Common genomic elements promote transcriptional and DNA replication roadblocks

Abstract

RNA Polymerase II (Pol II) transcription termination by the Nrd1p-Nab3p-Sen1p (NNS) pathway is critical for the production of stable non-coding RNAs and for the control of pervasive transcription in Saccharomyces cerevisiae. To uncover determinants that specify the precise locations of NNS termination, we mapped the 3'-ends of NNS-terminated transcripts genome-wide. We found that nucleosomes and various DNA-binding proteins, including Pol III transcription factors and the general regulatory factors (GRFs) Reb1p, Rap1p, and Abf1p, enhance the efficiency of NNS termination by physically blocking Pol II progression. Intriguingly, the same DNA-bound factors that promote NNS termination were shown previously to define the 3'-ends of Okazaki fragments during DNA replication. We demonstrate that abrogating DNA binding of these factors results in defective NNS termination and Pol II readthrough. Furthermore, inactivating NNS enables Pol II elongation through the same 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.