Headrick, C. (BMEB) – The Regulation of mRNA Cleavage in Nonsense-mediated mRNA Decay: From Inside (intra-pathway determinants) Out (extra-pathway regulation)

Nonsense-mediated mRNA decay (NMD) is a translation-coupled quality control pathway that degrades mRNAs that harbor a premature termination codon (PTC) and 5-30% of normal cellular mRNAs. The NMD field sits at a pivotal moment with recent developments that endonucleolytic cleavage is the primary mechanism of mRNA decay conserved across metazoans. Discovery of a conserved NMD cleavage mechanism sets the stage for a dissection of mRNA cleavage determinants and regulators.

To better understand how mRNA cleavage during NMD is regulated, I will use degradome-seq based approaches via 5’RACE-seq (Rapid Amplification of 5’ cDNA Ends) to isolate the cleavage products of the NMD pathway. I will first focus my analysis on core NMD factors and helicase UPF1, the binding site of NMD decay effectors, to examine how UPF1 enzymatic activity affects mRNA cleavage transcriptome-wide (Aim 1). In parallel, to assess extra-pathway regulation of mRNA cleavage during NMD, I will identify endogenous negative regulators of mRNA cleavage (Aim 2). Contemporary models of NMD are deprived of the functional impact of cellular NMD inhibitors. I will access this novel functional space with an innovative application of CRISPR screening and quantitative, high-throughput NGS, known as ReLiC (RNA-linked CRISPR) paired with degradome analysis.

Event Host: Camille Headrick, Ph.D. Student, Biomolecular Engineering & Bioinformatics 

Advisor: Joshua Arribere