To terminate transcripts with no poly(A) addition, we replaced the adh1 terminator in Construct 1 with the terminator of the snu2 gene, which encodes a small nuclear RNA (Brennwald et al, 1988; Zhou et al, 1999).
Thus, these three convergent gene pairs of R. prowazekii do not terminate transcripts at specific sites within the intervening region, as might be expected based on gene orientation.
The asterisk indicates a shorter terminated transcript that is the result of transcription initiating under the control of the transcribed-region −10 element when the σ-containing holoenzyme is present in the reaction.
Similar to snoRNA mediated termination, Rnt1 can provide 3′ end mediated termination, but in many more cases, NRD termination will step in, ensuring the immediate degradation of the improperly terminated transcript [182,207,210].
Therefore, dependent on the region in the gene where the probes are binding to measure expression of a reference gene, profound differences among conditions can be the result of alternatively spliced or terminated transcript variants.
As suggested by this study, a G1 checkpoint arrest signal might be maintained until subsequent transport of the prematurely terminated transcript for degradation at P-bodies and disassembly of the RNAPII-BRCA1-DSIF complex by ubiquitin-mediated degradation at the proteasome (Fig. 6E).
Thus, we conclude that a major fraction of the ∼35-nt RNA species, but not the full-length terminated transcript, is RNAP-associated.
We quantified the extent of pausing by dividing the signal associated with a pause RNA by the sum of this signal and the signal associated with the full-length terminated transcript (hereafter termed relative abundance).
The results indicate that a major fraction of the ∼35-nt RNA species, but not the full-length terminated transcript, was immunoprecipitated with an antibody against FLAG whether the cells lacked or contained plasmid encoded overproduced σ.
In addition, the full-length terminated transcript was at least as stable in stationary phase as in exponential phase, excluding the possibility that the increase in the relative abundance of the pause RNA might simply reflect a destabilization of the full-length transcript in stationary phase.
RNAs associated with paused transcription elongation complexes (TECs) (pause) and terminated transcripts (full length) are labeled.
