Conserved auxiliary elements are poorly enriched around G. lamblia cleavage sites. (A) Conserved pre-mRNA processing proteins and the sequences they recognize. The left panel shows the location and motifs of key sequences found around human cleavage sites. Right panel shows the human orthologs of core processing complexes for the recognition of poly(A) signals and surrounding sequences. Dots indicate whether an ortholog was readily identifiable in G. lamblia (black circle), whether ortholog identification was ambiguous (gray circle), or whether no orthologs were found (white circle). (B) The conserved UGUA motif is not enriched upstream of G. lamblia cleavage sites. Sequences 20 to 50 nt upstream of cleavage sites were used to count the frequency of UGUA or shuffled versions of the motif. Plotted is the number of times each motif was found in human (left) and G. lamblia (right) sequences. (C) GU-rich elements are not enriched downstream from G. lamblia cleavage sites. Sequences 40 nt up- and downstream from human and G. lamblia cleavage sites were used to count the occurrence of U- and GU-rich motifs enriched downstream from strong human cleavage sites (Hu et al. 2005). Plotted is the frequency of each motif upstream (gray) or downstream (green) of human (left) and G. lamblia (right) cleavage sites. (D) MA plot of enriched and depleted 6-mer sequences around polyadenylation signals. All single cleavage site genes from our data set that contain an AGUAAA were selected for this analysis. Sequences 50 nt upstream and downstream from the signal were used to search for all possible 6-nt motifs. Plotted is the average count of each motif versus its enrichment in downstream sequences. Red dots are motifs that showed at least a fourfold enrichment or depletion in downstream regions and with an average count of at least 15 occurrences.
