DSSS - Transposable elements: from parasites to symbionts

Nearly all eukaryotic genomes are replete with transposable elements (TEs). Since the discovery of TEs in maize by Barbara McClintock in the 1940s, our perception of TEs and of their biological impact has gone through major paradigm shifts. Each of these paradigms have had profound implications for our understanding of genome function and evolution. While McClintock viewed TEs as “normal components of the chromosomes” controlling differentially, the time and type of activity of individual genes” the 1980s and 1990s would be dominated by studies illustrating their mutagenic activity, supporting the concept of parasitic, selfish DNA. The shift from genetics to genomics at the turn of the millennium would trigger a seismic change in the study of TEs. Large-scale genome sequencing confirmed that eukaryotic genomes, including half of the human genome, are filled with TE sequences but the vast majority are clearly ancient fossils riddled with mutations and no longer capable of transposition. These findings led to the credence that most TEs are ‘junk DNA’: sequences devoid of obvious cellular function. Functional genomics however soon revealed that TEs made greater-than-expected contributions to the regulatory activity of the genome and to the complexity of the transcriptome. These findings overturned the idea that TEs are systematically silent and biochemically inert. Instead, a picture emerged of a genome in which TEs are dynamically responsive constituents –arching back to McClintock’s “genomic shock” theory, which postulated that TEs enable organisms to remodel their genome in times of stress. Continuous advances in our ability to map and manipulate the genome, such as CRISPR-based methods, have provided increasingly powerful tools to dissect the functional impact of TEs. Recent research is depicting TEs as diverse, sophisticated entities engaged in a continuum of interactions with their hosts, ranging from harmful to symbiotic. TE activities are no longer perceived as peripheral or merely competing with cellular functions, but as deeply integrated into the physiology, development and evolution of species.