High and uneven levels of 45S rDNA site-number variation across wild populations of a diploid plant genus (Anacyclus, Asteraceae)

Tandemly repeated ribosomal DNA (rDNA) arrays are among the most evolutionary dynamic loci of eukaryotic genomes. The loci code for essential cellular components, yet exhibit extensive copy number (CN) variation within and between species. CN might be partly determined by the requirement of dosage balance between the 5S and 45S rDNA arrays. The arrays are nonhomologous, physically unlinked in mammals, and encode functionally interdependent RNA components of the ribosome. Here we show that the 5S and 45S rDNA arrays exhibit concerted CN variation (cCNV). Despite 5S and 45S rDNA elements residing on different chromosomes and lacking sequence similarity, cCNV between these loci is strong, evolutionarily conserved in humans and mice, and manifested across individual genotypes in natural populations and pedigrees. Finally, we observe that bisphenol A induces rapid and parallel modulation of 5S and 45S rDNA CN. Our observations reveal a novel mode of genome variation, indicate that natural selection contributed to the evolution and conservation of cCNV, and support the hypothesis that 5S CN is partly determined by the requirement of dosage balance with the 45S rDNA array. We suggest that human disease variation might be traced to disrupted rDNA dosage balance in the genome.

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Comparative chromosomal localization of 45S and 5S rDNAs and implications for genome evolution in Cucumis

Genome ◽

10.1139/gen-2015-0207 ◽

2016 ◽

Vol 59 (7) ◽

pp. 449-457 ◽

Cited By ~ 15

Author(s):

Zhen-Tao Zhang ◽

Shu-Qiong Yang ◽

Zi-Ang Li ◽

Yun-Xia Zhang ◽

Yun-Zhu Wang ◽

...

Keyword(s):

Chromosomal Localization ◽

5S Rdna ◽

Chromosome Analysis ◽

45S Rdna ◽

Evolutionary Patterns ◽

Site Number ◽

Rdna Sites ◽

Wild Accessions ◽

Ribosomal Dnas

Ribosomal DNAs are useful cytogenetic markers for chromosome analysis. Studies investigating site numbers and distributions of rDNAs have provided important information for elucidating genome organization and chromosomal relationships of many species by fluorescence in situ hybridization. But relevant studies are scarce for species of the genus Cucumis, especially in wild species. In the present study, FISH was conducted to investigate the organization of 45S and 5S rDNA among 20 Cucumis accessions, including cultivars and wild accessions. Our results showed that the number of 45S rDNA sites varied from one to five pairs in different accessions, and most of these sites are located at the terminal regions of chromosomes. Interestingly, up to five pairs of 45S rDNA sites were observed in C. sativus var. sativus, the species which has the lowest chromosome number, i.e., 2n = 14. Only one pair of 5S rDNA sites was detected in all accessions, except for C. heptadactylus, C. sp, and C. spp that had two pairs of 5S rDNA sites. The distributions of 5S rDNA sites showed more variation than 45S rDNA sites. The phylogenetic analysis in this study showed that 45S and 5S rDNA have contrasting evolutionary patterns. We find that 5S rDNA has a polyploidization-related tendency towards the terminal location from an interstitial location but maintains a conserved site number, whereas the 45S rDNA showed a trend of increasing site number but a relatively conserved location.

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rDNA site number polymorphism and NOR inactivation in natural populations ofAllium schoenoprasum

Genetica ◽

10.1007/bf01429221 ◽

1994 ◽

Vol 94 (1) ◽

pp. 67-71 ◽

Cited By ~ 14

Author(s):

M. A. Garrido ◽

M. Jamilena ◽

R. Lozano ◽

C. Ruiz Rejon ◽

M. Ruiz Rejon ◽

...

Keyword(s):

Natural Populations ◽

Rdna Site ◽

Site Number

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Physical localization of 45S rDNA in Cymbopogon and the analysis of differential distribution of rDNA in homologous chromosomes of Cymbopogon winterianus

PLoS ONE ◽

10.1371/journal.pone.0257115 ◽

2021 ◽

Vol 16 (11) ◽

pp. e0257115

Author(s):

Shivangi Thakur ◽

Upendra Kumar ◽

Rashmi Malik ◽

Darshana Bisht ◽

Priyanka Balyan ◽

...

Keyword(s):

Chromosome Pair ◽

Interspecific Variation ◽

Rdna Site ◽

45S Rdna ◽

Differential Distribution ◽

Homologous Chromosomes ◽

Lemon Grass ◽

Cymbopogon Flexuosus ◽

Cymbopogon Winterianus ◽

Aromatic Grasses

Cymbopogon, commonly known as lemon grass, is one of the most important aromatic grasses having therapeutic and medicinal values. FISH signals on somatic chromosome spreads off Cymbopogon species indicated the localization of 45S rDNA on the terminal region of short arms of a chromosome pair. A considerable interspecific variation in the intensity of 45S rDNA hybridization signals was observed in the cultivars of Cymbopogon winterianus and Cymbopogon flexuosus. Furthermore, in all the varieties of C. winterianus namely Bio-13, Manjari and Medini, a differential distribution of 45S rDNA was observed in a heterologous pair of chromosomes 1. The development of C. winterianus var. Manjari through gamma radiation may be responsible for breakage of fragile rDNA site from one of the chromosomes of this heterologous chromosome pair. While, in other two varieties of C. winterianus (Bio-13 and Medini), this variability may be because of evolutionary speciation due to natural cross among two species of Cymbopogon which was fixed through clonal propagation. However, in both the situations these changes were fixed by vegetative method of propagation which is general mode of reproduction in the case of C. winterianus.

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Genetic context and proliferation determine contrasting patterns of copy number amplification and loss for 5S and 45S ribosomal DNA arrays in cancer

10.1101/154120 ◽

2017 ◽

Cited By ~ 1

Author(s):

Meng Wang ◽

Bernardo Lemos

Keyword(s):

Copy Number Variation ◽

Ribosomal Dna ◽

Copy Number ◽

5S Rdna ◽

45S Rdna ◽

Rdna Array ◽

Number Variation ◽

Proliferating Cell ◽

Rdna Copy ◽

Rdna Copy Number

AbstractThe multicopy 45S ribosomal DNA (45S rDNA) array gives origin to the nucleolus, the first discovered nuclear organelle, site of Poll I 45S rRNA transcription and key regulator of cellular metabolism, DNA repair response, genome stability, and global epigenetic states. The multicopy 5S ribosomal DNA array (5S rDNA) is located on a separate chromosome, encodes the 5S rRNA transcribed by Pol III, and exhibits concerted copy number variation (cCNV) with the 45S rDNA array in human blood. Here we combined genomic data from >700 tumors and normal tissues to provide a portrait of ribosomal DNA variation in human tissues and cancers of diverse mutational signatures. We show that most cancers undergo coupled 5S rDNA array amplification and 45S rDNA loss, with abundant inter-individual variation in rDNA copy number of both arrays, and concerted modulation of 5S-45S copy number in some but not all tissues. Analysis of genetic context revealed associations between the presence of specific somatic alterations, such as P53 mutations in stomach and lung adenocarcinomas, and coupled 5S gain / 45S loss. Finally, we show that increased proliferation rates along cancer lineages can partially explain contrasting copy number changes in the 5S and 45S rDNA arrays. We suggest that 5S rDNA amplification facilitates increased ribosomal synthesis in cancer, whereas 45S rDNA loss emerges as a byproduct of transcription-replication conflict in highly proliferating tumor cells. Our results highlight the tissue- specificity of concerted copy number variation and uncover contrasting changes in 5S and 45S rDNA copy number along rapidly proliferating cell lineages.Lay SummaryThe 45S and 5S ribosomal DNA (rDNA) arrays contain hundreds of rDNA copies, with substantial variability across individuals and species. Although physically unlinked, both arrays exhibit concerted copy number variation. However, whether concerted copy number is universally observed across all tissues is unknown. It also remains unknown if rDNA copy number may vary in tissues and cancer lineages. Here we showed that most cancers undergo coupled 5S rDNA array amplification and 45S rDNA loss, and concerted 5S-45S copy number variation in some but not all tissues. The coupled 5S amplification and 45S loss is associated with the presence of certain somatic genetic variations, as well as increased cancerous cell proliferation rate. Our research highlights the tissue- specificity of concerted copy number variation and uncover contrasting changes in rDNA copy number along rapidly proliferating cell lineages. Our observations raise the prospects of using 5S and 45S ribosomal DNA states as indicators of cancer status and targets in new strategies for cancer therapy.

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Dosage compensation can buffer copy-number variation in wild yeast

eLife ◽

10.7554/elife.05462 ◽

2015 ◽

Vol 4 ◽

Cited By ~ 57

Author(s):

James Hose ◽

Chris Mun Yong ◽

Maria Sardi ◽

Zhishi Wang ◽

Michael A Newton ◽

...

Keyword(s):

Copy Number Variation ◽

Gene Amplification ◽

Dosage Compensation ◽

Copy Number ◽

Gene Dosage ◽

Phenotypic Evolution ◽

Wild Populations ◽

Causal Gene ◽

Wild Yeast ◽

Number Variation

Aneuploidy is linked to myriad diseases but also facilitates organismal evolution. It remains unclear how cells overcome the deleterious effects of aneuploidy until new phenotypes evolve. Although laboratory strains are extremely sensitive to aneuploidy, we show here that aneuploidy is common in wild yeast isolates, which show lower-than-expected expression at many amplified genes. We generated diploid strain panels in which cells carried two, three, or four copies of the affected chromosomes, to show that gene-dosage compensation functions at 10–30% of amplified genes. Genes subject to dosage compensation are under higher expression constraint in wild populations—but they show elevated rates of gene amplification, suggesting that copy-number variation is buffered at these genes. We find that aneuploidy provides a clear ecological advantage to oak strain YPS1009, by amplifying a causal gene that escapes dosage compensation. Our work presents a model in which dosage compensation buffers gene amplification through aneuploidy to provide a natural, but likely transient, route to rapid phenotypic evolution.

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Binding site number variation and high-affinity binding consensus of Myb-SANT-like transcription factor Adf-1 in Drosophilidae

Nucleic Acids Research ◽

10.1093/nar/gkq504 ◽

2010 ◽

Vol 38 (19) ◽

pp. 6404-6417 ◽

Cited By ~ 4

Author(s):

Michael Lang ◽

Elvira Juan

Keyword(s):

Transcription Factor ◽

Binding Site ◽

Affinity Binding ◽

High Affinity Binding ◽

High Affinity ◽

Site Number ◽

Number Variation

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Physical localization of 45S rDNA in Cymbopogon and the analysis of differential distribution of rDNA in homologous chromosomes of Cymbopogon winterianus

10.1101/2021.08.25.457632 ◽

2021 ◽

Author(s):

Shivangi Thakur ◽

Upendra Kumar ◽

Rashmi Malik ◽

Darshana Bisht ◽

Priyanka Balyan ◽

...

Keyword(s):

Chromosome Pair ◽

Interspecific Variation ◽

Chromosome 1 ◽

Rdna Site ◽

45S Rdna ◽

Differential Distribution ◽

Homologous Chromosomes ◽

Cymbopogon Flexuosus ◽

Cymbopogon Winterianus ◽

Aromatic Grasses

AbstractCymbopogon, commonly known as lemon grass, is one of the most important aromatic grasses having therapeutic and medicinal values. FISH signals on somatic chromosome spreads off Cymbopogon species indicated the localization of 45S rDNA on the terminal region of short arms of a chromosome pair. A considerable interspecific variation in the intensity of 45S rDNA hybridization signals was observed in the cultivars of Cymbopogon winterianus and Cymbopogon flexuosus. Furthermore, in all the varieties of Cymbopogon winterianus namely Bio-13, Manjari and Medini, a differential distribution of 45S rDNA was observed in a heterologous pair of chromosome 1. The development of Cymbopogon winterianus var. Manjari through gamma radiation may be responsible for breakage of fragile rDNA site from one of the chromosomes of this heterologous chromosome pair. While, in other two varieties of Cymbopogon winterianus (Bio-13 and Medini), this variability may be because of evolutionary speciation due to natural cross among two species of Cymbopogon which was fixed through clonal propagation. However, in both the situations these changes were fixed by vegetative method of propagation which is general mode of reproduction in the case of Cymbopogon winterianus.

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Molecular Cytogenetic Analysis of Cucumis Wild Species Distributed in Southern Africa: Physical Mapping of 5S and 45S rDNA with DAPI

Cytogenetic and Genome Research ◽

10.1159/000433572 ◽

2015 ◽

Vol 146 (1) ◽

pp. 80-87 ◽

Cited By ~ 6

Author(s):

Kouhei Yagi ◽

Magdalena Pawełkowicz ◽

Paweł Osipowski ◽

Ewa Siedlecka ◽

Zbigniew Przybecki ◽

...

Keyword(s):

Cytogenetic Analysis ◽

Chromosomal Rearrangements ◽

Evolutionary Relationship ◽

Chromosomal Evolution ◽

Rdna Site ◽

45S Rdna ◽

Polyploid Evolution ◽

Molecular Cytogenetic ◽

Rdna Sites ◽

Cucumis Species

Wild Cucumis species have been divided into Australian/Asian and African groups using morphological and phylogenetic characteristics, and new species have been described recently. No molecular cytogenetic information is available for most of these species. The crossability between 5 southern African Cucumis species (C. africanus, C. anguria, C. myriocarpus, C. zeyheri, and C. heptadactylus) has been reported; however, the evolutionary relationship among them is still unclear. Here, a molecular cytogenetic analysis using FISH with 5S and 45S ribosomal DNA (rDNA) was used to investigate these Cucumis species based on sets of rDNA-bearing chromosomes (rch) types I, II and III. The molecular cytogenetic and phylogenetic results suggested that at least 2 steps of chromosomal rearrangements may have occurred during the evolution of tetraploid C. heptadactylus. In step 1, an additional 45S rDNA site was observed in the chromosome (type III). In particular, C. myriocarpus had a variety of rch sets. Our results suggest that chromosomal rearrangements may have occurred in the 45S rDNA sites. We propose that polyploid evolution occurred in step 2. This study provides insights into the chromosomal characteristics of African Cucumis species and contributes to the understanding of chromosomal evolution in this genus.

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