Predator-prey dynamics of transposable elements
Transposable elements (TEs), or transposons, are a class of mobile genetic elements that can either move or duplicate themselves in the genome, sometimes interfering with gene expression as a result. Some TEs can code all necessary enzymes for their transposition and are thus autonomous, while non-autonomous TEs are parasitic and must depend on the machinery of autonomous ones.
Transposable elements occupy roughly 45% of the human genome. Among them, are the autonomous/non-autonomous pair of L1 and Alu elements. Both L1 and Alu belong to the retrotransposon catogory. They use the corresponding mRNA molecule as a template and retrotranscribe the mRNA into DNA to complete a transposition. This copy-and-paste route results in the growth of the element copy number. L1 elements are autonomous and code all the necessary enzymes. Alu elements do not code any proteins and depend on the retrotranscriptase of the L1 elements to profiliate.
We develop and solve a stochastic model to describe the interaction between the Alu/L1 non- autonomous/autonomous pair. We predict noise-induced persistent quasi-cycles in their copy numbers, analogous to predator-prey dynamics in an ecosystem. These quasi-cycles can potentially be observed in the genomic age distribution or be realized in engineered fast dividing organisms (e.g. E. coli).