Characterizing the Role of the DEAD-box Protein Dbp2 in RNA Structure Remodeling and Pre-mRNA Processing
thesisposted on 10.06.2019, 18:37 by Yu-Hsuan Lai
RNA helicases are found in all kingdoms of life, functioning in all aspects of RNA biology mainly through modulating structures of RNA and ribonucleoprotein (RNP) complex. RNA structures have fundamental impacts on steps in gene expression, including transcription, pre-mRNA processing, and translation. However, the precise roles and regulatory mechanisms of RNA structures in co- and post-transcriptional processes remain elusive. By probing genome-wide RNA structures in vivo, a recent study suggested that ATP-dependent factors, such as RNA helicases, maintain the actively unfolded state of RNAs. Among all RNA helicases, DEAD-box proteins form the largest family in eukaryotes, and have been shown to remodel RNA/RNP structures both in vitro and in vivo. Nevertheless, for the majority of these enzymes, it is largely unclear what RNAs are targeted and where they modulate RNA/RNP structures to regulate co-transcriptional processes. To fill the gap, my research focused on identification of the RNAs and structures targeted by the DEAD-box protein Dbp2 in S. cerevisiae to uncover the cellular processes that Dbp2 is involved in.
My studies revealed a role of Dbp2 in transcriptional termination. Dbp2 binds to ~34% of yeast mRNAs and all snoRNAs, and loss of DBP2 leads to a termination defect as evidenced by RNA polymerase II (RNAPII) accumulation at 3’ ends of these genes. In addition, the binding pattern of Dbp2 in mRNAs is highly similar to Nrd1 and Nab3 in the Nrd1-Nab3-Sen1 (NNS) termination complex, and deletion of DBP2 leads to reduced recruitment of Nrd1 to its target genomic loci. In Dbp2 and NNS targeted 3’ UTRs, RNA structural changes resulted from DBP2 deletion also overlap polyadenylation elements and correlate with inefficient termination, and loss of stable structure in the 3’ UTR bypasses the requirement for Dbp2. These findings lead to a model that Dbp2 promotes efficient termination of transcription through RNA structure remodeling.
Interestingly, my research also revealed the requirement of DBP2 for efficient splicing, as loss of DBP2 leads to accumulation of unspliced pre-mRNAs. Moreover, this function is dependent on the helicase activity of Dbp2. Further studies are needed to characterize the molecular mechanism of how Dbp2 facilitates splicing in cells. Overall, my research demonstrated that DEAD-box RNA helicases remodel mRNA structure in vivo and that structural alteration can be essential for proper gene expression.