Mapping and Quantification of Non-Coding RNA Originating from the rDNA in Human Glioma Cells.

Ribosomal DNA is one of the most conserved parts of the genome, especially in its rRNA coding regions, but some puzzling pieces of its noncoding repetitive sequences harbor secrets of cell growth and development machinery. Disruptions in the neat mechanisms of rDNA orchestrating the cell functioning result in malignant conversion. In cancer cells, the organization of rRNA coding genes and their transcription somehow differ from that of normal cells, but little is known about the particular mechanism for this switch. In this study, we demonstrate that the region ~2 kb upstream of the rDNA promoter is transcriptionally active in one type of the most malignant human brain tumors, and we compare its expression rate to that of healthy human tissues and cell cultures. Sense and antisense non-coding RNA transcripts were detected and mapped, but their secondary structure and functions remain to be elucidated. We propose that the transcripts may relate to a new class of so-called promoter-associated RNAs (pRNAs), or have some other regulatory functions. We also hope that the expression of these non-coding RNAs can be used as a marker in glioma diagnostics and prognosis.

Evolutionary divergence of the pre-promotor region of ribosomal DNA in the great apes.

The human ribosomal intergenic spacer (rIGS) differs considerably on nucleotide sequence and regulatory elements positioning from their counterparts in the mouse, rat and Xenopus laevis. In the present study, we have PCR amplified, cloned and sequenced the rIGS fragments of about 4.5 kb length, located approximately 2 kb upstream of the rRNA transcription start point for the great apes, Pan paniscus, Pan troglodytes, Gorilla gorilla and Pongo pygmaeus. Alignment of the primates' orthologic nucleotide sequences reveals high extent of similarity, with the exception of highly repetitious region between the two Alu repeats, nearest to the onset of transcription. Data obtained have been analyzed for further understanding of the evolution of repetitive sequences. We have also shown, that MARs/SARs distribution patterns in the pre-promoter rIGSs of the great apes and the mouse are surprisingly similar in spite of an absence of similarity in the primary structure and regulatory elements organization in the region under study.

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

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.