scholarly journals Selective nucleolus organizer inactivation in Arabidopsis is a chromosome position-effect phenomenon

2016 ◽  
Vol 113 (47) ◽  
pp. 13426-13431 ◽  
Author(s):  
Gireesha Mohannath ◽  
Frederic Pontvianne ◽  
Craig S. Pikaard
Keyword(s):  
Position Effect ◽  
Nucleolus Organizer ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Chromosome 2 ◽  
Chromosome 4 ◽  
Base Pairs ◽  
Genomic Change ◽  
Nucleolus Organizer Regions ◽  
Chromosome Position

Nucleolus organizer regions (NORs) are chromosomal loci where hundreds of rRNA genes are clustered. Despite being nearly identical in sequence, specific rRNA genes are selected for silencing during development via choice mechanism(s) that remain unclear. In Arabidopsis thaliana, rRNA gene subtypes that are silenced during development were recently mapped to the NOR on chromosome 2, NOR2, whereas active rRNA genes map to NOR4, on chromosome 4. In a mutant line deficient for ATXR5 or ATXR6-dependent histone H3 lysine 27 (H3K27) monomethylation, we show that millions of base pairs of chromosome 4, including the telomere, TEL4N, and much of NOR4, have been converted to the corresponding sequences of chromosome 2. This genomic change places rRNA genes of NOR2, which are normally silenced, at the position on chromosome 4 where active rRNA genes are normally located. At their new location, NOR2-derived rRNA genes escape silencing, independent of the atxr mutations, indicating that selective rRNA gene silencing is chromosome 2-specific. The chromosome 2 position effect is not explained by the NOR2-associated telomere, TEL2N, which remains linked to the translocated NOR, implicating centromere-proximal sequences in silencing.

The nucleolus

2019 ◽  
pp. 147-152
Author(s):  
John C. Lucchesi
Keyword(s):  
Gene Silencing ◽  
Histone H1 ◽  
Nucleolus Organizer ◽  
Linker Histone ◽  
The Other ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Dna Repeats ◽  
Gene Arrays ◽  
Nucleolus Organizer Regions

The nucleolus forms at nucleolus organizer regions (NORs) that consist of clusters of repeated rRNA genes. Transcription of the rRNA genes and processing of the transcripts yields the three types of RNAs necessary for the biogenesis of ribosomes. Only subsets of the rRNA genes present in cells are transcribed. The linker histone H1 plays a specific role in the repression of inactive rRNA genes and in many of the other functions of the nucleolus. One of these functions is gene silencing—the nucleolus is surrounded by a zone of heterochromatin consisting of silenced rRNA gene arrays, DNA repeats that flank the centromeres and chromatin domains that include gene-poor, as well as silent, regions of the genome; any gene associating with this zone is subjected to repression. Other functions include the assembly of telomerase, the regulation of p53 stability and the synthesis of 5S and tRNAs whose genes form clusters in the nucleolus.

scholarly journals Targeted Enrichment of rRNA Gene Tandem Arrays for Ultra-Long Sequencing by Selective Restriction Endonuclease Digestion

2021 ◽  
Vol 12 ◽  
Author(s):  
Anastasia McKinlay ◽  
Dalen Fultz ◽  
Feng Wang ◽  
Craig S. Pikaard
Keyword(s):  
Ribosomal Rna ◽  
Reference Genome ◽  
Nucleolus Organizer ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Simple Method ◽  
Nucleolus Organizer Regions ◽  
Oxford Nanopore ◽  
Endonuclease Digestion ◽  
Targeted Enrichment

Large regions of nearly identical repeats, such as the 45S ribosomal RNA (rRNA) genes of Nucleolus Organizer Regions (NORs), can account for major gaps in sequenced genomes. To assemble these regions, ultra-long sequencing reads that span multiple repeats have the potential to reveal sets of repeats that collectively have sufficient sequence variation to unambiguously define that interval and recognize overlapping reads. Because individual repetitive loci typically represent a small proportion of the genome, methods to enrich for the regions of interest are desirable. Here we describe a simple method that achieves greater than tenfold enrichment of Arabidopsis thaliana 45S rRNA gene sequences among ultra-long Oxford Nanopore Technology sequencing reads. This method employs agarose-embedded genomic DNA that is subjected to restriction endonucleases digestion using a cocktail of enzymes predicted to be non-cutters of rRNA genes. Most of the genome is digested into small fragments that diffuse out of the agar plugs, whereas rRNA gene arrays are retained. In principle, the approach can also be adapted for sequencing other repetitive loci for which gaps exist in a reference genome.

The nucleolus organizer regions (Nor loci) of hexaploid wheat cultivars

1992 ◽  
Vol 43 (5) ◽  
pp. 889 ◽  
Author(s):  
CE May ◽  
R Appels
Keyword(s):  
Dna Sequences ◽  
Intergenic Spacer ◽  
Wheat Breeding ◽  
Nucleolus Organizer ◽  
Rrna Genes ◽  
F1 Hybrids ◽  
Dna Fragments ◽  
Wheat Cultivars ◽  
Nucleolus Organizer Regions ◽  
Spacer Dna

We have used the techniques of molecular genetics to analyse the nucleolus organizer regions (Nor loci) of a broad range of Australian, Chinese, and other hexaploid wheats (Triticum aestivum L. em Thell.). Genomic DNA was extracted from the leaves of 260 wheat cultivars, 94 different F1 hybrids, and from more than 800 F2 plants. Samples of the DNA were digested with the restriction enzyme TaqI and electrophoretically separated in agarose gels. The DNA fragments were then transferred to DNA filters by Southern blotting and assayed with the probe pTa250.4. This probe specifically detects the intergenic spacer DNA sequences which alternate with the ribosomal-RNA (rRNA) genes in highly repeated tandem arrays within the Nor loci. Analyses of the spacer DNA restriction fragments present in P, F1 and F2 plants show that allelic variants of the Nor loci can be distinguished by the existence of different lengths of spacer DNA fragments, different combinations of different length fragments, or differing amounts of the same length fragments. Eight alleles of the Nor-B1 locus on chromosome 1B (Nor-Bla to Nor-B1h) and 20 variants of the Nor-B2 locus on chromosome 6B (Nor-B2a to Nor-B2t) have been identified. The DNA fragments present in the different alleles are expressed in a co-dominant fashion to give phenotypic F2 ratios of 1 : 2 : 1 and 1 : 2 : 1 : 2 : 4 : 2 : 1 : 2 : 1, indicating segregation at one or two loci, respectively. With two exceptions, individual alleles segregated in a 1 : 1 ratio. On the basis of the presence of different combinations of Nor-B1 and Nor-B2 alleles, the wheat cultivars investigated were divided into 53 phenotypic groups. These groups clearly reflect the germplasm used in wheat breeding programs in different countries. Hybrid wheats could also be recognized and plants with new combinations of alleles were produced.

Two distant and precisely positioned domains promote transcription of Xenopus laevis rRNA genes: analysis with linker-scanning mutants

1986 ◽  
Vol 6 (12) ◽  
pp. 4585-4593
Author(s):  
J J Windle ◽  
B Sollner-Webb
Keyword(s):  
Xenopus Laevis ◽  
Promoter Activity ◽  
Promoter Sequence ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Unexpected Result ◽  
Base Pairs ◽  
S1 Nuclease ◽  
Transcriptional Initiation ◽  
Upstream Promoter

To examine the internal organization of the promoter of the Xenopus laevis rRNA gene, we constructed a series of linker-scanning mutants that traverse the rDNA initiation region. The mutant genes, which have 3 to 11 clustered base substitutions set within an otherwise unaltered rDNA promoter sequence, were injected into Xenopus oocyte nuclei, and their transcriptional capacity was assessed by S1 nuclease analysis of the resultant RNA. The data demonstrate that there are two essential promoter domains, the distal boundaries of which coincide with the promoter boundaries established previously by analysis of 5' and 3' deletion mutants. The upstream promoter domain is relatively small and extends from residues ca. -140 to -128. The downstream domain is considerably larger, encompassing residues ca. -36 to +10, and exactly corresponds in both size and position to the mammalian minimal promoter region. The Xenopus rDNA sequence between these two essential domains has a much smaller effect on the level of transcriptional initiation. In light of the fact that a large portion of this intervening region consists of a segment (residues -114 to -72) that is duplicated many times in the upstream spacer to form an rDNA enhancer sequence, it is noteworthy that a "-115/-77 linker scanner," in which virtually this entire segment is replaced by a polylinker sequence, has full promoter activity in the injected Xenopus borealis oocytes. Analysis of a parallel series of spacing change linker-scanning mutants revealed the unexpected result that the relative positions of the upstream and downstream promoter domains are very critical: all spacing alterations of more than 2 base pairs within this 100-base-pair region virtually abolish promoter activity. We conclude that the factors that bind to these two distant promoter domains must interact in a very precise stereospecific manner.

scholarly journals Two distant and precisely positioned domains promote transcription of Xenopus laevis rRNA genes: analysis with linker-scanning mutants.

1986 ◽  
Vol 6 (12) ◽  
pp. 4585-4593 ◽  
Author(s):  
J J Windle ◽  
B Sollner-Webb
Keyword(s):  
Xenopus Laevis ◽  
Promoter Activity ◽  
Promoter Sequence ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Unexpected Result ◽  
Base Pairs ◽  
S1 Nuclease ◽  
Transcriptional Initiation ◽  
Upstream Promoter

To examine the internal organization of the promoter of the Xenopus laevis rRNA gene, we constructed a series of linker-scanning mutants that traverse the rDNA initiation region. The mutant genes, which have 3 to 11 clustered base substitutions set within an otherwise unaltered rDNA promoter sequence, were injected into Xenopus oocyte nuclei, and their transcriptional capacity was assessed by S1 nuclease analysis of the resultant RNA. The data demonstrate that there are two essential promoter domains, the distal boundaries of which coincide with the promoter boundaries established previously by analysis of 5' and 3' deletion mutants. The upstream promoter domain is relatively small and extends from residues ca. -140 to -128. The downstream domain is considerably larger, encompassing residues ca. -36 to +10, and exactly corresponds in both size and position to the mammalian minimal promoter region. The Xenopus rDNA sequence between these two essential domains has a much smaller effect on the level of transcriptional initiation. In light of the fact that a large portion of this intervening region consists of a segment (residues -114 to -72) that is duplicated many times in the upstream spacer to form an rDNA enhancer sequence, it is noteworthy that a "-115/-77 linker scanner," in which virtually this entire segment is replaced by a polylinker sequence, has full promoter activity in the injected Xenopus borealis oocytes. Analysis of a parallel series of spacing change linker-scanning mutants revealed the unexpected result that the relative positions of the upstream and downstream promoter domains are very critical: all spacing alterations of more than 2 base pairs within this 100-base-pair region virtually abolish promoter activity. We conclude that the factors that bind to these two distant promoter domains must interact in a very precise stereospecific manner.

Karyotyping Melandrium album, a dioecious plant with heteromorphic sex chromosomes

Genome ◽  
1990 ◽  
Vol 33 (4) ◽  
pp. 556-562 ◽  
Author(s):  
D. D. Ciupercescu ◽  
J. Veuskens ◽  
A. Mouras ◽  
D. Ye ◽  
M. Briquet ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Sex Chromosomes ◽  
Nucleolus Organizer ◽  
Rrna Genes ◽  
Hybridization Technique ◽  
Metaphase Chromosomes ◽  
Nucleolus Organizer Regions ◽  
Melandrium Album ◽  
Group B

Mitotic metaphase chromosomes of Melandrium album obtained from root protoplasts were studied. Morphologically, the chromosomes were either metacentrics or submetacentrics. They were classified into three distinct groups: group A comprising six pairs of autosomal metacentrics, group B comprising five pairs of autosomal submetacentrics, and the sex chromosomes: X and Y. The X chromosome is a metacentric (r = 1.44), which accounts for more than 14% of the genome. The Y chromosome is a metacentric with, virtually, equal arms (r = 1.09) and accounts for 21% of the genome, being the largest of the complement. The Y:X ratio was 1.4. Ethidium bromide, caffeine, and vinblastine were used to obtain a better resolution and higher frequency of satellited chromosomes 7q and 9p. The proposed karyotype of M. album is 2n = 24, XX, s(7q;9p) for female and 2n = 24, XY, s(7q;9p) for male plants. Nucleolus organizer regions (NORs) were present at the telomeric sites of three chromosome pairs: 7q, 9p, and 10p. The NORs were polymorphic, particularly between the nonhomologous chromosomes. The in situ hybridization technique localized the rRNA genes on four chromosome pairs: 5p, 7q, 9p, and 10p. The discrepancy between the NORs and the hybridization signals was probably due to the fact that NORs were restricted only to transcriptionally active rRNA genes. It was concluded that for a complete description and characterization of rRNA genes, both NOR detection and in situ hybridization techniques, as complementary methods, should be employed.Key words: Melandrium album, karyotype, satellites, idiogram, nucleolus organizer regions, in situ hybridization.

scholarly journals The Control of Natural Variation in Cytosine Methylation in Arabidopsis

Genetics ◽  
2002 ◽  
Vol 162 (1) ◽  
pp. 355-363 ◽  
Author(s):  
Nicole C Riddle ◽  
Eric J Richards
Keyword(s):  
Copy Number ◽  
Natural Variation ◽  
Cytosine Methylation ◽  
Gene Copy Number ◽  
Nucleolus Organizer ◽  
Flowering Plant ◽  
Gene Copy ◽  
Rrna Gene ◽  
Nucleolus Organizer Regions ◽  
Plant Arabidopsis Thaliana

Abstract We explore the extent and sources of epigenetic variation in cytosine methylation in natural accessions of the flowering plant, Arabidopsis thaliana, by focusing on the methylation of the major rRNA gene repeats at the two nucleolus organizer regions (NOR). Our findings indicate that natural variation in NOR methylation results from a combination of genetic and epigenetic mechanisms. Genetic variation in rRNA gene copy number and trans-acting modifier loci account for some of the natural variation in NOR methylation. Our results also suggest that divergence and inheritance of epigenetic information, independent of changes in underlying nucleotide sequence, may play an important role in maintaining natural variation in cytosine methylation.

scholarly journals Chromosomal stasis in distinct families of marine Percomorpharia from South Atlantic

2017 ◽  
Vol 11 (2) ◽  
pp. 299-307 ◽  
Author(s):  
Fabilene Gomes Paim ◽  
Leandro Aragão da Hora Almeida ◽  
Paulo Roberto Antunes de Mello Affonso ◽  
Patrícia Elda Sobrinho-Scudeler ◽  
Claudio Oliveira ◽  
...  
Keyword(s):  
Nucleolus Organizer ◽  
Rrna Genes ◽  
Centromeric Heterochromatin ◽  
Single Pair ◽  
Nucleolus Organizer Regions ◽  
Chromosomal Data ◽  
Physical Barriers ◽  
5S Rrna Genes ◽  
Fish Group ◽  
Acrocentric Chromosomes

The weakness of physical barriers in the marine environment and the dispersal potential of fish populations have been invoked as explanations of the apparent karyotype stasis of marine Percomorpha, but several taxa remain poorly studied cytogenetically. To increase the chromosomal data in this fish group, we analyzed cytogenetically three widespread Atlantic species from distinct families: Chaetodipterusfaber Broussonet, 1782 (Ephippidae), Lutjanussynagris Linnaeus, 1758 (Lutjanidae) and Rypticusrandalli Courtenay, 1967 (Serranidae). The three species shared a karyotype composed of 2n=48 acrocentric chromosomes, single nucleolus organizer regions (NORs) and reduced amounts of centromeric heterochromatin. A single NOR-bearing pair was identified in all species by physical mapping of 18S rDNA while non-syntenic 5S rRNA genes were located at centromeric region of a single pair. The similar karyotypic macrostructure observed in unrelated groups of Percomorpharia reinforces the conservative karyoevolution of marine teleosteans. Nonetheless, the species could be differentiated based on the pair bearing ribosomal cistrons, revealing the importance of microstructural analyses in species with symmetric and stable karyotypes.

scholarly journals Karyotype structure and NOR activity in Brazilian Smilax Linnaeus, 1753 species (Smilacaceae)

2019 ◽  
Vol 13 (3) ◽  
pp. 245-263
Author(s):  
Daniel Pizzaia ◽  
Vanessa M. Oliveira-Maekawa ◽  
Aline R. Martins ◽  
Mateus Mondin ◽  
Margarida L. R. Aguiar-Perecin
Keyword(s):  
Silver Staining ◽  
Nucleolus Organizer ◽  
Raw Material ◽  
Chromosome 1 ◽  
Rrna Gene ◽  
Dioecious Species ◽  
Chromosomal Structure ◽  
Nucleolus Organizer Regions ◽  
Karyotype Structure ◽  
Secondary Constrictions

The genus Smilax Linnaeus, 1753 (Smilacaceae) is a large genus of dioecious plants distributed in tropical, subtropical and temperate regions. Some Smilax species have medicinal importance and their identification is important for the control of raw material used in the manufacture of phytotherapeutical products. The karyotypes of seven Brazilian Smilax species were investigated. Mitotic metaphases of roots from young plants were analysed in Feulgen-stained preparations. The karyotypes were asymmetric and modal with 2n = 2x = 32 chromosomes gradually decreasing in size. In S. goyazana A De Candolle & C De Candolle, 1878, a polyploid species, 2n = 4x = 64. In all the species, the large and medium-sized chromosomes were subtelocentric and submetacentric and the small chromosomes were submetacentric or metacentric. Their karyotypes were quite similar, with differences in the arm ratio of some chromosomes. S. fluminensis Steudel, 1841 differed from the other species by having a large metacentric chromosome 1. These findings suggest that evolution occurred without drastic changes in the chromosomal structure in the species analyzed. Terminal secondary constrictions were visualized on the short arm of some chromosomes, but they were detected only in one homologue of each pair. Due to the terminal location and the degree of chromosome condensation, secondary constrictions were not visualized in some species. The nucleolus organizer regions (NORs) were mapped by silver-staining and fluorescent in situ hybridization (FISH) in S. rufescens Grisebach, 1842 and S. fluminensis. Silver-staining and FISH signals were colocalized on the short arms of six chromosomes in S. rufescens and four chromosomes in S. fluminensis. In FISH preparations, one of the largest chromosomes had the secondary constrictions highly decondensed in some cells. This finding and the heteromorphism observed in Feulgen-stained chromosomes suggest that differential rRNA gene expression between homologous rDNA loci can occur in some cells, resulting in different degrees of ribosomal chromatin decondensation. The presence of a heteromorphic chromosome pair in S. rufescens, S. polyantha Grisebach, 1842 and S. goyazana suggests a chromosomal sex determination in these dioecious species.

Sign in / Sign up

Export Citation Format

Share Document