Real Time Transposable Element Activity in Individual Live Cells

The replication and propagation of transposable elements (TEs) disperses and disrupts coding and control regions of the host genome, generating genotypic and phenotypic diversity that plays an important role in evolution, development and the etiology of several human diseases including cancer. Nevertheless, quantitatively understanding TE activity and its governing factors has up to now been elusive. Current estimates of the rates and statistics of TE activity and their impact on evolution and epidemiology are primarily based on sequencing and other bulk analyses that generate averages over both time and ensembles of cells, and therefore the rates, statistics and controlling factors of TE activity and their dynamics in vivo remain poorly understood. Here we describe an experimental system based on the bacterial TE IS608 that permits direct observation and quantification of the rates and statistics of TE excision events in individual living cells in real time using fluorescent reporters. Using this system to quantitatively probe TE behavior, we find that TE activity rates are dynamic and highly variable throughout the lifetime of the cell, depending upon the TEu0027s orientation in the genome, the intracellular levels of the transposase protein responsible for its activity and the cellu0027s environment or history. These direct observations of growth-state dependent TE activity demonstrate that real-time live-cell imaging of evolution at the molecular level is achievable, and can be a powerful tool to address fundamental questions related to genome plasticity in stressed cells.