A simple signal element mediates transcription termination and mRNA 3′ end formation in the DEG1 gene of Saccharomyces cerevisiae

Abstract

DEG1 is a weakly transcribed gene of Saccharomyces cerevisiae, closely associated with CEN6. We mapped its major poly(A) site only 24 nucleotides (nt) downstream of the stop codon, and only 26 nt upstream of the CDEI centromere element. The deletion of this 50 nt stretch completely abolishes formation of the mRNA 3′ end. A shorter deletion of a 16 nt sequence in the 3′-untranslated region has the same effect on transcription termination and 3′-maturation function. A TATATA sequence within this 16 nt region is essential for both functions, while a TGTATA sequence has a weak compensating activity in 3′ end maturation if the TATATA stretch is deleted. We assume that the 3′ end formation signals of the DEG1 gene have this simple structure: a single essential element (TATATA, whether alone or with the few surrounding nucleotides), probably, but not necessarily, cooperating with the sequence at the poly(A) site. This simple structure differs from the emerging model for 3′ end-processing signals in that (i) it is shorter: 24 nt long at the most, while the model suggests 39 nt; (ii) there is no element located downstream of the TATATA signal to position the poly(A) site; and (iii) unlike the other naturally occurring signals studied, no cooperation among multiple TATATA-like elements is observed. We found that the same TATATA sequence also directs transcription termination, irrespective of promoter strength, and presumably without the cooperation of a downstream polymerase II pausing site. Taken together, these findings support the hypothesis that the DEG1 3′ end-forming signals are more condensed than in other yeast genes, probably because of their proximity to CEN6.