In human cells, each rDNA unit consists of the ~13 kb long ribosomal part and ~30 kb long intergenic spacer (IGS). The ribosomal part, transcribed by RNA polymerase I (pol I), includes genes coding for 18S, 5.8S, and 28S RNAs of the ribosomal particles, as well as their four transcribed spacers. Being highly repetitive, intensively transcribed, and abundantly methylated, rDNA is a very fragile site of the genome, with high risk of instability leading to cancer. Multiple small mutations, considerable expansion or contraction of the rDNA locus, and abnormally enhanced pol I transcription are usual symptoms of transformation. Recently it was found that both IGS and the ribosomal part of the locus contain many functional/potentially functional regions producing non-coding RNAs, which participate in the pol I activity regulation, stress reactions, and development of the malignant phenotype. Thus, there are solid reasons to believe that rDNA locus plays crucial role in carcinogenesis. In this review we discuss the data concerning the human rDNA and its closely associated factors as both targets and drivers of the pathways essential for carcinogenesis. We also examine whether variability in the structure of the locus may be blamed for the malignant transformation. Additionally, we consider the prospects of therapy focused on the activity of rDNA.

• Keywords
• IGS, cancer, copy number, human rDNA, non-coding RNA, ribosomal genes,
• MeSH
• Genetic Variation genetics   MeSH
• DNA, Intergenic genetics   MeSH
• Humans MeSH
• Mutation genetics   MeSH
• Neoplasms genetics   pathology   MeSH
• RNA, Untranslated genetics   MeSH
• DNA, Ribosomal genetics   MeSH
• Ribosomes genetics   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Review MeSH
• Names of Substances
• DNA, Intergenic MeSH
• RNA, Untranslated MeSH
• DNA, Ribosomal MeSH

In human cells, ribosomal DNA (rDNA) is arranged in ten clusters of multiple tandem repeats. Each repeat is usually described as consisting of two parts: the 13 kb long ribosomal part, containing three genes coding for 18S, 5.8S and 28S RNAs of the ribosomal particles, and the 30 kb long intergenic spacer (IGS). However, this standard scheme is, amazingly, often altered as a result of the peculiar instability of the locus, so that the sequence of each repeat and the number of the repeats in each cluster are highly variable. In the present review, we discuss the causes and types of human rDNA instability, the methods of its detection, its distribution within the locus, the ways in which it is prevented or reversed, and its biological significance. The data of the literature suggest that the variability of the rDNA is not only a potential cause of pathology, but also an important, though still poorly understood, aspect of the normal cell physiology.

• Keywords
• copy number, human rDNA, mutations, sequence variability,
• MeSH
• Genetic Variation * MeSH
• Genetic Loci MeSH
• Humans MeSH
• Promoter Regions, Genetic genetics   MeSH
• DNA, Ribosomal genetics   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Review MeSH
• Names of Substances
• DNA, Ribosomal MeSH

In human cells, the intergenic spacers (IGS), which separate ribosomal genes, are complex approximately 30 kb-long loci. Recent studies indicate that all, or almost all, parts of IGS may be transcribed, and that at least some of them are involved in the regulation of the ribosomal DNA (rDNA) transcription, maintenance of the nucleolar architecture, and response of the cell nucleus to stress. However, since each cell contains hundreds not quite identical copies of IGS, the structure and functions of this locus remain poorly understood, and the dynamics of its products has not been specially studied. In this work, we used quantitative PCR to measure the expression levels of various rDNA regions at different times after inhibition of the transcription by Actinomycin D applied in high doses. This approach allowed us to measure real or extrapolated half-life times of some IGS loci. Our study reveals characteristic dynamic patterns suggestive of various pathways of RNA utilization and decay.

• Keywords
• Intergenic spacer, Processing, RNA decay, lncRNAs, rDNA,
• MeSH
• HeLa Cells MeSH
• Humans MeSH
• DNA, Ribosomal Spacer chemistry   genetics   metabolism   MeSH
• RNA analysis   biosynthesis   genetics   isolation & purification   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• DNA, Ribosomal Spacer MeSH
• RNA MeSH

The role of the nucleolus and autophagy in maintenance of nuclear integrity is poorly understood. In addition, the mechanisms of nuclear destruction in cancer cells senesced after conventional chemotherapy are unclear. In an attempt to elucidate these issues, we studied teratocarcinoma PA1 cells treated with Etoposide (ETO), focusing on the nucleolus. Following treatment, most cells enter G2 arrest, display persistent DNA damage and activate p53, senescence, and macroautophagy markers. 2-5 µm sized nucleolar aggresomes (NoA) containing fibrillarin (FIB) and damaged rDNA, colocalized with ubiquitin, pAMPK, and LC3-II emerge, accompanied by heterochromatin fragments, when translocated perinuclearly. Microscopic counts following application of specific inhibitors revealed that formation of FIB-NoA is dependent on deficiency of the ubiquitin proteasome system coupled to functional autophagy. In contrast, the accompanying NoAs release of pericentric heterochromatin, which exceeds their frequency, is favored by debilitation of autophagic flux. Potential survivors release NoA in the cytoplasm during rare mitoses, while exit of pericentric fragments often depleted of H3K9Me3, with or without encompassing by NoA, occurs through the nucleolar protrusions and defects of the nuclear envelope. Foci of LC3-II are accumulated in the nucleoli undergoing cessation of rDNA transcription. As an origin of heterochromatin fragmentation, the unscheduled DNA synthesis and circular DNAs were found in the perinucleolar heterochromatin shell, along with activation and retrotransposition of ALU elements, colocalized with 45S rDNA in NoAs. The data indicate coordination of the basic nucleolar function with autophagy regulation in maintenance of the integrity of the nucleolus associated domains secured by inactivity of retrotransposons.

• Keywords
• ALU retrotransposition, LADs, NADs, aggresome, autophagy, cellular senescence, nucleolus, pericentric fragments, rRNA transcription, ubiquitin-proteasome,
• MeSH
• Autophagy drug effects   genetics   MeSH
• Cell Nucleolus drug effects   genetics   metabolism   MeSH
• Chromosomal Proteins, Non-Histone metabolism   MeSH
• Etoposide toxicity   MeSH
• Heterochromatin drug effects   metabolism   MeSH
• Cyclin-Dependent Kinase Inhibitor p16 metabolism   MeSH
• Cell Cycle Checkpoints drug effects   genetics   MeSH
• Humans MeSH
• Mutagens toxicity   MeSH
• Cell Line, Tumor MeSH
• DNA Damage MeSH
• Retroelements drug effects   genetics   MeSH
• DNA, Ribosomal genetics   metabolism   MeSH
• Cellular Senescence drug effects   genetics   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Chromosomal Proteins, Non-Histone MeSH
• Etoposide MeSH
• fibrillarin MeSH Browser
• Heterochromatin MeSH
• Cyclin-Dependent Kinase Inhibitor p16 MeSH
• Mutagens MeSH
• Retroelements MeSH
• DNA, Ribosomal MeSH