Molecular analysis of a NOR site polymorphism in brown trout (Salmo trutta): organization of rDNA intergenic spacers

Genome ◽  
1997 ◽  
Vol 40 (6) ◽  
pp. 916-922 ◽  
Author(s):  
Jaime Castro ◽  
Laura Sánchez ◽  
Paulino Martínez ◽  
Stefania De Lucchini ◽  
Irma Nardi
Keyword(s):  
Salmo Trutta ◽  
Organizer Region ◽  
Nucleolar Organizer Region ◽  
Nucleolar Organizer ◽  
Initial Step ◽  
Molecular Organization ◽  
Rrna Genes ◽  
28S Rrna ◽  
Intergenic Spacers ◽  
Brown Trout Salmo Trutta

Using restriction endonuclease mapping, we have analyzed the organization of rDNA (DNA coding for ribosomal RNA (rRNA)) units in the salmonid fish Salmo trutta, as an initial step toward understand the molecular basis of a nucleolar organizer region (NOR) site polymorphism detected in this species. The size of the rDNA units ranged between 15 and 23 kb, with remarkable variation both within individuals and between populations. Three regions of internal tandem repetitiveness responsible for this length polymorphism were located to the intergenic spacers. NOR site polymorphic individuals showed a higher number of length classes, in some cases forming a complete 1 kb fragment ladder. The amount of rRNA genes was as much as 8-fold higher in polymorphic individuals compared with standard individuals. All individuals from the most polymorphic population showed a 14-kb insertion of unknown nature in a small proportion (below 25%) of the 28S rRNA genes.Key words: rRNA genes, repetitive elements, molecular organization, rDNA amount.

scholarly journals Personal Perspectives on Plant Ribosomal RNA Genes Research: From Precursor-rRNA to Molecular Evolution

2021 ◽  
Vol 12 ◽  
Author(s):  
Vera Hemleben ◽  
Donald Grierson ◽  
Nikolai Borisjuk ◽  
Roman A. Volkov ◽  
Ales Kovarik
Keyword(s):  
Organizer Region ◽  
Nucleolar Organizer Region ◽  
Light And Electron Microscopy ◽  
Scientific Progress ◽  
5S Rdna ◽  
Molecular Organization ◽  
Rrna Genes ◽  
Detailed Knowledge ◽  
And Function ◽  
The Impact

The history of rDNA research started almost 90 years ago when the geneticist, Barbara McClintock observed that in interphase nuclei of maize the nucleolus was formed in association with a specific region normally located near the end of a chromosome, which she called the nucleolar organizer region (NOR). Cytologists in the twentieth century recognized the nucleolus as a common structure in all eukaryotic cells, using both light and electron microscopy and biochemical and genetic studies identified ribosomes as the subcellular sites of protein synthesis. In the mid- to late 1960s, the synthesis of nuclear-encoded rRNA was the only system in multicellular organisms where transcripts of known function could be isolated, and their synthesis and processing could be studied. Cytogenetic observations of NOR regions with altered structure in plant interspecific hybrids and detailed knowledge of structure and function of rDNA were prerequisites for studies of nucleolar dominance, epistatic interactions of rDNA loci, and epigenetic silencing. In this article, we focus on the early rDNA research in plants, performed mainly at the dawn of molecular biology in the 60 to 80-ties of the last century which presented a prequel to the modern genomic era. We discuss – from a personal view – the topics such as synthesis of rRNA precursor (35S pre-rRNA in plants), processing, and the organization of 35S and 5S rDNA. Cloning and sequencing led to the observation that the transcribed and processed regions of the rRNA genes vary enormously, even between populations and species, in comparison with the more conserved regions coding for the mature rRNAs. Epigenetic phenomena and the impact of hybridization and allopolyploidy on rDNA expression and homogenization are discussed. This historical view of scientific progress and achievements sets the scene for the other articles highlighting the immense progress in rDNA research published in this special issue of Frontiers in Plant Science on “Molecular organization, evolution, and function of ribosomal DNA.”

RIBOSOMAL GENE LOCALIZATION AND DISTRIBUTION (ARRANGEMENT) WITHIN THE NUCLEOLAR ORGANIZER REGION OF ZEA MAYS

Genetics ◽  
1975 ◽  
Vol 80 (3) ◽  
pp. 505-518
Author(s):  
Samuel A Ramirez ◽  
John H Sinclair
Keyword(s):  
Zea Mays ◽  
Organizer Region ◽  
Nucleolar Organizer Region ◽  
Nucleolar Organizer ◽  
B Chromosome ◽  
Ribosomal Gene ◽  
Ribosomal Genes ◽  
Rrna Genes ◽  
Gene Localization ◽  
Chromosome 6

ABSTRACT Cytogenetic and molecular hybridization techniques were used to examine the arrangement of rRNA genes at the nucleolar organizer region (NOR) of maize. TB-6a stocks involving a reciprocal translocation between a B chromosome and the NOR of chromosome 6 were used. The amount of rDNA in the different stocks used varied from 1.5 to 4 NOR equivalents depending on the number of B6 choromosomes present. Cytological measurements show that the medial break through the NOR results in an equal partitioning of the heterochromatic knob (the NOR) between chromosome 6 and the B chromosome to which it was translocated. DNA-rRNA hybridization experiments show a linear relationship between the amount of rRNA capable of hybridizing with DNA and the number of NOR equivalents present. The data confirm McClintock's conclusion that the heterochromatic knob, rather than the constricted portion, is the true NOR region. Further, they show that the number of ribosomal genes is correlated with the amount of cytologically visible NOR, suggesting a uniform distribution of genes throughout the locus.

Quantitative analysis of the variability of nucleolar organizer regions in Salmo trutta

Genome ◽  
1993 ◽  
Vol 36 (6) ◽  
pp. 1119-1123 ◽  
Author(s):  
P. Martínez ◽  
A. Viñas ◽  
C. Bouza ◽  
J. Castro ◽  
L. Sánchez
Keyword(s):  
Quantitative Analysis ◽  
Salmo Trutta ◽  
Chromosome Region ◽  
Organizer Region ◽  
Nucleolar Organizer Region ◽  
Size Variation ◽  
Nucleolar Organizer ◽  
Chromosome Length ◽  
Nucleolar Organizer Regions ◽  
Structural Polymorphism

A quantitative analysis combined with Ag staining was carried out to study the size variation of the main nucleolar organizer region (NOR) bearing chromosome pair 11 of Salmo trutta. A standardized NOR size measurement was developed by comparing the length of the short arm (NOR-bearing region) to the total chromosome length. Statistical procedures support arguments for the existence of a large and structural polymorphism within this species for this chromosome region. A minimum of five different chromosome classes were identified, which account for the total variation found. Size variation among classes was due both to changes in the number of NOR clusters as well as to the amount of rDNA genes within each cluster. NOR size values were normally distributed in the sample analyzed.Key words: nucleolar organizer region, size polymorphism, brown trout.

scholarly journals The number and location of genes for 5S ribonucleic acid within the genome of Drosophila melanogaster

1971 ◽  
Vol 123 (2) ◽  
pp. 227-233 ◽  
Author(s):  
R. V. Quincey
Keyword(s):  
Drosophila Melanogaster ◽  
Ribonucleic Acid ◽  
Organizer Region ◽  
Nucleolar Organizer Region ◽  
Nucleolar Organizer ◽  
Haploid Genome ◽  
28S Rrna ◽  
Wild Type ◽  
5S Rna ◽  
Type D

DNA was prepared from wild-type and two mutant stocks of Drosophila melanogaster that differed in their dosage of the nucleolar organizer region. The relative amounts of DNA from the nucleolar organizer region in these preparations of DNA were determined by hybridization with 3H-labelled 28S rRNA. As expected, the amount of 3H-labelled 28S rRNA that hybridized was directly related to the dosage of nucleolar organizer region. No positive correlation was observed between the amount of 3H-labelled 5S RNA that hybridized and the dosage of nucleolar organizer region. Thus genes for 5S RNA are located primarily, if not exclusively, outside the nucleolar organizer region. The haploid genome of the wild-type D. melanogaster used in this work has 106 genes for 28S rRNA and 96–105 genes for 5S RNA.

A NOR-associated repetitive element present in the genome of two Salmo species (salmo salar and Salmo trutta)

Genome ◽  
1996 ◽  
Vol 39 (4) ◽  
pp. 671-679 ◽  
Author(s):  
M. Abuín ◽  
P. Martínez ◽  
L. Sánchez ◽  
C. Clabby ◽  
F. Flavin ◽  
...  
Keyword(s):  
Atlantic Salmon ◽  
Cell Line ◽  
Salmo Salar ◽  
Brown Trout ◽  
Salmo Trutta ◽  
Repetitive Element ◽  
Organizer Region ◽  
Nucleolar Organizer Region ◽  
Nucleolar Organizer ◽  
Nucleotide Sequence Analysis

A repetitive element was isolated from the genome of Atlantic salmon. Nucleotide sequence analysis revealed the existence of variant monomers that range in length from approximately 200 to 230 bp. Repeat monomers contain regions of cryptic simplicity, internal repetition, and long direct repeats with deletions and insertions between individual units. The repetitive element was shown to have a tandem unit arrangement and was estimated to occupy between two and three percent of the Atlantic salmon genome. Southern blot analysis revealed the repetitive element to be unique to Atlantic salmon and brown trout species. In situ hybridization analysis showed this element to be localized at the main nucleolar organizer region bearing chromosomes of Atlantic salmon (Salmo salar), AS cell line (derived from S. salar), and brown trout (Salmo trutta). Key words : Atlantic salmon, brown trout, AS cell line, repeat DNA, NOR.

scholarly journals Comparative FISH analysis of Senna tora tandem repeats revealed insights into the chromosome dynamics in Senna

2021 ◽  
Vol 43 (3) ◽  
pp. 237-249 ◽  
Author(s):  
Thanh Dat Ta ◽  
Nomar Espinosa Waminal ◽  
Thi Hong Nguyen ◽  
Remnyl Joyce Pellerin ◽  
Hyun Hee Kim
Keyword(s):  
Tandem Repeats ◽  
Chromosomal Rearrangements ◽  
Organizer Region ◽  
Nucleolar Organizer Region ◽  
Nucleolar Organizer ◽  
Pericentromeric Region ◽  
Its2 Sequence ◽  
Fish Analysis ◽  
Chromosomal Distribution ◽  
Chromosome Dynamics

Abstract Background DNA tandem repeats (TRs) are often abundant and occupy discrete regions in eukaryotic genomes. These TRs often cause or generate chromosomal rearrangements, which, in turn, drive chromosome evolution and speciation. Tracing the chromosomal distribution of TRs could therefore provide insights into the chromosome dynamics and speciation among closely related taxa. The basic chromosome number in the genus Senna is 2n = 28, but dysploid species like Senna tora have also been observed. Objective To understand the dynamics of these TRs and their impact on S. tora dysploidization. Methods We performed a comparative fluorescence in situ hybridization (FISH) analysis among nine closely related Senna species and compared the chromosomal distribution of these repeats from a cytotaxonomic perspective by using the ITS1-5.8S-ITS2 sequence to infer phylogenetic relationships. Results Of the nine S. tora TRs, two did not show any FISH signal whereas seven TRs showed similar and contrasting patterns to other Senna species. StoTR01_86, which was localized in the pericentromeric regions in all S. tora, but not at the nucleolar organizer region (NOR) site, was colocalized at the NOR site in all species except in S. siamea. StoTR02_7_tel was mostly localized at chromosome termini, but some species had an interstitial telomeric repeat in a few chromosomes. StoTR05_180 was distributed in the subtelomeric region in most species and was highly amplified in the pericentromeric region in some species. StoTR06_159 was either absent or colocalized in the NOR site in some species, and StoIGS_463, which was localized at the NOR site in S. tora, was either absent or localized at the subtelomeric or pericentromeric regions in other species. Conclusions These data suggest that TRs play important roles in S. tora dysploidy and suggest the involvement of 45S rDNA intergenic spacers in “carrying” repeats during genome reshuffling.

scholarly journals The genomic structure of a human chromosome 22 nucleolar organizer region determined by TAR cloning

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jung-Hyun Kim ◽  
Vladimir N. Noskov ◽  
Aleksey Y. Ogurtsov ◽  
Ramaiah Nagaraja ◽  
Nikolai Petrov ◽  
...  
Keyword(s):  
Genomic Structure ◽  
Organizer Region ◽  
Nucleolar Organizer Region ◽  
Nucleolar Organizer ◽  
Chromosome 21 ◽  
Reference Sequence ◽  
Chromosome 22 ◽  
Rdna Variation ◽  
High Level ◽  
Tar Cloning

AbstractThe rDNA clusters and flanking sequences on human chromosomes 13, 14, 15, 21 and 22 represent large gaps in the current genomic assembly. The organization and the degree of divergence of the human rDNA units within an individual nucleolar organizer region (NOR) are only partially known. To address this lacuna, we previously applied transformation-associated recombination (TAR) cloning to isolate individual rDNA units from chromosome 21. That approach revealed an unexpectedly high level of heterogeneity in human rDNA, raising the possibility of corresponding variations in ribosome dynamics. We have now applied the same strategy to analyze an entire rDNA array end-to-end from a copy of chromosome 22. Sequencing of TAR isolates provided the entire NOR sequence, including proximal and distal junctions that may be involved in nucleolar function. Comparison of the newly sequenced rDNAs to reference sequence for chromosomes 22 and 21 revealed variants that are shared in human rDNA in individuals from different ethnic groups, many of them at high frequency. Analysis infers comparable intra- and inter-individual divergence of rDNA units on the same and different chromosomes, supporting the concerted evolution of rDNA units. The results provide a route to investigate further the role of rDNA variation in nucleolar formation and in the empirical associations of nucleoli with pathology.

Nucleolar organizer region staining patterns in paraffin-embedded tissue cells from human skin cancers

2005 ◽  
Vol 32 (5) ◽  
pp. 323-328 ◽  
Author(s):  
Rosana F. Romao-Correa ◽  
Durvanei A. Maria ◽  
Mithitaka Soma ◽  
Mirian N. Sotto ◽  
Jose Antonio Sanches ◽  
...  
Keyword(s):  
Human Skin ◽  
Organizer Region ◽  
Nucleolar Organizer Region ◽  
Nucleolar Organizer ◽  
Skin Cancers ◽  
Tissue Cells
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