Ribosomal DNA exhibits few alterations in human skin cancers

Romão-Corrêa, Rosana F; Maria, Durvanei Augusto; Ruiz, Itamar R. G.; Neto, Cyro Festa; Sanches, José Antônio

doi:10.1016/j.jdermsci.2003.11.009

Cited by 2 publications

(3 citation statements)

References 9 publications

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“…The findings presented here are in agreement with the view that rDNA genes are heterogeneous and dynamic Sylvester 1995, 2001;Kuo et al 1996;Grozdanov et al 2003;Romao-Correa et al 2004). Gonzalez and Sylvester analyzed the type of exchange that occurs in the rDNA region, and they reported the presence of very divergent IGS sequence classes (Gonzalez and Sylvester 1995).…”

Section: Discussionsupporting

confidence: 92%

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Human ribosomal RNA gene arrays display a broad range of palindromic structures

Caburet¹,

Conti²,

Schurra³

et al. 2005

Genome Res.

133

127

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The standard model of eukaryotic ribosomal RNA (rRNA) genes involves tandem arrays with hundreds of units in clusters, the nucleolus organizer regions (NORs). A first genomic overview for human cells is reported here for these regions, which have never been sequenced in their totality, by using molecular combing. The rRNA-coding regions are examined by fluorescence on single molecules of DNA with two specific probes that cover their entire length. The standard organization assumed for rDNA units is a transcribed region followed by a nontranscribed spacer. While we confirmed this arrangement in many cases, unorthodox patterns were also observed in normal individuals, with one-third of the rDNA units rearranged to form apparently palindromic structures (noncanonical units) independent of the age of the donors. In cells from individuals with a deficiency in the WRN RecQ helicase (Werner syndrome), the proportion of palindromes increased to one-half. These findings, supported by Southern blot analyses, show that rRNA genes are a mosaic of canonical and (presumably nonfunctional) palindromic units that may be altered by factors associated with genomic instability and pathology.

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Section: Discussionsupporting

confidence: 92%

“…4A, arrows). Upon digestion with HindIII, Southern blotting showed the expected band at ∼15 kb (Romao-Correa et al 2004). The bands previously described, ranging from 13.3 to 16.7, are not visible, because they require overexposure of the membrane and a higher separation (Krystal and Arnheim 1978).…”

Section: Southern Blotting Analysismentioning

confidence: 99%

Human ribosomal RNA gene arrays display a broad range of palindromic structures

Caburet¹,

Conti²,

Schurra³

et al. 2005

Genome Res.

133

127

View full text Add to dashboard Cite

show abstract

“…Additional studies in mice and rat cell lines report a lack of change in rDNA copy number with age [14][15][16] . In both cancer and aging studies, not all cancers and not all aging tissues or organisms appear to display changes in rDNA copy number 1,4,17,18 . In short, there is no universal agreement on whether rDNA copy number changes with age or cancer.…”

Section: Thousands Of High-quality Sequencing Samples Fail To Show Mementioning

confidence: 99%

Thousands of high-quality sequencing samples fail to show meaningful correlation between 5S and 45S ribosomal DNA arrays in humans

Hall

Turner

Queitsch

2021

Sci Rep

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The ribosomal RNA genes (rDNA) are tandemly arrayed in most eukaryotes and exhibit vast copy number variation. There is growing interest in integrating this variation into genotype–phenotype associations. Here, we explored a possible association of rDNA copy number variation with autism spectrum disorder and found no difference between probands and unaffected siblings. Because short-read sequencing estimates of rDNA copy number are error prone, we sought to validate our 45S estimates. Previous studies reported tightly correlated, concerted copy number variation between the 45S and 5S arrays, which should enable the validation of 45S copy number estimates with pulsed-field gel-verified 5S copy numbers. Here, we show that the previously reported strong concerted copy number variation may be an artifact of variable data quality in the earlier published 1000 Genomes Project sequences. We failed to detect a meaningful correlation between 45S and 5S copy numbers in thousands of samples from the high-coverage Simons Simplex Collection dataset as well as in the recent high-coverage 1000 Genomes Project sequences. Our findings illustrate the challenge of genotyping repetitive DNA regions accurately and call into question the accuracy of recently published studies of rDNA copy number variation in cancer that relied on diverse publicly available resources for sequence data.

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Ribosomal DNA exhibits few alterations in human skin cancers

Cited by 2 publications

References 9 publications

Human ribosomal RNA gene arrays display a broad range of palindromic structures

Human ribosomal RNA gene arrays display a broad range of palindromic structures

Thousands of high-quality sequencing samples fail to show meaningful correlation between 5S and 45S ribosomal DNA arrays in humans

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