Structural and compositional features of untranslated regions of eukaryotic mRNAs

The important role of 5′ and 3′ untranslated regions of eukaryotic mRNAs in gene regulation and expression is now widely accepted. In order to study the general structural and compositional features of these sequences we developed UTRdb, a specialized database of 5′ and 3′- UTR sequences from seven different taxonomic groups of eukaryotic mRNAs cleaned of redundancy. The analysis of the UTR sequences contained in this database showed that 5′- UTR sequences, on average 200 nucleotides long, are 1.5-3 times shorter than the corresponding 3′- UTR sequences in the various taxonomic groups considered here. As to their compositional properties on average 5′- UTR sequences resulted in all cases GC richer than 3′- UTR sequences, and significant correlations were found between the GC content of 5′ and 3′- UTR sequences and the GC content of the third silent codon positions of the corresponding protein coding genes. The dinucleotide analysis showed a differential depletion of CpG in vertebrate 5′ and 3′- UTR, with 5′- UTR sequences being more CpG-rich, and a generalized depletion of TpA in both 5′ and 3′- UTR was observed in all eukaryotic sequence collections.