The 3’ UTRs of eukaryotic genes
participate in a variety of post-transcriptional (and some transcriptional)
regulatory interactions. Some of these interactions are well characterised, but
an undetermined number remain to be discovered. While some regulatory sequences
in 3' UTRs may be conserved over long evolutionary time scales, others may have
only ephemeral functional significance as regulatory profiles respond to
changing selective pressures. Here we propose a sensitive segmentation
methodology for investigating patterns of composition and conservation 3’ UTRs
based on comparison of closely related species. We describe encodings of
pairwise and three-way alignments integrating information about conservation, GC
content and transition/transversion ratios and apply the method to three
closely related Drosophila species: D. melanogaster, D. simulans and D. yakuba.
Incorporating multiple data types greatly increased the number of segment
classes identified compared to similar methods based on conservation or GC
content alone. We propose that the number of segments and number of types of
segment identified by the method can be used as proxies for functional
complexity. Our main finding is that the number of segments and segment classes
identified in 3’ UTRs is greater than in the same length of protein-coding
sequence, suggesting greater functional complexity in 3’ UTRs. There is thus a
need for sustained and extensive efforts by bioinformaticians to delineate
functional elements in this important genomic fraction.