CAREER: Learning from NMD evasion by endogenous and viral transcripts

University Of Colorado At Denver, Aurora CO

Investigators

Abstract

Robustness in biological systems relies on quality control. An important quality control step in the flow of genetic information is to eliminate faulty and/or foreign messenger RNA (mRNA) molecules so that proteins that may be harmful to the cell are not produced. One of the ways that cells can identify faulty RNAs is by sensing the length of the sequence within an RNA that encodes for a protein versus not. While this mechanism works well in simple organisms such as yeast, the human genome has evolved to have naturally long regions of mRNAs that do not encode for a protein but serve regulatory purposes. How then does the cell know to not degrade such normal transcripts and yet identify potentially toxic RNAs that arise from mutated genes or viral genomes? This project will leverage evolutionary analysis, molecular biology, and genomics tools to identify and understand signals that could allow physiological RNAs that resemble aberrant RNAs to escape quality control. The project will also promote broader societal impacts by engaging 8th- and 9th-grade students in a local school in hands-on research to facilitate their training and exposure to scientific research. Nonsense-mediated RNA decay (NMD) is a quality control process that degrades transcripts containing premature termination codons (PTC) to prevent the production of toxic truncated proteins. NMD senses aberrant transcripts either via the presence of exon junction complexes (EJCs) downstream of the terminating ribosome or via the long 3’ untranslated region (UTR) generated by premature termination. Many non-aberrant endogenous transcripts and certain viral transcripts also mimic PTC-containing transcripts by virtue of possessing long 3’ UTRs and are also targeted by NMD. However, through the course of evolution, several transcripts with long UTRs, both viral and endogenous, have evolved mechanisms to bypass NMD by antagonizing the central NMD factor, UPF1. In this project, natural NMD evasion mechanisms will be investigated for novel insights into this fundamental quality control mechanism. The goals are to identify mechanisms of endogenous and viral bypass of long UTR NMD (Aim 1), determine the role of a mammal-specific UPF1 isoform in the arms race between NMD and its targets through experimental evolution in human and drosophila cells (Aim 2), and engage 8th-9th grade students from a local school in investigating the cross-regulation of different UPF1 paralogs and viral antagonists in yeast (Aim 3). This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.