Obstacles incurred by RNA polymerase II during primary transcript synthesis have 
been identified in vivo and in vitro. Transcription past these impediments 
requires SII, an RNA polymerase II-binding protein. SII also activates a 
nuclease in arrested elongation complexes and this nascent RNA shortening 
precedes transcriptional readthrough. Here we show that in the presence of SII 
and nucleotides, transcript cleavage is detected during SII-dependent elongation 
but not during SII-independent transcription. Thus, under typical transcription 
conditions, SII is necessary but insufficient to activate RNA cleavage. RNA 
cleavage could serve to move RNA polymerase II away from the transcriptional 
impediment and/or permit RNA polymerase II multiple attempts at RNA elongation. 
By mapping the positions of the 3'-ends of RNAs and the elongation complex on 
DNA, we demonstrate that upstream movement of RNA polymerase II is not required 
for limited RNA shortening (seven to nine nucleotides) and reactivation of an 
arrested complex. Arrested complexes become elongation competent after removal 
of no more than nine nucleotides from the nascent RNA's 3'-end. Further cleavage 
of nascent RNA, however, does result in "backward" translocation of the enzyme. 
We also show that one round of RNA cleavage is insufficient for full readthrough 
at an arrest site, consistent with a previously suggested mechanism of SII 
action.