RNA polymerase II (Pol II) transcription termination by the Nrd1p-Nab3p-Sen1p 
(NNS) pathway is critical for the production of stable noncoding RNAs and the 
control of pervasive transcription in Saccharomyces cerevisiae To uncover 
determinants of NNS termination, we mapped the 3'-ends of NNS-terminated 
transcripts genome-wide. We found that nucleosomes and specific DNA-binding 
proteins, including the general regulatory factors (GRFs) Reb1p, Rap1p, and 
Abf1p, and Pol III transcription factors enhance the efficiency of NNS 
termination by physically blocking Pol II progression. The same DNA-bound 
factors that promote NNS termination were shown previously to define the 3'-ends 
of Okazaki fragments synthesized by Pol δ during DNA replication. Reduced 
binding of these factors results in defective NNS termination and Pol II 
readthrough. Furthermore, inactivating NNS enables Pol II elongation through 
these roadblocks, demonstrating that effective Pol II termination depends on a 
synergy between the NNS machinery and obstacles in chromatin. Consistent with 
this finding, loci exhibiting Pol II readthrough at GRF binding sites are 
depleted for upstream NNS signals. Overall, these results underscore how RNA 
termination signals influence the behavior of Pol II at chromatin obstacles, and 
establish that common genomic elements define boundaries for both DNA and RNA 
synthesis machineries.