Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing
Open accessAbstract
Despite the key role of the human ribosome in protein biosynthesis, little is known about the extent of sequence variation in ribosomal DNA (rDNA) or its pre-rRNA and rRNA products. We recovered ribosomal DNA segments from a single human chromosome 21 using transformation-associated recombination (TAR) cloning in yeast. Accurate long-read sequencing of 13 isolates covering ∼0.82 Mb of the chromosome 21 rDNA complement revealed substantial variation among tandem repeat rDNA copies, several palindromic structures and potential errors in the previous reference sequence. These clones revealed 101 variant positions in the 45S transcription unit and 235 in the intergenic spacer sequence. Approximately 60% of the 45S variants were confirmed in independent whole-genome or RNA-seq data, with 47 of these further observed in mature 18S/28S rRNA sequences. TAR cloning and long-read sequencing enabled the accurate reconstruction of multiple rDNA units and a new, high-quality 44 838 bp rDNA reference sequence, which we have annotated with variants detected from chromosome 21 of a single individual. The large number of variants observed reveal heterogeneity in human rDNA, opening up the possibility of corresponding variations in ribosome dynamics.
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Within active NORs, some rRNA genes can be silent.
“Moreover, within the active NORs, some rRNA genes can be silent (19,20).”
From Impaired function of rDNA transcription initiation machinery leads to derepression of ribosomal genes with insertions of R2 retrotransposon (2022) · cites this paper as [19]
The Introduction (page unavailable) says that only 20–50% of rRNA genes are transcriptionally active in most human cells, supporting the point that some can be silent. It does not establish that silent genes occur specifically within active NORs, rather than elsewhere among the NORs. (LLM, conf=0.83)
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- Authors
- Kim, J.-H., Dilthey, A. T., Nagaraja, R., Lee, H.-S., Koren, S., Dudekula, D., Wood III, W. H., Piao, Y., Ogurtsov, A. Y., Utani, K., Noskov, V. N., Shabalina, S. A., Schlessinger, D., Phillippy, A. M., & Larionov, V.
- Affiliations
- National Cancer Institute (US)
- National Human Genome Research Institute (US)
- National Institute on Aging (US)
- National Institute on Aging, Laboratory of Genetics and Genomics, Baltimore, MD 21224, USA
- United States National Library of Medicine (US)
- Corresponding author
- Schlessinger, David
- Phillippy, Adam M
- Larionov, Vladimir
- ORCID
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-05-21
- Volume
- 46
- Issue
- 13
- Pages
- 6712-6725
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC6061828
- OpenAlex
- W2803553976
- Cited by
- 86
- References
- 73
- Citations by year
- 2026: 5 · 2025: 10 · 2024: 18 · 2023: 8 · 2022: 11 · 2021: 14 · 2020: 10 · 2019: 8 · 2018: 2
- FWCI
- 7.52
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- public-domain
- Locations
- Nucleic Acids Research (publishedVersion, public-domain)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- U.S. Department of Health and Human Services
- National Institutes of Health
- National Human Genome Research Institute
- National Cancer Institute
- U.S. National Library of Medicine
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- chromosome 21, ribosomal DNA, 45S rDNA, intergenic spacer, pre-rRNA, palindromic structure, ribosome heterogeneity, long-read sequencing
- MeSH terms
- Animals, Cell Line, Chromosomes, Human, Pair 21, Cloning, Molecular, DNA, Ribosomal, Humans, Nucleic Acid Conformation, Nucleolus Organizer Region, RNA, Ribosomal, Genetic Variation, Sequence Analysis, DNA, Genes, rRNA, DNA, Ribosomal Spacer, Mice
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