Processed pseudogenes: the ‘fossilized footprints’ of past gene expression

Although our knowledge of the genes and genomes of extinct organisms is improving as a result of progress in sequencing ancient DNA, the transcriptomes of extinct organisms remain inaccessible, owing to the rapid degradation of messenger RNA after death. We provide empirical evidence that gene expression levels in the reproductive tissues of mice and during early mouse development correlate highly with the rate of inherited retroposition: the source of processed pseudogenes in the genome. Thus, processed pseudogenes might serve as fossilized footprints of the expression of their parent genes, shedding light on ancient transcriptomes that could provide significant insights into the evolution of gene expression.