Nucleotide composition and RNA crosslinking likelihood centered on AGO1-4, QKI, PUM2, and IGF2BP1 interaction sites. The interaction site analysis is from all of the datasets: Quaking (QKI), Pumilio2 (PUM2), Insulin-like growth factor 2 binding protein 1 (IGF2BP1), and Argonaute 1 to 4 (AGO1 to -4). Heatmap: nucleotide composition, relative to a uniform background, of each individual binding site found in the respective genic regions. Barplot: likelihood of a T = > C conversion given that there is a 'T' at the given position. Unlike the heatmap, the barplot is not normalized by the number of reads mapping to an individual binding site. The red dotted line indicates the background conversion probability for all 'T's within the respective genic regions for each respective dataset. (a) Non-redundant seed-matches in 3' UTRs for the top 20 expressed miRNAs in the Argonaute dataset. 8 mer-m1 is a seed-match between the mRNA and nucleotides 1 to 8 of the miRNA seed sequence, 8 mer-A1 matches nucleotides 2 to 8 of the seed sequence paired with an A at position 1. 7 mer-1 m and 7 mer-A1 are similarly defined for nucleotides 1 to 7; 7 mer-m8 is a match utilizing nucleotides 2 to 8 of the seed sequence. 6 mer2-7 is a match utilizing nucleotides 2 to 7 of the seed sequence, and 6 mer3-8 utilizes nucleotides 3 to 8 of the sequence. (b) Motif matches for the two Quaking motifs in 3' UTRs, 5' UTRs, coding regions and introns. (c) Motif matches for the Pumilio 2 dataset in 3' UTRs, 5' UTRs, coding regions and introns. (d) Motif matches for the IGF2BP1 dataset in 3' UTRs, 5' UTRs, coding regions and introns.
Corcoran et al. Genome Biology 2011 12:R79 doi:10.1186/gb-2011-12-8-r79