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Journal articles on the topic '45S ribosomal RNA genes (45S rDNA)'

Author: Grafiati

Published: 4 June 2025

Last updated: 1 August 2025

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1

Delorme-Hinoux, Valérie, Assane Mbodj, Sophie Brando, et al. "45S rDNA Diversity In Natura as One Step towards Ribosomal Heterogeneity in Arabidopsis thaliana." Plants 12, no. 14 (2023): 2722. http://dx.doi.org/10.3390/plants12142722.

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The keystone of ribosome biogenesis is the transcription of 45S rDNA. The Arabidopsis thaliana genome contains hundreds of 45S rDNA units; however, they are not all transcribed. Notably, 45S rDNA units contain insertions/deletions revealing the existence of heterogeneous rRNA genes and, likely, heterogeneous ribosomes for rRNAs. In order to obtain an overall picture of 45S rDNA diversity sustaining the synthesis of rRNAs and, subsequently, of ribosomes in natura, we took advantage of 320 new occurrences of Arabidopsis thaliana as a metapopulation named At66, sampled from 0 to 1900 m of altitud

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Tran, Trang Thi Quynh, Trang Hien Do, Tung The Pham, et al. "Hypermethylation at 45S rDNA promoter in cancers." PLOS ONE 20, no. 1 (2025): e0311085. https://doi.org/10.1371/journal.pone.0311085.

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The ribosomal genes (rDNA genes) encode 47S rRNA which accounts for up to 80% of all cellular RNA. At any given time, no more than 50% of rDNA genes are actively transcribed, and the other half is silent by forming heterochromatin structures through DNA methylation. In cancer cells, upregulation of ribosome biogenesis has been recognized as a hallmark feature, thus, the reduced methylation of rDNA promoter has been thought to support conformational changes of chromatin accessibility and the subsequent increase in rDNA transcription. However, an increase in the heterochromatin state through rDN

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Gokhman, Vladimir E., and Valentina G. Kuznetsova. "Structure and Evolution of Ribosomal Genes of Insect Chromosomes." Insects 15, no. 8 (2024): 593. http://dx.doi.org/10.3390/insects15080593.

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Currently, clusters of 45S and 5S ribosomal DNA (rDNA) have been studied in about 1000 and 100 species of the class Insecta, respectively. Although the number of insect species with known 45S rDNA clusters (also referred to as nucleolus-organizing regions, or NORs) constitutes less than 0.1 percent of the described members of this enormous group, certain conclusions can already be drawn. Since haploid karyotypes with single 45S and 5S rDNA clusters predominate in both basal and derived insect groups, this character state is apparently ancestral for the class Insecta in general. Nevertheless, t

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Bi, Ke, James P. Bogart, and Jinzhong Fu. "A populational survey of 45S rDNA polymorphism in the Jefferson salamander Ambystoma jeffersonianum revealed by fluorescence in situ hybridization (FISH)." Current Zoology 55, no. 2 (2009): 145–49. http://dx.doi.org/10.1093/czoolo/55.2.145.

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Abstract The chromosomal localization of 45S ribosomal RNA genes in Ambystoma jeffersonianum was determined by fluorescence in situ hybridization with 18S rDNA fragment as a probe (FISH-rDNA). Our results revealed the presence of rDNA polymorphism among A. jeffersonianum populations in terms of number, location and FISH signal intensity on the chromosomes. Nine rDNA cytotypes were found in ten geographically isolated populations and most of them contained derivative rDNA sites. Our preliminary study provides strong indication of karyotypic diversification of A. Jeffersonianum that is demonstra

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5

Michalak, Katarzyna, Sebastian Maciak, Young Bun Kim, et al. "Nucleolar dominance and maternal control of 45S rDNA expression." Proceedings of the Royal Society B: Biological Sciences 282, no. 1820 (2015): 20152201. http://dx.doi.org/10.1098/rspb.2015.2201.

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Using a system of interspecies hybrids, trihybrids, and recombinants with varying proportions of genomes from three distinct Xenopus species, we provide evidence for de novo epigenetic silencing of paternal 45S ribosomal ribonucleic acid (rRNA) genes and their species-dependent expression dominance that escapes transcriptional inactivation after homologous recombination. The same pattern of imprinting is maintained in the offspring from mothers being genetic males (ZZ) sex-reversed to females, indicating that maternal control of ribosomal deoxyribonucleic acid (rDNA) expression is not sex-chro

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De, Bustos Alfredo. "Comparative FISH mapping of 45S and 5S rDNA in the genus Gambierdiscus advances understanding of the cytogenetic diversity and mitosis of dinoflagellates." European Journal of Phycology 57 (September 28, 2021): 264–76. https://doi.org/10.1080/09670262.2021.1964608.

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Dinoflagellates are protists with exceptionally large genomes and chromosomes that lack nucleosomes. To date, information on their genome organization is scarce. Studies investigating the distribution of ribosomal RNA genes (rDNA) in plants and animals by fluorescence in situ hybridization (FISH) have provided important information to elucidate the genome organization and evolution of many species. In the present study, FISH was used to analyse the chromosomal organization of 45S and 5S rDNA and the extent of rDNA variation among five species of Gambierdiscus (G. australes, G. excentricus

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Abirached-Darmency, Mona, Emilce Prado-Vivant, Liudmila Chelysheva, and Thomas Pouthier. "Variation in rDNA locus number and position among legume species and detection of 2 linked rDNA loci in the model Medicago truncatula by FISH." Genome 48, no. 3 (2005): 556–61. http://dx.doi.org/10.1139/g05-015.

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Within Fabaceae, legume species have a variable genome size, chromosome number, and ploidy level. The genome distribution of ribosomal genes, easily detectable by fluorescent in situ hybridization (FISH), is a good tool for anchoring physical and genetic comparative maps. The organisation of 45S rDNA and 5S loci was analysed by FISH in the 4 closely related species: Pisum sativum, Medicago truncatula, Medicago sativa (2 diploid taxa), and Lathyrus sativus. The 2 types of rDNA arrays displayed interspecific variation in locus number and location, but little intraspecific variation was detected.

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Dyomin, Alexander, Svetlana Galkina, Arina Ilina, and Elena Gaginskaya. "Single Copies of the 5S rRNA Inserted into 45S rDNA Intergenic Spacers in the Genomes of Nototheniidae (Perciformes, Actinopterygii)." International Journal of Molecular Sciences 24, no. 8 (2023): 7376. http://dx.doi.org/10.3390/ijms24087376.

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In the vast majority of Animalia genomes, the 5S rRNA gene repeats are located on chromosomes outside of the 45S rDNA arrays of the nucleolar organiser (NOR). We analysed the genomic databases available and found that a 5S rDNA sequence is inserted into the intergenic spacer (IGS) between the 45S rDNA repeats in ten species of the family Nototheniidae (Perciformes, Actinopterigii). We call this sequence the NOR-5S rRNA gene. Along with Testudines and Crocodilia, this is the second case of a close association between four rRNA genes within one repetitive unit in deuterostomes. In both cases, NO

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Coluccia, Elisabetta, Federica Deidda, Cinzia Lobina, et al. "Chromosome Mapping of 5S Ribosomal Genes in Indo-Pacific and Atlantic Muraenidae: Comparative Analysis by Dual Colour Fluorescence In Situ Hybridisation." Genes 11, no. 11 (2020): 1319. http://dx.doi.org/10.3390/genes11111319.

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The Muraenidae is one of the largest and most complex anguilliform families. Despite their abundance and important ecological roles, morays are little studied, especially cytogenetically, and both their phylogenetic relationships and the taxonomy of their genera are controversial. With the aim of extending the karyology of this fish group, the chromosomal mapping of the 5S ribosomal gene family was performed on seven species belonging to the genera Muraena and Gymnothorax from both the Atlantic and Pacific oceans. Fluorescence in situ hybridisation (FISH) experiments were realized using specie

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Choi, Young A., Ryutaro Tao, Keizo Yonemori, and Akira Sugiura. "Simultaneous Visualization of 5S and 45S rDNAs in Persimmon (Diospyros kaki) and Several Wild Relatives (Diospyros spp.) by Fluorescent in situ Hybridization (FISH) and MultiColor FISH (MCFISH)." Journal of the American Society for Horticultural Science 128, no. 5 (2003): 736–40. http://dx.doi.org/10.21273/jashs.128.5.0736.

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5S ribosomal DNA (rDNA) was visualized on the somatic metaphase chromosome of persimmon (Diospyros kaki) and ten wild Diospyros species by fluorescent in situ hybridization (FISH). The digoxigenin (DIG)-labeled 5S rDNA probe was hybridized onto the chromosomes and visualized by incubation with anti-DIG-fluorescein isothiocyanate (FITC). Strong signals of 5S rDNA probe were observed on several chromosomes of Diospyros species tested. Furthermore, multicolor FISH using 5S and 45S rDNA probes differently labeled with DIG and biotin, revealed separate localization of the two rDNA genes on differen

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Choi, Young A., Ryutaro Tao, Keizo Yonemori, and Akira Sugiura. "Simultaneous Visualization of 5S and 45S rDNAs in Persimmon (Diospyros kaki) and Several Wild Relatives (Diospyros spp.) by Fluorescent in situ Hybridization (FISH) and MultiColor FISH (MCFISH)." Journal of the American Society for Horticultural Science 128, no. 5 (2003): 736–40. https://doi.org/10.21273/jashs.128.5.736.

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5S ribosomal DNA (rDNA) was visualized on the somatic metaphase chromosome of persimmon (Diospyros kaki) and ten wild Diospyros species by fluorescent in situ hybridization (FISH). The digoxigenin (DIG)-labeled 5S rDNA probe was hybridized onto the chromosomes and visualized by incubation with anti-DIG-fluorescein isothiocyanate (FITC). Strong signals of 5S rDNA probe were observed on several chromosomes of Diospyros species tested. Furthermore, multicolor FISH using 5S and 45S rDNA probes differently labeled with DIG and biotin, revealed separate localization of the two rDNA genes on differen

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She, Chao-Wen, Xiang-Hui Jiang, and Chun-Ping He. "Comparative karyotype analysis of eight Cucurbitaceae crops using fluorochrome banding and 45S rDNA-FISH." Comparative Cytogenetics 17, no. (1) (2023): 31–58. https://doi.org/10.3897/compcytogen.v17.i1.99236.

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To have an insight into the karyotype variation of eight Cucurbitaceae crops including Cucumis sativus Linnaeus, 1753, Cucumis melo Linnaeus, 1753, Citrullus lanatus (Thunberg, 1794) Matsumura et Nakai, 1916, Benincasa hispida (Thunberg, 1784) Cogniaux, 1881, Momordica charantia Linnaeus, 1753, Luffa cylindrica (Linnaeus, 1753) Roemer, 1846, Lagenaria siceraria var. hispida (Thunberg, 1783) Hara, 1948 and Cucurbita moschata Duchesne ex Poiret, 1819, well morphologically differentiated mitotic metaphase chromosomes were prepared using the enzymatic maceration and flame-drying method, and the ch

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Lopez, Francesca B., Antoine Fort, Luca Tadini, et al. "Gene dosage compensation of rRNA transcript levels in Arabidopsis thaliana lines with reduced ribosomal gene copy number." Plant Cell 33, no. 4 (2021): 1135–50. http://dx.doi.org/10.1093/plcell/koab020.

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Abstract The 45S rRNA genes (rDNA) are among the largest repetitive elements in eukaryotic genomes. rDNA consists of tandem arrays of rRNA genes, many of which are transcriptionally silenced. Silent rDNA repeats may act as ‘back-up’ copies for ribosome biogenesis and have nuclear organization roles. Through Cas9-mediated genome editing in the Arabidopsis thaliana female gametophyte, we reduced 45S rDNA copy number (CN) to a plateau of ∼10%. Two independent lines had rDNA CNs reduced by up to 90% at the T7 generation, named low copy number (LCN) lines. Despite drastic reduction of rDNA copies,

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Symonová, Radka. "Integrative rDNAomics—Importance of the Oldest Repetitive Fraction of the Eukaryote Genome." Genes 10, no. 5 (2019): 345. http://dx.doi.org/10.3390/genes10050345.

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Nuclear ribosomal RNA (rRNA) genes represent the oldest repetitive fraction universal to all eukaryotic genomes. Their deeply anchored universality and omnipresence during eukaryotic evolution reflects in multiple roles and functions reaching far beyond ribosomal synthesis. Merely the copy number of non-transcribed rRNA genes is involved in mechanisms governing e.g., maintenance of genome integrity and control of cellular aging. Their copy number can vary in response to environmental cues, in cellular stress sensing, in development of cancer and other diseases. While reaching hundreds of copie

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Tang, Yan-Mei, Liang Xiao, Yasir Iqbal, et al. "Molecular cytogenetic characterization and phylogenetic analysis of four Miscanthus species (Poaceae)." Comparative Cytogenetics 13, no. (3) (2019): 211–30. https://doi.org/10.3897/CompCytogen.v13i3.35346.

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Chromosomes of four Miscanthus (Andersson, 1855) species including M. sinensis (Andersson, 1855), M. floridulus (Schumann & Lauterb, 1901), M. sacchariflorus (Hackel, 1882) and M. lutarioriparius (Chen & Renvoize, 2005) were analyzed using sequentially combined PI and DAPI (CPD) staining and fluorescence in situ hybridization (FISH) with 45S rDNA probe. To elucidate the phylogenetic relationship among the four Miscanthus species, the homology of repetitive sequences among the four species was analyzed by comparative genomic in situ hybridization (cGISH). Subsequently four Miscanthus sp

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She, Chao-Wen, Ying Mao, Xiang-Hui Jiang, and Chun-Ping He. "Comparative molecular cytogenetic characterization of five wild Vigna species (Fabaceae)." Comparative Cytogenetics 14, no. (2) (2020): 243–64. https://doi.org/10.3897/CompCytogen.v14i2.51154.

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To extend our knowledge on karyotype variation of the genus Vigna Savi, 1824, the chromosomal organization of rRNA genes and fluorochrome banding patterns of five wild Vigna species were studied. Sequential combined PI (propidium iodide) and DAPI (4',6-diamidino-2-phenylindole) (CPD) staining and fluorescence in situ hybridization (FISH) with 5S and 45S rDNA probes were used to analyze the karyotypes of V. luteola (Jacquin, 1771) Bentham, 1959, V. vexillata (Linnaeus, 1753) A. Richard, 1845, V. minima (Roxburgh, 1832) Ohwi & H. Ohashi, 1969, V. trilobata (Linnaeus, 1753) Verdcourt, 1968, a

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Wei, Yan-Fang, Xiang-Hui Jiang, Rong Song, and Chao-Wen She. "Molecular cytogenetic characterization of 9 populations of four species in the genus Polygonatum (Asparagaceae)." Comparative Cytogenetics 18 (May 16, 2024): 73–95. https://doi.org/10.3897/compcytogen.18.122399.

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To characterize the chromosomes of the four species of <i>Polygonatum</i> Miller, 1754, used in traditional Chinese medicine, <i>P. cyrtonema</i> Hua, 1892, <i>P. kingianum</i> Collett et Hemsley, 1890, <i>P. odoratum</i> (Miller, 1768) Druce, 1906, and <i>P. sibiricum</i> Redouté, 1811, and have an insight into the karyotype variation of the genus <i>Polygonatum</i>, fluorescence <i>in situ</i> hybridization (FISH) with 5S and 45S rDNA oligonucleotide probes was applied to analyze the karyotypes of 9 populations of the four species. Detailed molecular cytogenetic karyotypes of the 9 populatio

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Ferretti, Ana Beatriz Stein Machado, Francisco Ruiz Ruano, Juan Pedro Martinez Camacho, Vilma Loreto, and Diogo Cavalcanti Cabral de Mello. "Chromosomal dynamics, molecular organization and evolutionary patterns of major ribosomal DNA in the Grasshopper Abracris flavolineata (Acrididae)." Semina: Ciências Biológicas e da Saúde 38, no. 1supl (2018): 124. http://dx.doi.org/10.5433/1679-0367.2017v38n1suplp124.

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In the grasshopper Abracris flavolineata it was documented huge intrapopulation variation for 18S rDNA in individuals collected in six populations, but causes for this pattern was not understand yet. In this work we aimed to elucidate the molecular structure, evolutionary patterns of the rDNA 18S distribution and its causes in the genome of A. flavolineata. It was used a combination of classical cytogenetic techniques, mapping of18S rDNA through Fluorescence in situ hybridization (FISH) and genomics analyses from entire sequenced genome by Illumina hiseq 2000. It was analyzed 48 individuals co

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De, Bustos Alfredo. "The 5S rRNA genes in Alexandrium: their use as a FISH chromosomal marker in studies of the diversity, cell cycle and sexuality of dinoflagellates." Harmful Algae 98 (September 10, 2020): 101903. https://doi.org/10.1016/j.hal.2020.101903.

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Chromosomal markers of the diversity and evolution of dinoflagellates are scarce because the genomes of these organisms are unique among eukaryotes in terms of their base composition and chromosomal structure. Similarly, a lack of appropriate tools has hindered studies of the chromosomal localization of 5S ribosomal DNA (rDNA) in the nucleosome-less chromosomes of dinoflagellates. In this study, we isolated and cloned 5S rDNA sequences from various toxin-producing species of the genus Alexandrium and developed a fluorescence in situ hybridization (FISH) probe that allows their chromosomal loca

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Sadova, A. A., D. Yu Panteleev, and G. V. Pavlova. "Human rDNA Structure, Expression, and Non-Canonical Functions: the Role of Non-Coding Regions." Молекулярная биология 57, no. 3 (2023): 411–26. http://dx.doi.org/10.31857/s0026898423030084.

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The review is dedicated to analyzing and summarizing the data on the part of human genome encoding 45S rRNA. The sequences which seem evolutionary conserved on the first glance astonish one with their variability in structure and a variety of functions on closer examination. The major part of rDNA is non-coding and contains regulatory elements, protein binding sites, pseudogenes, repetitive sequences, and microRNA genes. Ribosomal intergenic spacers are not only in charge with the nucleolus morphology and functioning, namely, the rRNA expression and ribosome biogenesis, but also control nuclea

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SAVAŞ TUNA, Gülsemin, Gülru YÜCEL, Tansel KAYGISIZ AŞÇIOĞUL, et al. "Molecular cytogenetic characterization of common bean (Phaseolusvulgaris L.) accessions." TURKISH JOURNAL OF AGRICULTURE AND FORESTRY 44, no. 6 (2020): 612–30. http://dx.doi.org/10.3906/tar-1910-33.

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With an annual global production of approximately 25 million tons, the common bean (Phaseolus vulgaris L), a member of the genus Phaseolus, is one of the major protein sources used as food for humans. In this study, it was aimed to investigate the genome size of the common bean genetic resource collection (154 common bean accessions) in Turkey by flow cytometry (FCM) and determine whether geographical variables affected the genome size. In addition, the number and distribution of 5S and 45S ribosomal DNA loci were designated by performing a fluorescence in situ hybridization (FISH) analysis in

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Hett, Anne Kathrin, Mauro Nirchio, Claudio Oliveira, Zoila Raquel Siccha, Anna Rita Rossi, and Luciana Sola. "Karyotype characterization of Mugil incilis Hancock, 1830 (Mugiliformes: Mugilidae), including a description of an unusual co-localization of major and minor ribosomal genes in the family." Neotropical Ichthyology 9, no. 1 (2011): 107–12. http://dx.doi.org/10.1590/s1679-62252011005000005.

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This study reports the description of the karyotype of Mugil incilis from Venezuela. The chromosome complement is composed of 48 acrocentric chromosomes, which uniformly decrease in size. Therefore, the homologues can not be clearly identified, with the exception of one of the largest chromosome pairs, classified as number 1, whose homologues may show a subcentromeric secondary constriction, and of chromosome pair number 24, which is considerably smaller than the others. C-banding showed heterochromatic blocks at the centromeric/pericentromeric regions of all chromosomes, which were more consp

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Peška, Vratislav, Terezie Mandáková, Veronika Ihradská, and Jiří Fajkus. "Comparative Dissection of Three Giant Genomes: Allium cepa, Allium sativum, and Allium ursinum." International Journal of Molecular Sciences 20, no. 3 (2019): 733. http://dx.doi.org/10.3390/ijms20030733.

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Knowledge of the fascinating world of DNA repeats is continuously being enriched by newly identified elements and their hypothetical or well-established biological relevance. Genomic approaches can be used for comparative studies of major repeats in any group of genomes, regardless of their size and complexity. Such studies are particularly fruitful in large genomes, and useful mainly in crop plants where they provide a rich source of molecular markers or information on indispensable genomic components (e.g., telomeres, centromeres, or ribosomal RNA genes). Surprisingly, in Allium species, a c

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Kirtiklis, Lech, Konrad Ocalewicz, Michał Nowak, Marta Gwiazda-Orzoł, and Alicja Boroń. "Novel cytogenetic data in two gudgeons from the genera Gobio and Romanogobio (Teleostei: Cypriniformes: Gobionidae): chromosomal mapping of rDNAs and telomeric repeats." Folia Biologica 72, no. 4 (2024): 143–53. https://doi.org/10.3409/fb_72-4.14.

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The taxonomic status of gudgeons (Gobionidae) and the genetic relationships among them are still unclear. The current knowledge on the molecular cytogenetics of gudgeons is quite limited and concerns the basic parameters of their karyotype. Therefore, the main aim of this study was to obtain new data on the chromo- somes of two gudgeons – Gobio gobio and Romanogobio belingi – which would allow for characterising these species in a more precise way. Chromosomes of the examined species were analysed by conventional Giemsa staining and, for the first time, by fluorescence in situ hybridisation (F

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Singh, Mamta, Ravindra Kumar, N. S. Nagpure, B. Kushwaha, Indra Mani, and W. S. Lakra. "Extensive NOR site polymorphism in geographically isolated populations of Golden mahseer, Tor putitora." Genome 52, no. 9 (2009): 783–89. http://dx.doi.org/10.1139/g09-052.

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Analyses of nucleolar organizer region (NOR) site polymorphism using silver staining were carried out in 72 individuals of 5 geographically isolated populations of Tor putitora from India. All Ag-NORs analyzed were constituted by rDNA that was confirmed by the presence of positive fluorescence in situ hybridization (FISH) signals. Analyses of the extra NORs among the populations confirmed the hypothesis that multi-chromosomal NOR site polymorphism is not an exception but a rule. We found a negative correlation between the mean number of extra NORs and geographical distance from the Alaknanda R

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SOLA, L., A. R. ROSSI, F. ANNESI, and E. GORNUNG. "Cytogenetic studies in Sparus auratus (Pisces, Perciformes): molecular organization of 5S rDNA and chromosomal mapping of 5S and 45S ribosomal genes and of telomeric repeats." Hereditas 139, no. 3 (2004): 232–36. http://dx.doi.org/10.1111/j.1601-5223.2003.01814.x.

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Antônia, Campos Barros Luísa, Alves Cardoso de Aguiar Hiton Jeferson, Santos Ferreira Mariano Cléa dos, et al. "Cytogenetic data on six leafcutter ants of the genus Acromyrmex Mayr, 1865 (Hymenoptera, Formicidae, Myrmicinae): insights into chromosome evolution and taxonomic implications." Comparative Cytogenetics 10, no. (2) (2016): 229–43. https://doi.org/10.3897/CompCytogen.v10i2.7612.

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Cytogenetic data for the genus Acromyrmex Mayr, 1865 are available, to date, for a few species from Brazil and Uruguay, which have uniform chromosome numbers (2n = 38). The recent cytogenetic data of Acromyrmex striatus (Roger, 1863), including its banding patterns, showed a distinct karyotype (2n = 22), similar to earlier studied Atta Fabricius, 1804 species. Karyological data are still scarce for the leafcutter ants and many gaps are still present for a proper understanding of this group. Therefore, this study aimed at increasing cytogenetic knowledge of the genus through the characterizatio

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Harrington, C. A., and D. M. Chikaraishi. "Transcription of spacer sequences flanking the rat 45S ribosomal DNA gene." Molecular and Cellular Biology 7, no. 1 (1987): 314–25. http://dx.doi.org/10.1128/mcb.7.1.314-325.1987.

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The transcriptional activity of spacer sequences flanking the rat 45S ribosomal DNA (rDNA) gene were studied. Nascent RNA labeled in in vitro nuclear run-on reactions hybridized with both 5' and 3' spacer regions. The highest level of hybridization was seen with an rDNA fragment containing tandem repeats of a 130-base-pair sequence upstream of the 45S rRNA initiation site. Synthesis of RNA transcripts homologous to this internally repetitious spacer region was insensitive to high levels of alpha-amanitin, suggesting that it is mediated by RNA polymerase I. Analysis of steady-state RNA showed t

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Harrington, C. A., and D. M. Chikaraishi. "Transcription of spacer sequences flanking the rat 45S ribosomal DNA gene." Molecular and Cellular Biology 7, no. 1 (1987): 314–25. http://dx.doi.org/10.1128/mcb.7.1.314.

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The transcriptional activity of spacer sequences flanking the rat 45S ribosomal DNA (rDNA) gene were studied. Nascent RNA labeled in in vitro nuclear run-on reactions hybridized with both 5' and 3' spacer regions. The highest level of hybridization was seen with an rDNA fragment containing tandem repeats of a 130-base-pair sequence upstream of the 45S rRNA initiation site. Synthesis of RNA transcripts homologous to this internally repetitious spacer region was insensitive to high levels of alpha-amanitin, suggesting that it is mediated by RNA polymerase I. Analysis of steady-state RNA showed t

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Gibbons, John G., Alan T. Branco, Susana A. Godinho, Shoukai Yu, and Bernardo Lemos. "Concerted copy number variation balances ribosomal DNA dosage in human and mouse genomes." Proceedings of the National Academy of Sciences 112, no. 8 (2015): 2485–90. http://dx.doi.org/10.1073/pnas.1416878112.

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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 residin

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Chang, Yu-Chu, Chou-Tou Shii, and Mei-Chu Chung. "Variations in Ribosomal RNA Gene Loci in Spider Lily (Lycoris spp.)." Journal of the American Society for Horticultural Science 134, no. 5 (2009): 567–73. http://dx.doi.org/10.21273/jashs.134.5.567.

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Lycoris species of the Amaryllidaceae are important ornamental and medicinal plants in Asia. Karyotypes of Lycoris species have been studied extensively since the time when their chromosome numbers were first counted over 80 years ago. Based on karyotype, Lycoris taxa can be classified into the monomorphic A group, dimorphic MT group, and the sterile dikaryotype MT-A group. Numerous reports dealing with karyotype analysis and phylogenetic relationship in the genus Lycoris have been published. However, there are disputes and controversies regarding karyotype evolution resulting from lacking eff

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Capesius, I., and R. Appels. "The direct measurement of ribosomal RNA gene activity in wheat–rye hybrids." Genome 32, no. 2 (1989): 343–46. http://dx.doi.org/10.1139/g89-452.

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Cloned rDNA segments, from wheat (Triticum aestivum) and rye (Secale cereale), which included the entire spacer region plus parts of the flanking 18S and 26S rRNA genes, were used to assay transcripts formed in the nuclei from wheat–rye hybrids. The tetraploid triticales (× Triticosecale Wittmack) carrying a complete rye chromosome complement and a combination of wheat chromosomes, as well as wheat and rye per se, were studied. Nuclei isolated from young leaves were incubated in the presence of [32P]UTP for 10 min, after which the total RNA was isolated. Hybridization of this radioactive RNA t

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Jehangir, Maryam, Syed Farhan Ahmad, Adauto Lima Cardoso, Guilherme Targino Valente, and Cesar Martins. "FISH mapping of 45S rRNA and IHHB genes on autosomes and B chromosome of cichlid fish Astatotilapia latifasciata." Semina: Ciências Biológicas e da Saúde 38, no. 1supl (2018): 175. http://dx.doi.org/10.5433/1679-0367.2017v38n1suplp175.

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B chromosomes (B) are supernumerary, additional and non-homologous to standard (A) chromosomes. Significant biological questions concerning the origin and structural organization of Bs are under discussion. Previous reports found that B chromosomes are enriched with repetitive elements and can carry functional genes. The present study is aimed to extend our knowledge of the structure and composition of B chromosomes. We have combined cytogenetics and genomics approaches to undertsand the B chromosome problem. Cytogenetics analysis, applied to cichlid fish Astatotilapia latifasciata, revealed t

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Malimpensa, Geovana C., Josiane B. Traldi, Danyelle Toyama, Flávio Henrique-Silva, Marcelo R. Vicari, and Orlando Moreira-Filho. "Chromosomal Mapping of Repeat DNA in Bergiaria westermanni (Pimelodidae, Siluriformes): Localization of 45S rDNA in B Chromosomes." Cytogenetic and Genome Research 154, no. 2 (2018): 99–106. http://dx.doi.org/10.1159/000487652.

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The occurrence of repetitive DNA in autosomes and B chromosomes of Bergiaria westermanni was examined using conventional and molecular cytogenetic techniques. This species exhibited 2n = 56 chromosomes, with intra- and interindividual variation in the number of heterochromatic B chromosomes (from 0 to 4). The 5S rDNA was localized in pairs 1 and 5, and histone probes (H1, H3, and H4) and U2 small nuclear RNA were syntenic with 5S rDNA in pair 5. Histone sequences were also located in chromosome pair 14. The (GATA)n sequence was dispersed throughout the autosomes and B chromosomes, with cluster

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Michalak, Pawel. "Evidence for maternal imprinting of 45S ribosomal RNA genes in Xenopus hybrids." Development Genes and Evolution 224, no. 2 (2014): 125–28. http://dx.doi.org/10.1007/s00427-014-0464-1.

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Donald, Tamzin M., Andreas Houben, Carolyn R. Leach, and Jeremy N. Timmis. "Ribosomal RNA genes specific to the B chromosomes in Brachycome dichromosomatica are not transcribed in leaf tissue." Genome 40, no. 5 (1997): 674–81. http://dx.doi.org/10.1139/g97-089.

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Ribosomal RNA genes are present near the end of the short arm and, to a lesser extent, near the centromere of the B chromosomes of some populations of Brachycome dichromosomatica. The internal transcribed spacer (ITS2) was amplified by PCR from total leaf DNA using primers within the conserved regions encoding the 5.8S and 25S stable rRNA species. Comparison of PCR amplified ITS2 sequences from several individual plants without B chromosomes with corresponding sequences derived from microdissected B chromosomes revealed two consistent differences between the rDNA of A and B chromosomes. One of

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Vallejos, C. E., S. D. Tanksley, and R. Bernatzky. "LOCALIZATION IN THE TOMATO GENOME OF DNA RESTRICTION FRAGMENTS CONTAINING SEQUENCES HOMOLOGOUS TO THE rRNA (45S), THE MAJOR CHLOROPHYLL a/b BINDING POLYPEPTIDE AND THE RIBULOSE BISPHOSPHATE CARBOXYLASE GENES." Genetics 112, no. 1 (1986): 93–105. http://dx.doi.org/10.1093/genetics/112.1.93.

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ABSTRACT DNA restriction fragments containing sequences homologous to the ribosomal RNA (45s), the major chlorophyll a/b binding polypeptide (CAB) and the small subunit of ribulose bisphosphate carboxylase (RBCS) genes have been localized and mapped in the tomato nuclear genome by linkage analysis. Ribosomal RNA genes map to a single locus, R45s, which resides in a terminal position on the short arm of chromosome 2 and corresponds to the Nucleolar Organizer Region. The size of the 45s repeating unit is estimated to be approximately 9 kb in Lycopersicon esculentum and 11 kb in Lycopersicon penn

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Maciak, Sebastian, Katarzyna Michalak, Shiv D. Kale, and Pawel Michalak. "Nucleolar Dominance and Repression of 45S Ribosomal RNA Genes in Hybrids between Xenopus borealis and X. muelleri (2n = 36)." Cytogenetic and Genome Research 149, no. 4 (2016): 290–96. http://dx.doi.org/10.1159/000450665.

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Nucleolar dominance is a dramatic disruption in the formation of nucleoli and the expression of ribosomal RNA (rRNA) genes, characteristic of some plant and animal hybrids. Here, we report that F1 hybrids produced from reciprocal crosses between 2 sister species of Xenopus clawed frogs, X. muelleri and X. borealis, undergo nucleolar dominance somewhat distinct from a pattern previously reported in hybrids between phylogenetically more distant Xenopus species. Patterns of nucleolar development, 45S rRNA expression, and gene copy inheritance were investigated using a combination of immunostainin

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Jung, Ji Hoon, Eun Jung Sohn, Eun Ah Shin, et al. "Melatonin Suppresses the Expression of 45S Preribosomal RNA and Upstream Binding Factor and Enhances the Antitumor Activity of Puromycin in MDA-MB-231 Breast Cancer Cells." Evidence-Based Complementary and Alternative Medicine 2013 (2013): 1–8. http://dx.doi.org/10.1155/2013/879746.

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Since the dysregulation of ribosome biogenesis is closely associated with tumor progression, in the current study, the critical role of ribosome biogenesis related signaling was investigated in melatonin and/or puromycin induced apoptosis in MDA-MB-231 breast cancer cells. Despite its weak cytotoxicity, melatonin from 3 mM attenuated the expression of 45S pre-ribosomal RNA (pre-rRNA), UBF as a nucleolar transcription factor, and fibrillarin at mRNA level and consistently downregulated nucleolar proteins such as UBF and fibrillarin at protein level in MDA-MB-231 cells. Furthermore, immunofluore

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Tseng, H., J. A. Biegel, and R. S. Brown. "Basonuclin is associated with the ribosomal RNA genes on human keratinocyte mitotic chromosomes." Journal of Cell Science 112, no. 18 (1999): 3039–47. http://dx.doi.org/10.1242/jcs.112.18.3039.

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Basonuclin is a zinc finger protein mainly expressed in keratinocytes of the basal layer of epidermis and the outer root sheath of hair follicles. It is also found in abundance in the germ cells of testis and ovary. In cultured keratinocytes, basonuclin is associated with chromatin in all phases of the cell cycle, including mitosis. By immunocytochemical methods, we demonstrate here that in mitosis basonuclin is associated with the short arms of the acrocentric chromosomes and with other loci on many metaphase chromosomes of human keratinocytes. Using the evolutionarily highly conserved N-term

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Tek, Ahmet L., Sevim D. Kara Öztürk, Hümeyra Yıldız, and Didem Karalar. "Novel Centromeric and Subtelomeric Repetitive DNA Sequences for Karyotyping the Bambara Groundnut (<b><i>Vigna subterranea</i></b> L. Verdc.)." Cytogenetic and Genome Research 161, no. 12 (2021): 585–94. http://dx.doi.org/10.1159/000521398.

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Bambara groundnut (<i>Vigna subterranea</i> L. Verdc.) is an underutilized minor legume crop with climate resilience and great potential use in world agriculture. This study aimed to cytogenetically characterize the genome and chromosome properties of Bambara groundnut. We cloned, sequenced, and mapped a 50-bp centromere-specific tandem repeat on all chromosomes. In addition, a 400-bp subtelomeric repeat was discovered and mapped on a single pair of chromosomes. A Bambara groundnut karyotype was constructed using these novel repeats along with ribosomal RNA genes (45S and 5S) and

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Valinsky, Lea, Gianluca Della Vedova, Tao Jiang, and James Borneman. "Oligonucleotide Fingerprinting of rRNA Genes for Analysis of Fungal Community Composition." Applied and Environmental Microbiology 68, no. 12 (2002): 5999–6004. http://dx.doi.org/10.1128/aem.68.12.5999-6004.2002.

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ABSTRACT Thorough assessments of fungal diversity are currently hindered by technological limitations. Here we describe a new method for identifying fungi, oligonucleotide fingerprinting of rRNA genes (OFRG). ORFG sorts arrayed rRNA gene (ribosomal DNA [rDNA]) clones into taxonomic clusters through a series of hybridization experiments, each using a single oligonucleotide probe. A simulated annealing algorithm was used to design an OFRG probe set for fungal rDNA. Analysis of 1,536 fungal rDNA clones derived from soil generated 455 clusters. A pairwise sequence analysis showed that clones with

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А.В., ПИМЕНОВ, ГОРЯЧКИНА О.В., СЕДЕЛЬНИКОВА Т.С. та МУРАТОВА Е.Н. "КАРИОЛОГИЧЕСКИЕ И ЦИТОГЕНЕТИЧЕСКИЕ ИССЛЕДОВАНИЯ ХВОЙНЫХ В ЭКСТРЕМАЛЬНЫХ УСЛОВИЯХ ПРОИЗРАСТАНИЯ". Сибирский экологический журнал 30, № 5 (2023): 591–602. http://dx.doi.org/10.15372/sej20230502.

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Обобщены результаты кариологических и цитогенетических исследований в популяциях видов хвойных семейств Pinaceae и Cupressaceae из экстремальных условий произрастания. У хвойных, произрастающих у южной и северной границ ареалов на экологическом пределе распространения, в антропогенно нарушенных экосистемах, в условиях интродукции, выявлена хромосомная изменчивость, обнаружены геномные и хромосомные мутации различного типа. Отмечены высокая частота изменений числа хромосом (миксоплоидия, анеуплоидия и полиплоидия) и их морфологии. Найдены различные типы хромосомных аномалий (кольцевые и полицен

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Iwakawa, Hidekazu, Hiro Takahashi, Yasunori Machida, and Chiyoko Machida. "Roles of ASYMMETRIC LEAVES2 (AS2) and Nucleolar Proteins in the Adaxial–Abaxial Polarity Specification at the Perinucleolar Region in Arabidopsis." International Journal of Molecular Sciences 21, no. 19 (2020): 7314. http://dx.doi.org/10.3390/ijms21197314.

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Leaves of Arabidopsis develop from a shoot apical meristem grow along three (proximal–distal, adaxial–abaxial, and medial–lateral) axes and form a flat symmetric architecture. ASYMMETRIC LEAVES2 (AS2), a key regulator for leaf adaxial–abaxial partitioning, encodes a plant-specific nuclear protein and directly represses the abaxial-determining gene ETTIN/AUXIN RESPONSE FACTOR3 (ETT/ARF3). How AS2 could act as a critical regulator, however, has yet to be demonstrated, although it might play an epigenetic role. Here, we summarize the current understandings of the genetic, molecular, and cellular

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Ma, Xinyuan, Paula Agudelo, Vincent P. Richards, and J. Antonio Baeza. "Genome survey sequencing of the phyto-parasitic nematode Hoplolaimus galeatus." PeerJ 10 (January 18, 2022): e12749. http://dx.doi.org/10.7717/peerj.12749.

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Background Hoplolaimus galeatus is a plant-parasite nematode with a broad range of hosts. This nematode is known to damage cotton, corn, and soybean crops. Hoplolaimus galeatus is also an economically important pest of turfgrasses. Despite its economical importance, no genomic resources exist for this parasite. Methods Using 300 bp paired-end short read sequencing, this study estimated genome size, analyzed a nearly complete mitochondrial chromosome, and explored nuclear repetitive elements, including microsatellites, in H. galeatus for the first time. The phylogenetic placement of H. galeatus

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Baeza, J. Antonio, José Luis Molina-Quirós, and Sebastián Hernández-Muñoz. "Genome Survey Sequencing of an Iconic ‘Trophy’ Sportfish, the Roosterfish Nematistius pectoralis: Genome Size, Repetitive Elements, Nuclear RNA Gene Operon, and Microsatellite Discovery." Genes 12, no. 11 (2021): 1710. http://dx.doi.org/10.3390/genes12111710.

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The ‘Pez Gallo’ or the Roosterfish, Nematistius pectoralis, is an ecologically relevant species in the shallow water soft-bottom environments and a target of a most lucrative recreational sport fishery in the Central Eastern Pacific Ocean. According to the International Union for Conservation of Nature, N. pectoralis is assessed globally as Data Deficient. Using low-coverage short Illumina 300 bp pair-end reads sequencing, this study reports, for the first time, the genome size, single/low-copy genome content, and nuclear repetitive elements, including the 45S rRNA DNA operon and microsatellit

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Baeza, Juan Antonio, Mei Lin Neo, and Danwei Huang. "Genomic Survey and Resources for the Boring Giant Clam Tridacna crocea." Genes 13, no. 5 (2022): 903. http://dx.doi.org/10.3390/genes13050903.

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The boring giant clam Tridacna crocea is an evolutionary, ecologically, economically, and culturally important reef-dwelling bivalve targeted by a profitable ornamental fishery in the Indo-Pacific Ocean. In this study, we developed genomic resources for T. crocea. Using low-pass (=low-coverage, ~6×) short read sequencing, this study, for the first time, estimated the genome size, unique genome content, and nuclear repetitive elements, including the 45S rRNA DNA operon, in T. crocea. Furthermore, we tested if the mitochondrial genome can be assembled from RNA sequencing data. The haploid genome

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Ogo, Ogo A., John Tyson, Simon J. Cockell, Alison Howard, Ruth A. Valentine, and Dianne Ford. "The Zinc Finger Protein ZNF658 Regulates the Transcription of Genes Involved in Zinc Homeostasis and Affects Ribosome Biogenesis through the Zinc Transcriptional Regulatory Element." Molecular and Cellular Biology 35, no. 6 (2015): 977–87. http://dx.doi.org/10.1128/mcb.01298-14.

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We previously identified the ZTRE ( z inc t ranscriptional r egulatory e lement) in genes involved in zinc homeostasis and showed that it mediates transcriptional repression in response to zinc. We now report that ZNF658 acts at the ZTRE. ZNF658 was identified by matrix-assisted laser desorption ionization–time of flight mass spectrometry of a band excised after electrophoretic mobility shift assay using a ZTRE probe. The protein contains a KRAB domain and 21 zinc fingers. It has similarity with ZAP1 from Saccharomyces cerevisiae , which regulates the response to zinc restriction, including a

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Farrar, Jason, Michelle Nater, Emi Caywood, et al. "A Large Ribosomal Subunit Protein Abnormality in Diamond-Blackfan Anemia (DBA)." Blood 110, no. 11 (2007): 422. http://dx.doi.org/10.1182/blood.v110.11.422.422.

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Abstract DBA is an inherited bone marrow failure syndrome characterized by hypoproliferative anemia, congenital abnormalities and cancer predisposition. Ribosomal genes RPS19 and 24 are mutated in 25% and 3% of DBA patients respectively. To identify additional genetic abnormalities in DBA, we evaluated 2 unrelated children with DBA and sub-telomeric deletions of chromosome 3q by comparative genomic hybridization. The larger deletion spanned 11 Mb from 3q28 to the telomeric region and included 72 gene candidates. The second deletion involved 4 Mb from 3q29 to the telomeric end and included 52 k

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NEBEL, MARKUS E., SEBASTIAN WILD, MICHAEL HOLZHAUSER, et al. "JAGUC — A SOFTWARE PACKAGE FOR ENVIRONMENTAL DIVERSITY ANALYSES." Journal of Bioinformatics and Computational Biology 09, no. 06 (2011): 749–73. http://dx.doi.org/10.1142/s0219720011005781.

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Background: The study of microbial diversity and community structures heavily relies on the analyses of sequence data, predominantly taxonomic marker genes like the small subunit of the ribosomal RNA (SSU rRNA) amplified from environmental samples. Until recently, the "gold standard" for this strategy was the cloning and Sanger sequencing of amplified target genes, usually restricted to a few hundred sequences per sample due to relatively high costs and labor intensity. The recent introduction of massive parallel tag sequencing strategies like pyrosequencing (454 sequencing) has opened a new w

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