In a study published in eLife, Biological Systems and Engineering (BSE) postdoctoral researcher Grace Lee and senior scientist Gary Karpen investigated the extent to which transposons—bits of DNA that copy themselves and jump to other locations in the genome—harm organisms through epigenetic means, such as changing the way DNA is packaged in cells, and whether this influences how transposons evolve. In a Q&A with the journal, Lee explained the background of the research, the specific question she and Karpen were interested in, and the most illuminating result among their findings.
How would you introduce your research to someone unfamiliar with your field?
Most transposable elements (TEs) have no important functions and are usually harmful to organisms. Accordingly, they are widely known as “genomic parasites.” Despite their harmful effects, TEs are present in the genomes of almost all organisms, and their number varies greatly between individuals and species. Organisms have evolved ways to package TE sequences into heterochromatin, which reduces the ability of TEs to multiply. However, this packaging of TEs into heterochromatin sometimes spreads to neighboring genes, which becomes harmful to organisms. This effect on neighboring genes is mediated through changing the DNA packaging, and is therefore an epigenetic effect induced by TEs.
What exact question did you set out to answer?
While we have a good understanding of the harmful genetic effects of TEs (e.g. jumping into gene sequences), the epigenetic effects of TEs have been largely unexplored. We wanted to understand how often and to what extent TEs are harmful through epigenetic effects, and whether this effect in turn influences the evolution of TEs.
What is the most important finding of your paper?
In wild type fruit flies, we found that more than 50 percent of TEs lead to packaging of nearby sequences into heterochromatin, which can negatively impact up to 20 percent of genes in the genome. As a result, TEs with harmful epigenetic effects are more often removed from the population by natural selection. The epigenetic effect of TEs inversely correlates with the number of TEs in two closely related fruit fly species. The association between stronger epigenetic effects on neighboring genes and fewer numbers of TEs in the genome provides a new way to understand why TE numbers vary among organisms.