An Intergenic Non-Coding rRNA Correlated with Expression of the rRNA and Frequency of an rRNA Single Nucleotide Polymorphism in Lung Cancer Cells

Abstract

BackgroundRibosomal RNA (rRNA) is a central regulator of cell growth and may control cancer development. A cis noncoding rRNA (nc-rRNA) upstream from the 45S rRNA transcription start site has recently been implicated in control of rRNA transcription in mouse fibroblasts. We investigated whether a similar nc-rRNA might be expressed in human cancer epithelial cells, and related to any genomic characteristics.Methodology/Principal FindingsUsing quantitative rRNA measurement, we demonstrated that a nc-rRNA is transcribed in human lung epithelial and lung cancer cells, starting from approximately −1000 nucleotides upstream of the rRNA transcription start site (+1) and extending at least to +203. This nc-rRNA was significantly more abundant in the majority of lung cancer cell lines, relative to a nontransformed lung epithelial cell line. Its abundance correlated negatively with total 45S rRNA in 12 of 13 cell lines (P = 0.014). During sequence analysis from −388 to +306, we observed diverse, frequent intercopy single nucleotide polymorphisms (SNPs) in rRNA, with a frequency greater than predicted by chance at 12 sites. A SNP at +139 (U/C) in the 5′ leader sequence varied among the cell lines and correlated negatively with level of the nc-rRNA (P = 0.014). Modelling of the secondary structure of the rRNA 5′-leader sequence indicated a small increase in structural stability due to the +139 U/C SNP and a minor shift in local configuration occurrences.Conclusions/SignificanceThe results demonstrate occurrence of a sense nc-rRNA in human lung epithelial and cancer cells, and imply a role in regulation of the rRNA gene, which may be affected by a +139 SNP in the 5′ leader sequence of the primary rRNA transcript.

Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing

“…Comparison of the rDNA promoter sequence of U13369.1 and the new reference sequence showed significant differences (16 SNPs and INDELs), and in all cases the whole-genome validation datasets confirmed the new reference. These results are also in agreement with previously published rDNA promoter sequences ( 59 , 60 ).…”

“…Notably, sequence variants in the 5′ ETS lie near processing sites (e.g. sites 01 and 1 in 5′ETS and between sites 3 and E in ITS1; Supplementary Figure S12 ) and might affect pre-rRNA processing through modification of RNA folding ( 59 ). In addition, in the pre-rRNA promoter region, several variants modify CpG sites that show differential methylation status in some tumor samples ( 60 ) ( Supplementary Figure S12 ).…”

Single nucleotide polymorphisms and cancer susceptibility

“…Mutations in the mitochondrial tRNA genes are associated with mitochondrial dysfunction in breast cancer [ 119 ]. A cis non-coding rRNA (nc-rRNA), upstream of the 45S rRNA transcriptional start site is implicated in altered rRNA transcription in human lung epithelial cancer cells due to changes in its secondary structure [ 120 ]. Mitochondrial SNPs (mtSNPs) in the rRNA and tRNAs, MT-ND2 and haplogroup T are associated with CRC risk in European Americans (OR = 1.66, 95% CI: 1.19–2.33, P = 0.003) [ 121 ].…”

Dynamic Localisation of Mature MicroRNAs in Human Nucleoli is Influenced by Exogenous Genetic Materials

“…The nucleolus is a very dynamic structure [21], [39]. Activities of a wide range of proteins, including MDM2 [40], ADAR2 [41], HAND1 [42] and RelA [43], are controlled by their nucleolar localisation, possibly through a mechanism mediated by a noncoding RNA encoded in the ribosomal intergenic region [44]. Moreover, the nucleolar structure can be reversibly disrupted in response to cellular stress, which allows sequestered nucleolar factors to disperse out [34], [45]–[46].…”