The ‘moving target’ of transposon landscape changes in aging Drosophila

Genetic mechanisms that strongly repress transposable elements (TEs) in young animals decline during aging because TE transcripts become reactivated. Does TE transcriptional reactivation during aging then alter and damage the genome? To test this hypothesis, we quantified Transposon Landscape (TLs) via deeply sequencing genomes of young and aged Drosophila strains of wild-type and mutant backgrounds. We quantified TLs in aging whole flies as well as dissected brains, and we validated the feasibility of our approach in detecting increases in new TE insertions in aging Drosophila genomes when RNAi and Piwi pathways are compromised. By also incorporating droplet digital PCR as an important validation methodology for measuring genomic TE loads, we now show that genetic mutations that strongly reactivate TE RNA expression only exhibit modest genomic TL changes. Additionally, we examine a new frontier of extra-chromosomal DNA circles (eccDNAs) as a source of accumulating TE copies and describe new sequencing methods to quantify eccDNAs in Drosophila. Our analysis suggests that small RNA surveillance mechanisms still prevent genomic TL expansion despite the increase in transposon transcripts during aging. However, to combat the natural progression of increased TE expression during animal aging we show that knocking down the PAF1 complex that regulates RNA Pol II elongation and transcription termination, can reduce aging related TE expression increases.