Understanding how transposons generate new immune gene protein-coding splice variants

Project Summary Transposons are ubiquitous genomic elements that can mobilize, replicate, and integrate within the host genome. Extensive research has focused on how transposons impact their host, revealing instances of both deleterious and selectively advantageous roles. While transposon exonization (defined as the inclusion of transposon-derived exons into cellular transcripts through alternative splicing) is common, the biological relevance of transposon-derived transcript isoforms remains unclear and controversial. Here, I propose to investigate transposon exonization in coding regions as an important, recurrent evolutionary mechanism that drives adaptive proteome diversification, specifically in the context of host-pathogen arms races. In preliminary studies, I re-analyzed long-read transcriptome data from human macrophages and discovered hundreds of poorly characterized isoforms derived from transposon exonization events for genes involved in immune and inflammatory responses. These include a transposon-derived isoform of the type I interferon receptor subunit 2 gene (IFNAR2), which I have experimentally shown to act as a novel immune decoy receptor. I will use alternative splicing of the IFNAR2 gene as a model to reconstruct the genomic events that can lead to the successful exonization of transposons to form functional protein isoforms (Aim 1), with the goal of reconstructing the genetic basis of the “road to co-option” of exonized transposons. Using IFNAR2 as a model, I will then investigate which mechanisms and factors are involved in the regulation of alternative splicing and expression of transcribed transposon-derived coding alternative exons (Aim 2). Finally, I will compare long-read RNA sequencing de novo transcriptome assemblies from multiple species of the vertebrate tree of life to evaluate the incidence of proteins that evolved through the inclusion of transposons in coding sequences (Aim 3). Taken together, these aims will establish an experimental framework to test the role of transposable elements in adaptive proteome diversification, and shed light on the process of how transposons can evolve novel functions beneficial for their host (transposon co-option) through their inclusion in coding regions. Additionally, they will provide me with new training in: 1) techniques for testing and validating mechanisms of mRNA and alternative splicing regulation; 2) how to design and perform immunological assays, including viral infections; and 3) the execution and troubleshooting of genome-scale screens for phenotypes of interest and training in primary cell culture and genome engineering. Additionally, I will learn how to perform high throughput long-read RNA sequencing and isoform-specific transcriptome assembly for model and non-model species. The research and training provided by this proposal will prepare me to launch my own research group studying how transposon co-option shapes the evolution of vertebrate proteomes.