Transposable elements (TEs) are sequences that can move and multiply along the chromosomes. Considered for a long time as genomic parasites, they are now acknowledged as key players of genome function and evolution. Accordingly, the presence of TEs in a genome may affect the chromatin structure of the regions in which they are inserted. TEs allow us to revisit self and nonself distinction at the genomic level, through the complex relationships they display with the genome and the epigenome and their interaction with the environment.