The Dynamic Interplay between Ribosomal DNA and Transposable Elements: A Perspective from Genomics and Cytogenetics.

Although both are salient features of genomes, at first glance ribosomal DNAs (rDNAs) and transposable elements (TEs) are genetic elements with not much in common: whereas rDNAs are mainly viewed as housekeeping genes that uphold all prime genome functions, TEs are generally portrayed as selfish and disruptive. These opposing characteristics are also mirrored in other attributes: organization in tandem (rDNAs) versus organization in a dispersed manner (TEs); evolution in a concerted manner (rDNAs) versus evolution by diversification (TEs); and activity that prolongs genomic stability (rDNAs) versus activity that shortens it (TEs). Re-visiting relevant instances in which rDNA-TE interactions have been reported, we note that both repeat types share at least four structural and functional hallmarks: (1) they are repetitive DNAs that shape genomes in evolutionary timescales; (2) they exchange structural motifs and can enter co-evolution processes; (3) they are tightly controlled genomic stress sensors playing key roles in senescence/aging; and (4) they share common epigenetic marks such as DNA methylation and histone modification. Here, we give an overview of the structural, functional and evolutionary characteristics of both rDNAs and TEs, discuss their roles and interactions, and highlight trends and future directions as we move forward in understanding rDNA-TE associations.