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

Abstract

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.

Zooming in: PAGE-Northern Blot Helps to Analyze Anti-Sense Transcripts Originating from Human rIGS under Transcriptional Stress

“…It is demonstrated that the pre-promoter region of human rDNA is transcribed in cancer cells [20]. We also have shown that the region ~2 kb upstream of the rRNA promoter is transcriptionally active in normal human cell lines, as well as in glioma and glioblastoma cell cultures [21]. The sequences are given in the Table A1.…”

Variability of Human rDNA

“…Recent studies suggest that IGS has a complex functional organization. RNA-seq analysis of human and murine rDNA has revealed a specific pattern of low-abundance expression over the entire spacer region [15][16][17][18][19][20][21]. One prominent transcription unit includes a 2 kb long segment at the 3 end of IGS, and probably stretches into 5 ETS area [15,20,[22][23][24].…”

“…RNA-seq analysis of human and murine rDNA has revealed a specific pattern of low-abundance expression over the entire spacer region [15][16][17][18][19][20][21]. One prominent transcription unit includes a 2 kb long segment at the 3 end of IGS, and probably stretches into 5 ETS area [15,20,[22][23][24]. This region is transcribed by pol I and is involved in rDNA silencing [10,22,[25][26][27][28][29][30][31][32].…”

“…Alu sequences scattered over the spacer also produce transcripts, which may be involved in the maintenance of the nucleolar structure [43,44]. Other regions of IGS have been recently described as potentially functional [20,45]. Thus, rDNA is characterized by the multiplicity of copies and complex structure of each copy, which includes many other repetitive elements.…”

Antagonising Chromatin Remodelling Activities in the Regulation of Mammalian Ribosomal Transcription

“…Similar enrichment of RNA pol I factors has been found in human cells approximately 800 bp upstream of transcription start site, with an enrichment of CTCF [ 37 , 48 ]. In the human IGS, a third promoter two kb upstream of the transcription start site in human cells was identified, from which an antisense RNA of unknown function is produced [ 50 ]. The open structure organised with UBF is particularly abundant in ES cells (embryonic stem cells) and mouse embryonic fibroblasts (MEFs), where few histone marks are found in the 47S rRNA gene repeat (35, 37), whereas that of differentiated cells may contain more histones (49).…”