ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2019
Intragenomic heterogeneity of intergenic ribosomal DNA spacers in Cucurbita moschata is determined by DNA minisatellites with variable potential to form non-canonical DNA conformations.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed.
- G-quadruplex stabilization induces DNA breaks in pericentromeric repetitive DNA sequences in B lymphocytes.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- DDX41 resolves G-quadruplexes to maintain erythroid genome integrity and prevent cGAS-mediated cell death.Nature communications · 2025Article
- Does time matter? Intraspecific diversity of ribosomal RNA genes in lineages of the allopolyploid model grass Brachypodium hybridum with different evolutionary ages.BMC plant biology · 2024Article
- Transcriptional Silencing of 35S rDNA inInternational journal of molecular sciences · 2024Article
- The 'genetic zipper' method offers a cost-effective solution for aphid control.Frontiers in insect science · 2024Article
- Non-canonical DNA structures in the human ribosomal DNA.Histochemistry and cell biology · 2023Review
- Intragenomic rDNA variation - the product of concerted evolution, mutation, or something in between?Heredity · 2023Review
- The Divergence of Chromosome Structures and 45S Ribosomal DNA Organization inPlants (Basel, Switzerland) · 2022Article
- Challenges and Approaches to Genotyping Repetitive DNA.G3 (Bethesda, Md.) · 2020Article
- G4 Structures in Control of Replication and Transcription of rRNA Genes.Frontiers in plant science · 2020Article
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5 authors.
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Abstract
The intergenic spacer (IGS) of rDNA is frequently built of long blocks of tandem repeats. To estimate the intragenomic variability of such knotty regions, we employed PacBio sequencing of the Cucurbita moschata genome, in which thousands of rDNA copies are distributed across a number of loci. The rRNA coding regions are highly conserved, indicating intensive interlocus homogenization and/or high selection pressure. However, the IGS exhibits high intragenomic structural diversity. Two repeated blocks, R1 (300-1250 bp) and R2 (290-643 bp), account for most of the IGS variation. They exhibit minisatellite-like features built of multiple periodically spaced short GC-rich sequence motifs with the potential to adopt non-canonical DNA conformations, G-quadruplex-folded and left-handed Z-DNA. The mutual arrangement of these motifs can be used to classify IGS variants into five structural families. Subtle polymorphisms exist within each family due to a variable number of repeats, suggesting the coexistence of an enormous number of IGS variants. The substantial length and structural heterogeneity of IGS minisatellites suggests that the tempo of their divergence exceeds the tempo of the homogenization of rDNA arrays. As frequently occurring among plants, we hypothesize that their instability may influence transcription regulation and/or destabilize rDNA units, possibly spreading them across the genome.
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