Analysis of conserved translational regulatory elements in 3’-UTR from multiple alignments of Drosophila families

A hypothesis that many potential Translational Control Elements (TCEs) may have stable secondary structures which are conserved across closely related genomes has been investigated. The 3’-UTR sequences and PAC (Poly-Adenylation Cleavage) sites information of Human and Mouse orthologous genes have been analyzed. It has been found that orthologous genes usually have very similar 3’-UTR sequences. In order to test the hypothesis of conserved secondary structure, multiple sequence alignments of 3’-UTR sequences of genes that had been confirmed to be highly expressed in Drosophila melanogaster testis, in which post-transcriptional regulation are dominant, have been compiled and tested. Unlike initial expectation, however, only 11.7% of such 3’-UTRs from testis specific gene sets had stable RNA secondary structures, while 15.7% of all the other non-testis 3’-UTRs had such structures. Possible reasons for this phenomenon have been explored with respect to the accuracy of obtained putative 3’UTR sequences from other genomes than Drosophila melanogaster.