IDENTIFICATION AND CHARACTERIZATION OF A SEQUENCE MOTIF INVOLVED IN NONSENSE-MEDIATED MESSENGER-RNA DECAY

In both prokaryotes and eukaryotes, nonsense mutations in a gene can e nhance the decay rate or reduce the abundance of the mRNA transcribed from that gene, and we call this process nonsense-mediated mRNA decay. We have been investigating the cis-acting sequences involved in this decay pathway. Previous experiments have demonstrated that, in additio n to a nonsense codon, specific sequences 3' of a nonsense mutation, w hich have been defined as downstream elements, are required for mRNA d estabilization. The results presented here identify a sequence motif ( TGYYGATGYYYYY, where Y stands for either T or C) that can predict regi ons in genes that, when positioned 3' of a nonsense codon, promote rap id decay of its mRNA. Sequences harboring two copies of the motif from five regions in the PGK1, ADE3, and HIS4 genes were able to function as downstream elements. In addition, four copies of this motif can fun ction as an independent downstream element. The sequences flanking the motif played a more significant role in modulating its activity when fewer copies of the sequence motif were present. Our results indicate the sequences 5' of the motif can modulate its activity by maintaining a certain distance between the sequence motif and the termination cod on. We also suggest that the sequences 3' of the motif modulate the ac tivity of the downstream element by forming RNA secondary structures. Consistent with this view, a stem-loop structure positioned 3' of the sequence motif can enhance the activity of the downstream element. Thi s sequence motif is one of the few elements that have been identified that can predict regions in genes that can be involved in mRNA turnove r. The role of these sequences in mRNA decay is discussed.