Deletions in (CCCT)_n repeat regions belonging to the human pRNA gene inhibit its expression

Ribosomal DNA (rDNA), the most abundantly expressed locus in the human genome, is represented by hundreds of units per cell. Each unit includes a 13 kb long region (47S rDNA) containing the genes of ribosomal particles, and a 30 kb long intergenic spacer (IGS). The 47S rDNA is transcribed with varying intensity in different units, some of which remain permanently silent. A key intermediator of this silencing is the promoter-associated RNA (pRNA) produced from a 2 kb long gene situated upstream of the rDNA transcription start site. Recent studies, including ours, suggest that the sequence variability, which normally occurs in mammalian cells, may account for the selective transcription of different rDNA units. The present work is based on the deep sequencing of a pRNA gene fragment and its RNA product and subsequent bioinformatic analysis.

We found that a certain SNV, which converts the CCC motif into CCT, as well as deletions which reduce the number of (CCCT) tandem repeats, were significantly more frequent in the DNA than in the respective transcripts.

These findings allowed us to establish directly the inhibitory effect of DNA variants on the expression of pRNA and thus (indirectly) the promoting effect on the production of ribosomal RNA. Our results also suggest that (CCCT)_n/(GGGA)_n DNA repeats and the respective (GGGA)_n RNA repeats may form triplex structures, facilitating the function of pRNA.