Plant 5S rDNA has multiple alternative nucleosome positions

Genome ◽  
2006 ◽  
Vol 49 (7) ◽  
pp. 840-850 ◽  
Author(s):  
Jaroslav Fulnecek ◽  
Roman Matyasek ◽  
Ales Kovarik
Keyword(s):  
Tandem Repeats ◽  
5S Rdna ◽  
Nicotiana Sylvestris ◽  
Micrococcal Nuclease ◽  
Dna Curvature ◽  
Cleavage Sites ◽  
Computer Prediction ◽  
Theoretical Computer ◽  
Nontranscribed Spacer ◽  
Multiple Alternative

In plants, 5S ribosomal DNA (5S rDNA) is typically found in hundreds of copies of tandemly arranged units. Nucleotide database searches revealed that the majority of 5S genes (>90%) have repeat lengths that are not simple multiples of a plant nucleosomal unit, ranging in plants from 175–185 bp. To get insight into the chromatin structure, we have determined positions of nucleosomes in the Nicotiana sylvestris and Nicotiana tomentosiformis 5S rDNA units with repeat lengths of about 430 and 645 bp, respectively. Mapping experiments carried out on isolated nucleo somal DNA revealed many (>50) micrococcal nuclease cleavage sites in each class of repeats. Permutation analysis and theoretical computer prediction showed multiple DNA bend sites, mostly located in the nontranscribed spacer region. The distance between bend sites, however, did not correspond to the average spacing of nucleosomes in 5S chromatin (~180 bp). These data indicate that 5S rDNA does not have fixed nucleosomal positioning sites and that units can be wrapped in a number of alternative nucleosome frames. Consequently, accessibility of transcription factors to cognate motifs might vary across the tandem array, potentially influencing gene expression.Key words: Nicotiana, 5S rDNA, heterochromatin, tandem repeats, nucleosomes, DNA curvature.

The 5S rDNA units in Kengyilia (Poaceae: Triticeae): diversity of the nontranscribed spacer and genomic relationships

2000 ◽  
Vol 78 (12) ◽  
pp. 1571-1579 ◽  
Author(s):  
Bernard R Baum ◽  
L Grant Bailey
Keyword(s):  
Concerted Evolution ◽  
Low Frequency ◽  
Pcr Amplification ◽  
5S Rdna ◽  
Nontranscribed Spacer ◽  
Unit Classes ◽  
Unit Class ◽  
5S Dna ◽  
Genomic Relationships ◽  
Single Clone

The sequences of eighty 5S rDNA clones were obtained by polymerase chain reaction (PCR) amplification of DNA from 12 accessions representing eight species of Kengyilia. Orthologous sequences were grouped into five unit classes: long P1, long S1, long {Y1, short P1, and short S1. Both the long P1 and long S1 classes are prevalent in Kengyilia, whereas the rest are rare. The short S1 class has not been described previously in other Kengyilia species. Two clones represent the long {Y1 class, with only one clone reported previously in Kengyilia alatavica (Drobow) J.L. Yang, Yen & Baum and a single clone found in this investigation. The long H1 unit class reported earlier for Kengyilia rigidula (Keng and S.L. Chen) J.L. Yang, Yen & Baum, but not for K. alatavica, was not found in any of the eight species investigated. Therefore, its presence in K. rigidula may be the result of introgression from Elymus nutans Grisebach, an HS-genome species containing the long H1 unit class; the two are often found growing together and are known to yield sterile hybrids in those populations. The specific 5S DNA unit classes, except for the ones that were found in very low frequency and in few samples, may have a potential not only as markers for the identification of haplomes but also of hybrids containing a combination of genomes. This investigation indicated, along with previous studies, that the 5S unit classes either form integral parts of haplomes or remain conserved and identifiable within haplomes originating from distant species, indicating that concerted evolution in the 5S gene plays only a partial role as an evolutionary force.Key words: 5S DNA gene, molecular diversity, Kengyilia, Triticeae, concerted evolution.

Organization of the 5S rRNA genes in the soybean Glycine max (L.) Merrill and conservation of the 5S rDNA repeat structure in higher plants

Genome ◽  
1990 ◽  
Vol 33 (4) ◽  
pp. 486-494 ◽  
Author(s):  
S. G. Gottlob-McHugh ◽  
M. Lévesque ◽  
K. MacKenzie ◽  
M. Olson ◽  
O. Yarosh ◽  
...  
Keyword(s):  
Glycine Max ◽  
Tandem Repeats ◽  
Higher Plants ◽  
5S Rdna ◽  
Rdna Sequence ◽  
5S Rrna ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Glycine Max L ◽  
5S Rdna Sequence

The 5S rRNA gene of the soybean Glycine max (L.) Merr. has been cloned on a 556-bp fragment of DNA and sequenced. This fragment contains two copies of the soybean 5S rDNA sequence, one intact and one truncated, separated by noncoding DNA. We have used this clone to investigate the organization of the 5S genes within the soybean genome and the extent of their methylation. Our results demonstrate that soybean 5S genes are clustered, organized into tandem repeats of 330 bp, and extensively methylated. Hybridization of the 5S sequence to Southern transfers of soybean DNA digested with BamHI reveals a striking ladderlike pattern. Hybridization of the soybean 5S sequence to a wide variety of plant DNAs results in similar patterns, suggesting that the 5S rDNA sequence, gene organization, and methylation pattern are conserved in many higher plants.Key words: 5S rDNA, sequence, methylation, soybean, repeat conservation.

A thermal denaturation study of chromatin and nuclease-produced chromatin fragments

1977 ◽  
Vol 55 (7) ◽  
pp. 736-746 ◽  
Author(s):  
Peter N. Lewis
Keyword(s):  
Thermal Denaturation ◽  
Micrococcal Nuclease ◽  
Melting Transition ◽  
Cleavage Sites ◽  
Main Determinant ◽  
Calf Thymus ◽  
Sulfhydryl Oxidation ◽  
Thermal Denaturation Study ◽  
Lower Temperature ◽  
Mechanical Shearing

Calf thymus chromatin and nuclease-produced chromatin fragments have been examined by thermal denaturation measurements. Native chromatin gave a series of distinct melting transitions at 64, 73, 79, and 85 °C in 0.25 mM EDTA pH 8. Treatments such as dialysis, mechanical shearing, or sulfhydryl oxidation of histone H3 carried out on native chromatin significantly altered the derivative melting profiles by blurring the distinct transitions and shifting the highest melting transition to a lower temperature. Derivative melting profiles for electrophoretically purified chromatin fragments, monomer through hexamer, all resembled that obtained from dialyzed chromatin. These results suggest that higher order structures exist in chromatin that are easily disrupted. Since the products of micrococcal nuclease (EC 3.1.4.7) digestion of the altered chromatins did not exhibit any major electrophoretic differences from those obtained from nuclei, then most likely the primary arrangements of histones along the DNA are the main determinant for cleavage sites.

scholarly journals Characterizing the Celery Genome with DNA-based Genetic Markers

1995 ◽  
Vol 120 (5) ◽  
pp. 747-751 ◽  
Author(s):  
Xiaofeng Yang ◽  
Carlos F. Quiros
Keyword(s):  
Rapd Markers ◽  
Tandem Repeats ◽  
Southern Hybridization ◽  
5S Rdna ◽  
Positive Association ◽  
Restriction Enzymes ◽  
Apium Graveolens ◽  
Base Substitution ◽  
Rflp Markers ◽  
Cdna Clones

To characterize the celery (Apium graveolens L. var. dulce, 2n = 2x = 22) genome, 126 celery cDNA clones and 340 random 10-mer primers were used to generate restriction fragment-length polymorphism (RFLP) and randomly amplified polymorphic DNA (RAPD) markers between two cultivated types. Different abundance classes of the genomic sequences represented by the cDNA clones and the RAPD markers were observed. Most of the cDNA clones were single-copy sequences, suggesting the true diploid nature of the celery genome. Nearly half of the 39 RAPD markers tested by Southern hybridization were multiple-copy sequences. Of the RAPD markers tested, 28% was single- and low-copy, and 26% was high-copy sequences. The polymorphism level of the cDNA clones was 23% when tested with four restriction enzymes (Eco RI, Eco RV, Hin dIII, and Hae III). A positive association was observed between RFLP level and the size of cDNA inserts or hybridized restriction fragments. Deletion, insertion, and base substitution were important in the formation of the RFLP markers. Eighty-two (23%) of the 340 primers tested yielded useful RAPD markers, but only 3.8% of the amplified products were polymorphic. Base substitution may be the most important mechanism for the RAPD markers in celery. The RAPD fragments revealed no RFLP markers when tested by Southern hybridization, implying that RAPD markers are an important complement to RFLP markers in genomic mapping in celery. Random methylation of cytosine was determined in 5S rDNA on Bam HI and Hin dIII cutting sites that produced ladder patterns characteristic of tandem repeats.

scholarly journals Mosaic Arrangement of the 5S rDNA in the Aquatic Plant Landoltia punctata (Lemnaceae)

2021 ◽  
Vol 12 ◽  
Author(s):  
Guimin Chen ◽  
Anton Stepanenko ◽  
Nikolai Borisjuk
Keyword(s):  
5S Rdna ◽  
Class Ii ◽  
Class I ◽  
Length Variation ◽  
Wastewater Remediation ◽  
Nontranscribed Spacer ◽  
Pharmaceutical Proteins ◽  
G Quadruplex ◽  
Molecular Forces ◽  
Nucleotide Repeats

Duckweeds are a group of monocotyledonous aquatic plants in the Araceae superfamily, represented by 37 species divided into five genera. Duckweeds are the fastest growing flowering plants and are distributed around the globe; moreover, these plants have multiple applications, including biomass production, wastewater remediation, and making pharmaceutical proteins. Dotted duckweed (Landoltia punctata), the sole species in genus Landoltia, is one of the most resilient duckweed species. The ribosomal DNA (rDNA) encodes the RNA components of ribosomes and represents a significant part of plant genomes but has not been comprehensively studied in duckweeds. Here, we characterized the 5S rDNA genes in L. punctata by cloning and sequencing 25 PCR fragments containing the 5S rDNA repeats. No length variation was detected in the 5S rDNA gene sequence, whereas the nontranscribed spacer (NTS) varied from 151 to 524 bp. The NTS variants were grouped into two major classes, which differed both in nucleotide sequence and the type and arrangement of the spacer subrepeats. The dominant class I NTS, with a characteristic 12-bp TC-rich sequence present in 3–18 copies, was classified into four subclasses, whereas the minor class II NTS, with shorter, 9-bp nucleotide repeats, was represented by two identical sequences. In addition to these diverse subrepeats, class I and class II NTSs differed in their representation of cis-elements and the patterns of predicted G-quadruplex structures, which may influence the transcription of the 5S rDNA. Similar to related duckweed species in the genus Spirodela, L. punctata has a relatively low rDNA copy number, but in contrast to Spirodela and the majority of other plants, the arrangement of the 5S rDNA units demonstrated an unusual, heterogeneous pattern in L. punctata, as revealed by analyzing clones containing double 5S rDNA neighboring units. Our findings may further stimulate the research on the evolution of the plant rDNA and discussion of the molecular forces driving homogenization of rDNA repeats in concerted evolution.

scholarly journals Molecular Karyotyping on Populus simonii × P. nigra and the Derived Doubled Haploid

2021 ◽  
Vol 22 (21) ◽  
pp. 11424
Author(s):  
Bo Liu ◽  
Sui Wang ◽  
Xiaoyan Tao ◽  
Caixia Liu ◽  
Guanzheng Qu ◽  
...  
Keyword(s):  
Doubled Haploid ◽  
Tandem Repeats ◽  
Doubled Haploids ◽  
Repetitive Sequences ◽  
5S Rdna ◽  
Molecular Karyotyping ◽  
Populus Simonii ◽  
Homologous Chromosomes ◽  
Significant Difference ◽  
Molecular Karyotype

The molecular karyotype could represent the basic genetic make-up in a cell nucleus of an organism or species. A doubled haploid (DH) is a genotype formed from the chromosome doubling of haploid cells. In the present study, molecular karyotype analysis of the poplar hybrid Populus simonii × P. nigra (P. xiaohei) and the derived doubled haploids was carried out with labeled telomeres, rDNA, and two newly repetitive sequences as probes by fluorescence in situ hybridization (FISH). The tandem repeats, pPC349_XHY and pPD284_XHY, with high-sequence homology were used, and the results showed that they presented the colocalized distribution signal in chromosomes. For P. xiaohei, pPD284_XHY produced hybridizations in chromosomes 1, 5, 8, and 9 in the hybrid. The combination of pPD284_XHY, 45S rDNA, and 5S rDNA distinctly distinguished six pairs of chromosomes, and the three pairs of chromosomes showed a significant difference in the hybridization between homologous chromosomes. The repeat probes used produced similar FISH hybridizations in the DH; nevertheless, pPD284_XHY generated an additional hybridization site in the telomere region of chromosome 14. Moreover, two pairs of chromosomes showed differential hybridization distributions between homologous chromosomes. Comparisons of the distinguished chromosomes between hybrid and DH poplar showed that three pairs of chromosomes in the DH presented hybridization patterns that varied from those of the hybrid. The No. 8 chromosome in DH and one of the homologous chromosomes in P. xiaohei shared highly similar FISH patterns, which suggested the possibility of intact or mostly partial transfer of the chromosome between the hybrid and DH. Our study will contribute to understanding the genetic mechanism of chromosomal variation in P. xiaohei and derived DH plants.

scholarly journals Condensin Loaded onto the Replication Fork Barrier Site in the rRNA Gene Repeats during S Phase in a FOB1-Dependent Fashion To Prevent Contraction of a Long Repetitive Array in Saccharomyces cerevisiae

2006 ◽  
Vol 26 (6) ◽  
pp. 2226-2236 ◽  
Author(s):  
Katsuki Johzuka ◽  
Masahiro Terasawa ◽  
Hideyuki Ogawa ◽  
Tomoko Ogawa ◽  
Takashi Horiuchi
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Copy Number ◽  
Replication Fork ◽  
Tandem Repeats ◽  
S Phase ◽  
Rrna Gene ◽  
Nontranscribed Spacer ◽  
Condensin Complex ◽  
Unknown System ◽  
Average Copy

ABSTRACT An average of 200 copies of the rRNA gene (rDNA) is clustered in a long tandem array in Saccharomyces cerevisiae. FOB1 is known to be required for expansion/contraction of the repeats by stimulating recombination, thereby contributing to the maintenance of the average copy number. In Δfob1 cells, the repeats are still maintained without any fluctuation in the copy number, suggesting that another, unknown system acts to prevent repeat contraction. Here, we show that condensin acts together with FOB1 in a functionally complemented fashion to maintain the long tandem repeats. Six condensin mutants possessing severely contracted rDNA repeats were isolated in Δfob1 cells but not in FOB1 + cells. We also found that the condensin complex associated with the nontranscribed spacer region of rDNA with a major peak coincided with the replication fork barrier (RFB) site in a FOB1-dependent fashion. Surprisingly, condensin association with the RFB site was established during S phase and was maintained until anaphase. These results indicate that FOB1 plays a novel role in preventing repeat contraction by regulating condensin association and suggest a link between replication termination and chromosome condensation and segregation.

5S rDNA genome regions of Lens species

Genome ◽  
2005 ◽  
Vol 48 (5) ◽  
pp. 937-942 ◽  
Author(s):  
M Fernández ◽  
M L Ruiz ◽  
C Linares ◽  
A Fominaya ◽  
M Pérez de la Vega
Keyword(s):  
Lens Culinaris ◽  
Organizer Region ◽  
Nucleolar Organizer Region ◽  
Pcr Amplification ◽  
Intergenic Spacer ◽  
5S Rdna ◽  
Nucleolar Organizer ◽  
Repeated Sequence ◽  
Nontranscribed Spacer ◽  
Selective Hybridization

The length variability of the nontranscribed spacer (NTS) of the 5S rDNA repeats was analyzed in species of the genus Lens by means of PCR amplification. The NTS ranged from ~227 to ~952 bp. The polymorphism detected was higher than previous NTS polymorphisms described in this genus. Three NTS length variants from Lens culinaris subsp. culinaris and 2 from Lens culinaris subsp. orientalis were sequenced. The culinaris NTS fragment lengths were 239, 371, and 838 bp, whereas the orientalis ones were 472 bp and 506 bp, respectively. As a result of sequence similarities, 2 families of sequences were distinguished, 1 including the sequences of 838 and 506 bp, and others with the sequences of 239, 371, and 472 bp. The 1st family was characterized by the presence of a repeated sequence designated A, whereas the 2nd family showed a single A sequence and other repeated sequences designated B, C, and D. The presence of an (AT)n microsatellite was also observed in the 2nd family of sequences. The fragments, which included the 239-bp and 838-bp NTS sequences, as well as the intergenic spacer (IGS) of the 18S–5.8S–26S ribosomal DNA also from L. culinaris subsp. culinaris, were used to localize the nucleolar organizer region (NOR) and the 5S rDNA loci in the chromosomes of several species of the genus Lens by means of fluorescence in situ hybridization (FISH). The selective hybridization of the 2 NTS probes allowed us to distinguish between different 5S rDNA chromosomal loci.Key words: Lens, lentil, ribosomal loci, 5S, FISH, NTS polymorphism, NOR.

scholarly journals Species Identification of Crassostrea and Ostrea Oysters by Polymerase Chain Reaction Amplification of the 5S rRNA Gene

2006 ◽  
Vol 89 (1) ◽  
pp. 144-148 ◽  
Author(s):  
Ismael Cross ◽  
Laureana Rebordinos ◽  
Edgardo Diaz
Keyword(s):  
Polymerase Chain Reaction ◽  
Polymerase Chain Reaction Amplification ◽  
5S Rdna ◽  
Universal Primers ◽  
Rrna Gene ◽  
Chain Reaction ◽  
Nontranscribed Spacer ◽  
Crassostrea Angulata ◽  
Polymerase Chain ◽  
Species Specific

Abstract A specific multiplex polymerase chain reaction (PCR) was developed for the identification of Crassostrea angulata, C. gigas, Ostrea edulis, and O. stentina oyster species. Universal primers were used for the amplification of complete repetition units of 5S rDNA in each of the 4 species. The alignment of the obtained sequences was the basis for the specific design of species-specific primers (ED1, ED2, ST1, ST2, CR1, and CR2) located in the nontranscribed spacer regions. The different sizes of the species-specific amplicons, separated by agarose gel electrophoresis, allowed identification of Crassostrea and Ostrea species. A multiplex PCR with a set of the 6 designed primers showed that they did not interfere with each other and bound specifically to the DNA target. This genetic marker can be very useful for traceability of the species, application in the management of oyster cultures, and conservation of the genetic resources of the species.

Chromosomal mapping and nucleotide sequence of two tandem repeats of Atlantic salmon 5S rDNA

1994 ◽  
Vol 67 (1) ◽  
pp. 31-36 ◽  
Author(s):  
A.M. Pendas ◽  
P. Moran ◽  
J.P. Freije ◽  
E. Garcia-Vazquez
Keyword(s):  
Nucleotide Sequence ◽  
Atlantic Salmon ◽  
Tandem Repeats ◽  
5S Rdna ◽  
Chromosomal Mapping
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