Non-canonical ribosomal DNA segments in the human genome, and nucleoli functioning

• We mapped the bonds susceptible to disruption in the human rIGS.
• We showed an accumulation of these bonds near rIGS stimuli-specific inducible loci.
• Most active break points are located upstream and downstream of Alu fragments.
• A multitude of identical short DNA segments enter into groups of coding genes.

Ribosomal DNA (rDNA) in the human genome is represented by tandem repeats of 43 kb nucleotide sequences that form nucleoli organizers (NORs) on each of five pairs of acrocentric chromosomes. RDNA-similar segments of different lengths are also present on (NOR)− chromosomes. Many of these segments contain nucleotide substitutions, supplementary microsatellite clusters, and extended deletions. Recently, it was shown that, in addition to ribosome biogenesis, nucleoli exhibit additional functions, such as cell-cycle regulation and response to stresses. In particular, several stress-inducible loci located in the ribosomal intergenic spacer (rIGS) produce stimuli-specific noncoding nucleolus RNAs. By mapping the 5′/3′ ends of the rIGS segments scattered throughout (NOR)− chromosomes, we discovered that the bonds in the rIGS that were most often susceptible to disruption in the rIGS were adjacent to, or overlapped with stimuli-specific inducible loci. This suggests the interconnection of the two phenomena — nucleoli functioning and the scattering of rDNA-like sequences on (NOR)− chromosomes.