifs are indicated.