Genome-Wide Discovery of DEAD-Box RNA Helicase Targets Reveals RNA Structural Remodeling in Transcription Termination

RNA helicases are a class of enzymes that unwind RNA duplexes in vitro but whose cellular functions are largely enigmatic. Here, we provide evidence that the DEAD-box protein remodels RNA-protein complex (RNP) structure to facilitate efficient termination of transcription in Saccharomyces cerevisiae via the Nrd1-Nab3-Sen1 (NNS) complex. First, we find that loss of results in RNA polymerase II accumulation at the 3 ' ends of small nucleolar RNAs and a subset of mRNAs. In addition, associates with RNA sequence motifs and regions bound by and can promote its recruitment to NNS-targeted regions. Using Structure-seq, we find altered RNA/RNP structures in increment cells that correlate with inefficient termination. We also show a positive correlation between the stability of structures in the 3 ' ends and a requirement for in termination. Taken together, these studies provide a role for RNA remodeling by and further suggests a mechanism whereby RNA structure is exploited for gene regulation.