Nucleotide sequence of the genetically labile repeated elements 5' to the origin of mouse rRNA transcription.

We have determined the complete nucleotide sequence of a cloned Balb/c mouse rDNA NTS fragment containing 13 tandem copies of a 135 bp subrepeating segment. This repetitious region (VrDNA) lies close to the origin of ribosomal RNA transcription. Analyses of these VrDNA subrepeats from Balb/c and a related species, Mus pahari, reveal regions of inverted repeat DNA as well as large poly T tracts, either of which may be significant to the generation of the high levels of VrDNA copy number variation found in wild and inbred mice and/or the modulation of rRNA synthesis. Unlike the highly homogeneous subrepeats in the Xenopus laevis NTS repetitious regions, the VrDNA subrepeats differ from one another on the average by about 13%. Sequence analysis and Southern hybridization studies have also shown that, unlike the Xenopus and Drosophila NTS, extensive duplications of sequences found surrounding the mouse rRNA initiation site are found neither in the VrDNA region nor 6 kb further upstream in the NTS.