Maintenance of long-term transposable element activity in genomes through regulation by nonautonomous elements

Abstract

AbstractTransposable elements are DNA sequences that can move and replicate within genomes. Broadly speaking, two element types exist: autonomous elements, which encode the necessary enzymes for transposition, and nonautonomous elements that rely on these enzymes produced by autonomous elements for their transposition. Nonautonomous elements have been proposed to regulate transposable element numbers, which is a possible explanation for continued transposition activity over long evolutionary times. However, previous modeling studies indicate that interactions between autonomous and nonautonomous elements usually result in the extinction of one type. Here, we study a stochastic model that allows for stable coexistence of autonomous and nonautonomous elements. We determine the conditions for coexistence and derive an analytical expression for the stationary distribution of their copy numbers, showing that nonautonomous elements regulate stochastic fluctuations and the number of autonomous elements in stationarity. We find that the stationary variances of each element can be expressed as a function of transposable element copy number averages and their covariance, enabling data comparison and model validation. These results suggest that besides silencing or domestication of transposable elements, continued regulated transposition by nonautonomous elements may be an alternative evolutionary outcome that could for example explain the long co-evolutionary history of autonomousLINE1and nonautonomousAluelement transposition in the human ancestry.