Poster abstracts
Poster number 42 submitted by Debadrita Paul
Identification of Cis-elements and Trans-factors that govern UPF3-independent Nonsense-Mediated mRNA Decay (NMD)
Debadrita Paul (The Ohio State University)
Abstract:
Nonsense-mediated mRNA decay (NMD) identifies and eliminates aberrant transcripts with premature termination codons (PTCs) while regulating normal physiological transcripts. Dysregulation of NMD links to neurodevelopmental defects and cancer. Core factors UPF1, UPF2, and UPF3 are essential for yeast NMD, targeting long 3’UTR transcripts. Multicellular organisms have an additional NMD regulator called Exon Junction complex (EJC), which strongly triggers NMD downstream of a PTC, constituting the major EJC-dependent NMD branch, alongside the EJC-independent one in yeast. UPF3, less conserved among UPF proteins, bridges the terminating ribosome and downstream EJCs, leading to UPF1 activation and subsequent mRNA degradation mediated by SMG5/7 and SMG6. While UPF3 is essential for yeast NMD, its loss in humans results in neurodevelopmental defects without lethality. Previous research highlighted UPF3's non-essential role in NMD. Some transcripts in the EJC-dependent branch rely on UPF3 (UPF3-dependent NMD), while others undergo UPF3-independent NMD. My analysis reveals that EJC-independent NMD can occur via both UPF3-dependent and -independent mechanisms. My research aims to unravel the cis-elements and trans-factors dictating UPF3-independent NMD. Investigation into the roles of cis-elements such as mRNA GC-content, stop codon identity, penultimate codons and other factors influencing ribosome termination efficiency will help understand the basis of UPF3 independence in NMD. Moreover, we aim to understand how UPF3-independent NMD relies on trans-factors like SMG5/7 and SMG6 to elucidate its degradation pathway. Finally, using fluorescent NMD reporters in a genome-wide CRISPR screen, we aim to identify novel proteins for EJC sensing in the absence of UPF3. Unraveling UPF3-independent NMD mechanisms and identifying transcripts will enable precise therapeutic targeting, especially for genetic diseases caused by nonsense mutations, by inhibiting specific NMD branches.
References:
Yi, Zhongxia, René M. Arvola, Sean Myers, Corinne N. Dilsavor, Rabab Abu Alhasan, Bayley N. Carter, Robert D. Patton, Ralf Bundschuh, and Guramrit Singh. 2022. “Mammalian UPF3A and UPF3B Can Activate Nonsense-Mediated mRNA Decay Independently of Their Exon Junction Complex Binding.” The EMBO Journal 41 (10): e109202.
Wallmeroth, Damaris, Jan-Wilm Lackmann, Sabrina Kueckelmann, Janine Altmüller, Christoph Dieterich, Volker Boehm, and Niels H. Gehring. 2022. “Human UPF3A and UPF3B Enable Fault-Tolerant Activation of Nonsense-Mediated mRNA Decay.” The EMBO Journal 41 (10): e109191.
Karousis, Evangelos D., Sofia Nasif, and Oliver Mühlemann. 2016. “Nonsense-Mediated mRNA Decay: Novel Mechanistic Insights and Biological Impact.” Wiley Interdisciplinary Reviews. RNA 7 (5): 661–82.
Keywords: UPF3-independent NMD, translation termination, SMG6