Poster abstracts
Poster number 164 submitted by Maria Zea
Crosstalk between DEAD box RNA helicase Dbp2 and RNA Pol II kinetics on transcription termination
Maria Zea (Purdue University), Subhadeep Das (Purdue University), Elizabeth Tran (Purdue University)
Abstract:
Dead box RNA helicases are a class of enzymes that play a crucial role in RNA duplex unwinding and modulation of interactions between RNA molecules and proteins. The association of these helicases with various disease states, including neurological disorders, viral infections, and multiple cancer types, suggests a potential link between RNA and/or ribonucleoprotein (RNP) structures and human pathologies. While the involvement of DEAD-box proteins in nuclear gene expression steps has been demonstrated in the budding yeast Saccharomyces cerevisiae, the specific function of Dbp2 in efficient termination of RNAPII transcription remains unclear. In this study, we aim to investigate the impact of RNA helicases on RNA polymerase II (RNAPII) dynamics. Our primary objective is to determine whether RNA helicases are essential for RNAPII efficient termination. To address this, we have developed Chip-seq experiments to examine the occupancy of Dbp2 in the 3' untranslated region (UTR) downstream, which was further validated by a reporter assay demonstrating readthrough in YOP1, YNL190W, and RBG1 genes at a 150 bp annotation site. Interestingly when using TTseq—a method designed to capture full-length nascent RNA transcripts—we did not observe this readthrough in these genes. TTseq involves blocking RNA polymerase activity and selectively labeling and sequencing newly synthesized RNA transcripts, enabling investigations into transcription dynamics. Additionally, our gene ontology (GO) analysis revealed that differentially expressed genes at the 100 bp region were associated with translation. Our primary objective is to identify and analyze potential candidates from the bioinformatics data through biological validation methods to confirm their readthrough. Additionally, we aim to investigate whether the presence of RNA polymerase in the 3' UTR is predominantly influenced by stability rather than readthrough. By examining the interactions between RNA helicases, RNA polymerase dynamics, and their critical role in cellular processes, this research has the potential to advance our understanding of the molecular mechanisms involved in human diseases associated with RNA structure and processing.
References:
Lai YH, Choudhary K, Cloutier SC, Xing Z, Aviran S, Tran EJ. Genome-Wide Discovery of DEAD-Box RNA Helicase Targets Reveals RNA Structural Remodeling in Transcription Termination. Genetics. 2019 May;212(1):153-174. doi: 10.1534/genetics.119.302058. Epub 2019 Mar 22. PMID: 30902808; PMCID: PMC6499532.
This project is funded by National institute of health (NIH) grant
Keywords: readthrough, dbp2