Poster abstracts
Poster number 126 submitted by Michael Schiff
Understanding Connections between PYM1 Function in Exon Junction Complex Binding and Gene Architecture
Michael Schiff (Department of Physics, The Ohio State University), Manu Sanjeev (Department of Molecular Genetics, The Ohio State University), Ralf Bundschuh (Department of Physics, The Ohio State University), Guramrit Singh (Department of Molecular Genetics, The Ohio State University)
Abstract:
The exon junction complex (EJC) is a protein complex deposited near the junction of two exons during pre-mRNA splicing. The EJC is a hallmark of spliced RNAs and plays many important roles in RNA processes including mRNA surveillance. It has been previously suggested that PYM1 acts as an EJC disassembly factor through a direct interaction with the EJC [1]. However, recent experiments from our group suggest no role for PYM1 in translation dependent EJC disassembly. To better understand PYM1's function and effect on EJC occupancy and/or stability, we have generated and analyzed RNA-seq and EJC-footprinting data under conditions that limit EJC-PYM1 interaction. An exploratory analysis of these data has suggested a link between gene architecture and altered gene expression and EJC occupancy upon loss of EJC-PYM1 interaction. We thus set out to use a machine learning based, unbiased approach to identify which specific aspects of gene architecture are most relevant for the observed differences. RNA-seq and EJC-footprint foldchanges between samples from different conditions were predicted using gene architecture features as the predictors. The importance of each feature in the learned models was subsequently measured. A feature appearing important to the model thus could shed light on the role of PYM1 in EJC occupancy. This method was tested using synthetic data to verify that known predictors are indeed identified by this approach. Current progress on experimentally obtained data thus far has pointed to a connection between PYM1 effect on EJC occupancy and the GC content, which previously has been linked with gene architecture [2]. Thus, PYM1 function in regulating EJC's RNA binding is likely dependent on gene architectural features such as GC content.
References:
[1] Gehring NH, Lamprinaki S, Kulozik AE, Hentze MW. Disassembly of exon junction complexes by PYM. Cell. 2009 May;137(3):536-548. DOI: 10.1016/j.cell.2009.02.042. PMID: 19410547
[2] Mordstein, C., Savisaar, R., Young, R. S., Bazile, J., Talmane, L., Luft, J., Liss, M., Taylor, M. S., Hurst, L. D., & Kudla, G. (2020). Codon usage and splicing jointly influence mrna localization. Cell Systems, 10(4). https://doi.org/10.1016/j.cels.2020.03.001
Keywords: Exon Junction Complex (EJC), PYM1, Machine Learning