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

Yu Hsuan Lai, Krishna Choudhary, Sara C. Cloutier, Zheng Xing, Sharon Aviran, Elizabeth J. Tran

Research output: Contribution to journalArticle

1 Scopus citations

Abstract

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 Dbp2 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 DBP2 results in RNA polymerase II accumulation at the 3' ends of small nucleolar RNAs and a subset of mRNAs. In addition, Dbp2 associates with RNA sequence motifs and regions bound by Nrd1 and can promote its recruitment to NNS-targeted regions. Using Structure-seq, we find altered RNA/RNP structures in dbp2∆ 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 Dbp2 in termination. Taken together, these studies provide a role for RNA remodeling by Dbp2 and further suggests a mechanism whereby RNA structure is exploited for gene regulation.

Original languageEnglish (US)
Pages (from-to)153-174
Number of pages22
JournalGenetics
Volume212
Issue number1
DOIs
StatePublished - May 1 2019

Keywords

  • DEAD-box
  • RNA helicase
  • RNA structure
  • termination
  • transcription

ASJC Scopus subject areas

  • Genetics

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