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Zhukova A, Zakharov G, Pavlova O, Saifitdinova A. Description of the complete rDNA repeat unit structure of Coturnixjaponica Temminck et Schlegel, 1849 (Aves). COMPARATIVE CYTOGENETICS 2024; 18:183-198. [PMID: 39363903 PMCID: PMC11447458 DOI: 10.3897/compcytogen.18.127373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 08/29/2024] [Indexed: 10/05/2024]
Abstract
Ribosomal RNA (18S, 5.8S, 28S) gene clusters in genomes form regions that consist of multiple tandem repeats. They are located on a single or several pairs of chromosomes and play an important role in the formation of the nucleolus responsible for the assembly of ribosome subunits. The rRNA gene cluster sequences are widely used for taxonomic studies, however at present, complete information on the avian rDNA repeat unit structure including intergenic spacer sequence is available only for the chicken (Gallusgallusdomesticus Linnaeus, 1758). The GC enrichment and high-order repeats peculiarities within the intergenic spacer described for the chicken rDNA cluster may be responsible for these failures. The karyotype of the Japanese quail (Coturnixjaponica Temminck et Schlegel, 1849) deserves close attention because, unlike most birds, it has three pairs of nucleolar organizer bearing chromosomes, two of which are microchromosomes enriched in repeating elements and heterochromatin that carry translocated terminal nucleolar organizers. Here we assembled and annotated the complete Japanese quail ribosomal gene cluster sequence of 21166 base pairs (GenBank under the registration tag BankIt2509210 CoturnixOK523374). This is the second deciphered avian rDNA cluster after the chicken. Despite the revealed high similarity with the chicken corresponding sequence, it has a number of specific features, which include a slightly lower degree of GC content and the presence of bendable elements in the content of both the transcribed spacer I and the non-transcribed intergenic spacer.
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Affiliation(s)
- Alina Zhukova
- Herzen State Pedagogical University of Russia, Saint Petersburg, RussiaHerzen State Pedagogical University of RussiaSaint PetersburgRussia
| | - Gennadii Zakharov
- Pavlov Institute of Physiology, Russian Academy of Sciences, Saint Petersburg, RussiaPavlov Institute of Physiology, Russian Academy of SciencesSaint PetersburgRussia
- EPAM Systems Inc., Saint Petersburg, RussiaEPAM Systems Inc.Saint PetersburgRussia
| | - Olga Pavlova
- International Centre for Reproductive Medicine, Saint Petersburg, RussiaInternational Centre for Reproductive MedicineSaint PetersburgRussia
- Beagle Ltd., Saint Petersburg, RussiaBeagle Ltd.Saint PetersburgRussia
| | - Alsu Saifitdinova
- Herzen State Pedagogical University of Russia, Saint Petersburg, RussiaHerzen State Pedagogical University of RussiaSaint PetersburgRussia
- International Centre for Reproductive Medicine, Saint Petersburg, RussiaInternational Centre for Reproductive MedicineSaint PetersburgRussia
- Saint Petersburg State University, Saint Petersburg, RussiaSaint Petersburg State UniversitySaint PetersburgRussia
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2
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Gokhman VE, Kuznetsova VG. Structure and Evolution of Ribosomal Genes of Insect Chromosomes. INSECTS 2024; 15:593. [PMID: 39194798 DOI: 10.3390/insects15080593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 07/25/2024] [Accepted: 08/02/2024] [Indexed: 08/29/2024]
Abstract
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, the number, chromosomal location, and other characteristics of both 45S and 5S rDNA sites substantially vary across different species, and sometimes even within the same species. There are several main factors and molecular mechanisms that either maintain these parameters or alter them on the short-term and/or long-term scale. Chromosome structure (i.e., monocentric vs. holokinetic chromosomes), excessive numbers of rRNA gene copies per cluster, interactions with transposable elements, pseudogenization, and meiotic recombination are perhaps the most important among them.
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Affiliation(s)
| | - Valentina G Kuznetsova
- Department of Karyosystematics, Zoological Institute, Russian Academy of Sciences, St. Petersburg 199034, Russia
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3
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Wu HY, Wong KL, Law STS, Nong W, Chan KT, Hui JHL, Lin G, Chan WH, Shaw PC. Determination of ITS1 haplotypes of Fritillariae Cirrhosae Bulbus by amplicon sequencing. Chin Med 2024; 19:33. [PMID: 38419104 PMCID: PMC10900738 DOI: 10.1186/s13020-024-00911-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 02/16/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Fritillariae Cirrhosae Bulbus is an antitussive and expectorant Chinese medicinal material derived from the dried bulbs of six Fritillaria species. In the 2015 edition of the Chinese Pharmacopoeia, the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) is the officially listed method for their authenfication. Specifically, the ~ 300-bp ITS1 amplicon of only Fritillariae Cirrhosae Bulbus but not other Fritillaria species can be cleaved into two smaller fragments with restriction enzyme SmaI. Considering repeated reported cases of incomplete digestion of ITS1 amplicon, this study aims to investigate the possibility of heterogeneous ITS1 sequences contained in the Fritillariae Cirrhosae Bulbus. METHODS In this study, ITS1 amplicons of Fritillaria Cirrhosae Bulbus and four other Fritillaria species were sequenced on Illumina platform. We utilised high-throughout amplicon sequencing to determine ITS1 haplotypes and their frequencies in Fritillaria genomes. RESULTS Our results showed that all six botanical sources of Fritillariae Cirrhosae Bulbus indeed possess ITS1 haplotypes with no SmaI restriction site, and the average percentages of ITS1 reads containing SmaI restriction site ranged from 63.60% to 91.81%. CONCLUSION Our findings suggest that the incomplete digestion in PCR-RFLP analysis of Fritillariae Cirrhosae Bulbus is caused by the presence of ITS1 haplotypes without SmaI restriction site due to intragenomic heterogeneity.
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Affiliation(s)
- Hoi-Yan Wu
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Ka-Lok Wong
- Government Chinese Medicines Testing Institute, Chinese Medicine Regulatory Office, Department of Health, Shatin, N.T., Hong Kong, China
| | - Sean Tsz-Sum Law
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Wenyang Nong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Kwun-Tin Chan
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Jerome Ho-Lam Hui
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Ge Lin
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Wing-Han Chan
- Government Chinese Medicines Testing Institute, Chinese Medicine Regulatory Office, Department of Health, Shatin, N.T., Hong Kong, China
| | - Pang-Chui Shaw
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China.
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China.
- State Key Laboratory of Research on Bioactivities and Clinical Applications of Medicinal Plants (The Chinese University of Hong Kong) and Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China.
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4
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Veiko NN, Ershova ES, Veiko RV, Umriukhin PE, Kurmyshev MV, Kostyuk GP, Kutsev SI, Kostyuk SV. Mild cognitive impairment is associated with low copy number of ribosomal genes in the genomes of elderly people. Front Genet 2022; 13:967448. [PMID: 36199570 PMCID: PMC9527325 DOI: 10.3389/fgene.2022.967448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
Introduction: Mild cognitive impairments (MCI) accompanying aging are associated with oxidative stress. The ability of cells to respond to stress is determined by the protein synthesis level, which depends on the ribosomes number. Ribosomal deficit was documented in MCI. The number of ribosomes depends, together with other factors, on the number of ribosomal genes copies. We hypothesized that MCI is associated with low rDNA CN in the elderly person genome. Materials and Methods: rDNA CN and the telomere repeat (TR) content were determined in the DNA of peripheral blood leukocytes of 93 elderly people (61–91 years old) with MCI and 365 healthy volunteers (16–91 years old). The method of non-radioactive quantitative hybridization of DNA with biotinylated DNA probes was used for the analysis. Results: In the MCI group, rDNA CN (mean 329 ± 60; median 314 copies, n = 93) was significantly reduced (p < 10–15) compared to controls of the same age with preserved cognitive functions (mean 412 ± 79; median 401 copies, n = 168) and younger (16–60 years) control group (mean 426 ± 109; median 416 copies, n = 197). MCI is also associated with a decrease in TR DNA content. There is no correlation between the content of rDNA and TR in DNA, however, in the group of DNA samples with rDNA CN > 540, TR content range was significantly narrowed compared to the rest of the sample. Conclusion: Mild cognitive impairment is associated with low ribosomal genes copies in the elderly people genomes. A low level of rDNA CN may be one of the causes of ribosomal deficit that was documented in MCI. The potential possibilities of using the rDNA CN indicator as a prognostic marker characterizing human life expectancy are discussed.
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Affiliation(s)
| | - Elizaveta S. Ershova
- Research Centre for Medical Genetics (RCMG), Moscow, Russia
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, V.A. Negovsky Research Institute of General Reanimatology, Moscow, Russia
- *Correspondence: Elizaveta S. Ershova,
| | - Roman V. Veiko
- Research Centre for Medical Genetics (RCMG), Moscow, Russia
| | - Pavel E. Umriukhin
- Research Centre for Medical Genetics (RCMG), Moscow, Russia
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
- P.K. Anokhin Institute of Normal Physiology, Moscow, Russia
| | | | - Georg P. Kostyuk
- Mental-health Clinic No1 Named After N.A. Alexeev, Moscow, Russia
| | | | - Svetlana V. Kostyuk
- Research Centre for Medical Genetics (RCMG), Moscow, Russia
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, V.A. Negovsky Research Institute of General Reanimatology, Moscow, Russia
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5
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Fan W, Eklund E, Sherman RM, Liu H, Pitts S, Ford B, Rajeshkumar NV, Laiho M. Widespread genetic heterogeneity of human ribosomal RNA genes. RNA (NEW YORK, N.Y.) 2022; 28:478-492. [PMID: 35110373 PMCID: PMC8925967 DOI: 10.1261/rna.078925.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 12/28/2021] [Indexed: 05/28/2023]
Abstract
Polymorphism drives survival under stress and provides adaptability. Genetic polymorphism of ribosomal RNA (rRNA) genes derives from internal repeat variation of this multicopy gene, and from interindividual variation. A considerable amount of rRNA sequence heterogeneity has been proposed but has been challenging to estimate given the scarcity of accurate reference sequences. We identified four rDNA copies on chromosome 21 (GRCh38) with 99% similarity to recently introduced reference sequence KY962518.1. We customized a GATK bioinformatics pipeline using the four rDNA loci, spanning a total 145 kb, for variant calling and used high-coverage whole-genome sequencing (WGS) data from the 1000 Genomes Project to analyze variants in 2504 individuals from 26 populations. We identified a total of 3791 variant positions. The variants positioned nonrandomly on the rRNA gene. Invariant regions included the promoter, early 5' ETS, most of 18S, 5.8S, ITS1, and large areas of the intragenic spacer. A total of 470 variant positions were observed on 28S rRNA. The majority of the 28S rRNA variants were located on highly flexible human-expanded rRNA helical folds ES7L and ES27L, suggesting that these represent positions of diversity and are potentially under continuous evolution. Several variants were validated based on RNA-seq analyses. Population analyses showed remarkable ancestry-linked genetic variance and the presence of both high penetrance and frequent variants in the 5' ETS, ITS2, and 28S regions segregating according to the continental populations. These findings provide a genetic view of rRNA gene array heterogeneity and raise the need to functionally assess how the 28S rRNA variants affect ribosome functions.
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Affiliation(s)
- Wenjun Fan
- Department of Radiation Oncology and Molecular Radiation Sciences, and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Eetu Eklund
- Department of Radiation Oncology and Molecular Radiation Sciences, and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Rachel M Sherman
- Department of Computer Science, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Hester Liu
- Department of Radiation Oncology and Molecular Radiation Sciences, and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Stephanie Pitts
- Department of Radiation Oncology and Molecular Radiation Sciences, and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Brittany Ford
- Drug Research Program, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland
| | - N V Rajeshkumar
- Department of Radiation Oncology and Molecular Radiation Sciences, and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Marikki Laiho
- Department of Radiation Oncology and Molecular Radiation Sciences, and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
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6
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Abstract
The complete, ungapped sequence of the short arms of human acrocentric chromosomes (SAACs) is still unknown almost 20 years after the near completion of the Human Genome Project. Yet these short arms of Chromosomes 13, 14, 15, 21, and 22 contain the ribosomal DNA (rDNA) genes, which are of paramount importance for human biology. The sequences of SAACs show an extensive variation in the copy number of the various repetitive elements, the full extent of which is currently unknown. In addition, the full spectrum of repeated sequences, their organization, and the low copy number functional elements are also unknown. The Telomere-to-Telomere (T2T) Project using mainly long-read sequence technology has recently completed the assembly of the genome from a hydatidiform mole, CHM13, and has thus established a baseline reference for further studies on the organization, variation, functional annotation, and impact in human disorders of all the previously unknown genomic segments, including the SAACs. The publication of the initial results of the T2T Project will update and improve the reference genome for a better understanding of the evolution and function of the human genome.
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Affiliation(s)
- Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical Faculty, 1211 Geneva, Switzerland
- Foundation Campus Biotech, 1202 Geneva, Switzerland
- Medigenome, Swiss Institute of Genomic Medicine, 1207 Geneva, Switzerland
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7
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Fernandes MA, Cioffi MDB, Bertollo LAC, da Costa GWWF, da Motta-Neto CC, Borges AT, Soares RX, de Souza AS, Pinthong K, Supiwong W, Tanomtong A, Molina WF. Evolutionary Tracks of Chromosomal Diversification in Surgeonfishes (Acanthuridae: Acanthurus) Along the World's Biogeographic Domains. Front Genet 2021; 12:760244. [PMID: 34777477 PMCID: PMC8586516 DOI: 10.3389/fgene.2021.760244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
Fishes of the genus Acanthurus (Acanthuridae) are strongly related to reef environments, in a broad biogeographic context worldwide. Although their biological aspects are well known, cytogenetic information related to this genus remains incipient. In this study, Acanthurus species from populations inhabiting coastal regions of the Southwest Atlantic (SWA), South Atlantic oceanic islands (Fernando de Noronha Archipelago and Trindade Island), Greater Caribbean (GC), and Indo-Pacific Ocean (the center of the origin of the group) were analyzed to investigate their evolutionary differentiation. For this purpose, we employed conventional cytogenetic procedures and fluorescence in situ hybridization of 18S rDNA, 5S rDNA, and H3 and H2B-H2A histone sequences. The Atlantic species (A. coeruleus, A. chirurgus, and A. bahianus) did not show variations among them, despite their vast continental and insular distribution. In contrast, A. coeruleus from SWA and GC diverged from each other in the number of 18S rDNA sites, a condition likely associated with the barrier created by the outflows of the Amazonas/Orinoco rivers. The geminate species A. tractus had a cytogenetic profile similar to that of A. bahianus. However, the chromosomal macrostructures and the distribution of rDNA and hisDNA sequences revealed moderate to higher rates of diversification when Acanthurus species from recently colonized areas (Atlantic Ocean) were compared to A. triostegus, a representative species from the Indian Ocean. Our cytogenetic data covered all Acanthurus species from the Western Atlantic, tracked phylogenetic diversification throughout the dispersive process of the genus, and highlighted the probable diversifying role of ocean barriers in this process.
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Affiliation(s)
- Maria Aparecida Fernandes
- Department of Cell Biology and Genetics, Biosciences Center, Federal University of Rio Grande do Norte, Natal, Brazil
| | | | | | | | - Clóvis Coutinho da Motta-Neto
- Department of Cell Biology and Genetics, Biosciences Center, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Amanda Tôrres Borges
- Department of Cell Biology and Genetics, Biosciences Center, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Rodrigo Xavier Soares
- Department of Cell Biology and Genetics, Biosciences Center, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Allyson Santos de Souza
- Department of Cell Biology and Genetics, Biosciences Center, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Krit Pinthong
- Department of Fundamental Science, Faculty of Science and Technology, Surindra Rajabhat University, Muang, Thailand
| | - Weerayuth Supiwong
- Applied Science Program, Faculty of Interdisciplinary Studies, Khon Kaen University, Nong Khai Campus, Nong Khai, Thailand
| | - Alongklod Tanomtong
- Program of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Wagner Franco Molina
- Department of Cell Biology and Genetics, Biosciences Center, Federal University of Rio Grande do Norte, Natal, Brazil
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8
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Hori Y, Shimamoto A, Kobayashi T. The human ribosomal DNA array is composed of highly homogenized tandem clusters. Genome Res 2021; 31:1971-1982. [PMID: 34407983 PMCID: PMC8559705 DOI: 10.1101/gr.275838.121] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/09/2021] [Indexed: 11/25/2022]
Abstract
The structure of the human ribosomal DNA (rDNA) cluster has traditionally been hard to analyze owing to its highly repetitive nature. However, the recent development of long-read sequencing technology, such as Oxford Nanopore sequencing, has enabled us to study the large-scale structure of the genome. Using this technology, we found that human cells have a quite regular rDNA structure. Although each human rDNA copy has some variations in its noncoding region, contiguous copies of rDNA are similar, suggesting that homogenization through gene conversion frequently occurs between copies. Analysis of rDNA methylation by Nanopore sequencing further showed that all the noncoding regions are heavily methylated, whereas about half of the coding regions are clearly unmethylated. The ratio of unmethylated copies, which are speculated to be transcriptionally active, was lower in individuals with a higher rDNA copy number, suggesting that there is a mechanism that keeps the active copy number stable. In addition, the rDNA in progeroid syndrome patient cells with reduced DNA repair activity had more unstable copies compared with control normal cells, although the rate was much lower than previously reported using a fiber-FISH method. Collectively, our results clarify the view of rDNA stability and transcription regulation in human cells, indicating the presence of mechanisms for both homogenizations to ensure sequence quality and maintenance of active copies for cellular functions.
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Affiliation(s)
- Yutaro Hori
- Institute for Quantitative Biosciences, the University of Tokyo, Tokyo 133-0032, Japan
| | - Akira Shimamoto
- Faculty of Pharmaceutical Sciences, Sanyo-Onoda City University, Sanyo Onoda, Yamaguchi 756-0884, Japan
| | - Takehiko Kobayashi
- Institute for Quantitative Biosciences, the University of Tokyo, Tokyo 133-0032, Japan
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9
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The genomic structure of a human chromosome 22 nucleolar organizer region determined by TAR cloning. Sci Rep 2021; 11:2997. [PMID: 33542373 PMCID: PMC7862453 DOI: 10.1038/s41598-021-82565-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 01/18/2021] [Indexed: 12/13/2022] Open
Abstract
The 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.
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10
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Smirnov E, Chmúrčiaková N, Liška F, Bažantová P, Cmarko D. Variability of Human rDNA. Cells 2021; 10:cells10020196. [PMID: 33498263 PMCID: PMC7909238 DOI: 10.3390/cells10020196] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 12/15/2022] Open
Abstract
In human cells, ribosomal DNA (rDNA) is arranged in ten clusters of multiple tandem repeats. Each repeat is usually described as consisting of two parts: the 13 kb long ribosomal part, containing three genes coding for 18S, 5.8S and 28S RNAs of the ribosomal particles, and the 30 kb long intergenic spacer (IGS). However, this standard scheme is, amazingly, often altered as a result of the peculiar instability of the locus, so that the sequence of each repeat and the number of the repeats in each cluster are highly variable. In the present review, we discuss the causes and types of human rDNA instability, the methods of its detection, its distribution within the locus, the ways in which it is prevented or reversed, and its biological significance. The data of the literature suggest that the variability of the rDNA is not only a potential cause of pathology, but also an important, though still poorly understood, aspect of the normal cell physiology.
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11
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Seal RL, Chen LL, Griffiths-Jones S, Lowe TM, Mathews MB, O'Reilly D, Pierce AJ, Stadler PF, Ulitsky I, Wolin SL, Bruford EA. A guide to naming human non-coding RNA genes. EMBO J 2020; 39:e103777. [PMID: 32090359 PMCID: PMC7073466 DOI: 10.15252/embj.2019103777] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/23/2020] [Accepted: 01/30/2020] [Indexed: 12/15/2022] Open
Abstract
Research on non-coding RNA (ncRNA) is a rapidly expanding field. Providing an official gene symbol and name to ncRNA genes brings order to otherwise potential chaos as it allows unambiguous communication about each gene. The HUGO Gene Nomenclature Committee (HGNC, www.genenames.org) is the only group with the authority to approve symbols for human genes. The HGNC works with specialist advisors for different classes of ncRNA to ensure that ncRNA nomenclature is accurate and informative, where possible. Here, we review each major class of ncRNA that is currently annotated in the human genome and describe how each class is assigned a standardised nomenclature.
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Affiliation(s)
- Ruth L Seal
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Science, Shanghai, China
| | - Sam Griffiths-Jones
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Todd M Lowe
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Michael B Mathews
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Dawn O'Reilly
- Computational Biology and Integrative Genomics Lab, MRC/CRUK Oxford Institute and Department of Oncology, University of Oxford, Oxford, UK
| | - Andrew J Pierce
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.,Institute of Theoretical Chemistry, University of Vienna, Vienna, Austria.,Facultad de Ciencias, Universidad National de Colombia, Sede Bogotá, Colombia.,Santa Fe Institute, Santa Fe, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Sandra L Wolin
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Elspeth A Bruford
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
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12
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Life time of some RNA products of rDNA intergenic spacer in HeLa cells. Histochem Cell Biol 2019; 152:271-280. [DOI: 10.1007/s00418-019-01804-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2019] [Indexed: 12/21/2022]
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13
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Salim D, Gerton JL. Ribosomal DNA instability and genome adaptability. Chromosome Res 2019; 27:73-87. [DOI: 10.1007/s10577-018-9599-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 01/03/2023]
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14
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Learning-induced ribosomal RNA is required for memory consolidation in mice-Evidence of differentially expressed rRNA variants in learning and memory. PLoS One 2018; 13:e0203374. [PMID: 30281601 PMCID: PMC6169870 DOI: 10.1371/journal.pone.0203374] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 08/20/2018] [Indexed: 12/01/2022] Open
Abstract
The transition from short-term to long-term forms of synaptic plasticity requires protein synthesis and new gene expression. Most efforts to understand experience-induced changes in neuronal gene expression have focused on the transcription products of RNA polymerase II—primarily mRNAs and the proteins they encode. We recently showed that nucleolar integrity and activity-dependent ribosomal RNA (rRNA) synthesis are essential for the maintenance of hippocampal long-term potentiation (LTP). Consequently, the synaptic plasticity and memory hypothesis predicts that nucleolar integrity and activity dependent rRNA synthesis would be required for Long-term memory (LTM). We tested this prediction using the hippocampus-dependent, Active Place Avoidance (APA) spatial memory task and found that training induces de novo rRNA synthesis in mouse dorsal hippocampus. This learning-induced increase in nucleolar activity and rRNA synthesis persists at least 24 h after training. In addition, intra-hippocampal injection of the Pol I specific inhibitor, CX-5461 prior to training, revealed that de novo rRNA synthesis is required for 24 h memory, but not for learning. Using qPCR to assess activity-dependent changes in gene expression, we found that of seven known rRNA expression variants (v-rRNAs), only one, v-rRNA IV, is significantly upregulated right after training. These data indicate that learning induced v-rRNAs are crucial for LTM, and constitute the first evidence that differential rRNA gene expression plays a role in memory.
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Kim JH, Dilthey AT, Nagaraja R, Lee HS, Koren S, Dudekula D, Wood Iii WH, Piao Y, Ogurtsov AY, Utani K, Noskov VN, Shabalina SA, Schlessinger D, Phillippy AM, Larionov V. Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing. Nucleic Acids Res 2018; 46:6712-6725. [PMID: 29788454 PMCID: PMC6061828 DOI: 10.1093/nar/gky442] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 05/08/2018] [Indexed: 12/31/2022] Open
Abstract
Despite the key role of the human ribosome in protein biosynthesis, little is known about the extent of sequence variation in ribosomal DNA (rDNA) or its pre-rRNA and rRNA products. We recovered ribosomal DNA segments from a single human chromosome 21 using transformation-associated recombination (TAR) cloning in yeast. Accurate long-read sequencing of 13 isolates covering ∼0.82 Mb of the chromosome 21 rDNA complement revealed substantial variation among tandem repeat rDNA copies, several palindromic structures and potential errors in the previous reference sequence. These clones revealed 101 variant positions in the 45S transcription unit and 235 in the intergenic spacer sequence. Approximately 60% of the 45S variants were confirmed in independent whole-genome or RNA-seq data, with 47 of these further observed in mature 18S/28S rRNA sequences. TAR cloning and long-read sequencing enabled the accurate reconstruction of multiple rDNA units and a new, high-quality 44 838 bp rDNA reference sequence, which we have annotated with variants detected from chromosome 21 of a single individual. The large number of variants observed reveal heterogeneity in human rDNA, opening up the possibility of corresponding variations in ribosome dynamics.
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MESH Headings
- Animals
- Cell Line
- Chromosomes, Human, Pair 21
- Cloning, Molecular
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/isolation & purification
- DNA, Ribosomal Spacer/chemistry
- Genes, rRNA
- Genetic Variation
- Humans
- Mice
- Nucleic Acid Conformation
- Nucleolus Organizer Region/chemistry
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/metabolism
- Sequence Analysis, DNA
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Affiliation(s)
- Jung-Hyun Kim
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD 20892, USA
| | - Alexander T Dilthey
- National Human Genome Research Institute, Computational and Statistical Genomics Branch, Bethesda, MD 20892, USA
| | - Ramaiah Nagaraja
- National Institute on Aging, Laboratory of Genetics and Genomics, Baltimore, MD 21224, USA
| | - Hee-Sheung Lee
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD 20892, USA
| | - Sergey Koren
- National Human Genome Research Institute, Computational and Statistical Genomics Branch, Bethesda, MD 20892, USA
| | - Dawood Dudekula
- National Institute on Aging, Laboratory of Genetics and Genomics, Baltimore, MD 21224, USA
| | - William H Wood Iii
- National Institute on Aging, Laboratory of Genetics and Genomics, Baltimore, MD 21224, USA
| | - Yulan Piao
- National Institute on Aging, Laboratory of Genetics and Genomics, Baltimore, MD 21224, USA
| | - Aleksey Y Ogurtsov
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20892, USA
| | - Koichi Utani
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD 20892, USA
| | - Vladimir N Noskov
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD 20892, USA
| | - Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20892, USA
| | - David Schlessinger
- National Institute on Aging, Laboratory of Genetics and Genomics, Baltimore, MD 21224, USA
| | - Adam M Phillippy
- National Human Genome Research Institute, Computational and Statistical Genomics Branch, Bethesda, MD 20892, USA
| | - Vladimir Larionov
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD 20892, USA
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Sochorová J, Garcia S, Gálvez F, Symonová R, Kovařík A. Evolutionary trends in animal ribosomal DNA loci: introduction to a new online database. Chromosoma 2018; 127:141-150. [PMID: 29192338 PMCID: PMC5818627 DOI: 10.1007/s00412-017-0651-8] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 11/24/2022]
Abstract
Ribosomal DNA (rDNA) loci encoding 5S and 45S (18S-5.8S-28S) rRNAs are important components of eukaryotic chromosomes. Here, we set up the animal rDNA database containing cytogenetic information about these loci in 1343 animal species (264 families) collected from 542 publications. The data are based on in situ hybridisation studies (both radioactive and fluorescent) carried out in major groups of vertebrates (fish, reptiles, amphibians, birds, and mammals) and invertebrates (mostly insects and mollusks). The database is accessible online at www.animalrdnadatabase.com . The median number of 45S and 5S sites was close to two per diploid chromosome set for both rDNAs despite large variation (1-74 for 5S and 1-54 for 45S sites). No significant correlation between the number of 5S and 45S rDNA loci was observed, suggesting that their distribution and amplification across the chromosomes follow independent evolutionary trajectories. Each group, irrespective of taxonomic classification, contained rDNA sites at any chromosome location. However, the distal and pericentromeric positions were the most prevalent (> 75% karyotypes) for 45S loci, while the position of 5S loci was more variable. We also examined potential relationships between molecular attributes of rDNA (homogenisation and expression) and cytogenetic parameters such as rDNA positions, chromosome number, and morphology.
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Affiliation(s)
- Jana Sochorová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, CZ-61265, Brno, Czech Republic
| | - Sònia Garcia
- Institut Botànic de Barcelona (IBB-CSIC-ICUB), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
| | - Francisco Gálvez
- Bioscripts-Centro de Investigación y Desarrollo de Recursos Científicos, 41012, Sevilla, Andalusia, Spain
| | - Radka Symonová
- Faculty of Science, University of Hradec Kralove, Hradecka 1285, CZ-50003, Hradec Kralove, Czech Republic
| | - Aleš Kovařík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, CZ-61265, Brno, Czech Republic.
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Rabanal FA, Mandáková T, Soto-Jiménez LM, Greenhalgh R, Parrott DL, Lutzmayer S, Steffen JG, Nizhynska V, Mott R, Lysak MA, Clark RM, Nordborg M. Epistatic and allelic interactions control expression of ribosomal RNA gene clusters in Arabidopsis thaliana. Genome Biol 2017; 18:75. [PMID: 28464948 PMCID: PMC5414317 DOI: 10.1186/s13059-017-1209-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 04/06/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Ribosomal RNA (rRNA) accounts for the majority of the RNA in eukaryotic cells, and is encoded by hundreds to thousands of nearly identical gene copies, only a subset of which are active at any given time. In Arabidopsis thaliana, 45S rRNA genes are found in two large ribosomal DNA (rDNA) clusters and little is known about the contribution of each to the overall transcription pattern in the species. RESULTS By taking advantage of genome sequencing data from the 1001 Genomes Consortium, we characterize rRNA gene sequence variation within and among accessions. Notably, variation is not restricted to the pre-rRNA sequences removed during processing, but it is also present within the highly conserved ribosomal subunits. Through linkage mapping we assign these variants to a particular rDNA cluster unambiguously and use them as reporters of rDNA cluster-specific expression. We demonstrate that rDNA cluster-usage varies greatly among accessions and that rDNA cluster-specific expression and silencing is controlled via genetic interactions between entire rDNA cluster haplotypes (alleles). CONCLUSIONS We show that rRNA gene cluster expression is controlled via complex epistatic and allelic interactions between rDNA haplotypes that apparently regulate the entire rRNA gene cluster. Furthermore, the sequence polymorphism we discovered implies that the pool of rRNA in a cell may be heterogeneous, which could have functional consequences.
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Affiliation(s)
- Fernando A Rabanal
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria.
| | - Terezie Mandáková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Luz M Soto-Jiménez
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | | | - David L Parrott
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | - Stefan Lutzmayer
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Joshua G Steffen
- Department of Natural Sciences, Colby-Sawyer College, New London, NH, USA
| | - Viktoria Nizhynska
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Richard Mott
- Genetics Institute, University College London (UCL), Gower Street, London, WC1E 6BT, UK
| | - Martin A Lysak
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Richard M Clark
- Department of Biology, University of Utah, Salt Lake City, UT, USA
- Center for Cell and Genome Science, University of Utah, Salt Lake City, UT, USA
| | - Magnus Nordborg
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria.
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Abstract
Nucleoli are formed on the basis of ribosomal genes coding for RNAs of ribosomal particles, but also include a great variety of other DNA regions. In this article, we discuss the characteristics of ribosomal DNA: the structure of the rDNA locus, complex organization and functions of the intergenic spacer, multiplicity of gene copies in one cell, selective silencing of genes and whole gene clusters, relation to components of nucleolar ultrastructure, specific problems associated with replication. We also review current data on the role of non-ribosomal DNA in the organization and function of nucleoli. Finally, we discuss probable causes preventing efficient visualization of DNA in nucleoli.
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Devis D, Firth SM, Liang Z, Byrne ME. Dosage Sensitivity of RPL9 and Concerted Evolution of Ribosomal Protein Genes in Plants. FRONTIERS IN PLANT SCIENCE 2015; 6:1102. [PMID: 26734020 PMCID: PMC4679983 DOI: 10.3389/fpls.2015.01102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 11/22/2015] [Indexed: 05/19/2023]
Abstract
The ribosome in higher eukaryotes is a large macromolecular complex composed of four rRNAs and eighty different ribosomal proteins. In plants, each ribosomal protein is encoded by multiple genes. Duplicate genes within a family are often necessary to provide a threshold dose of a ribosomal protein but in some instances appear to have non-redundant functions. Here, we addressed whether divergent members of the RPL9 gene family are dosage sensitive or whether these genes have non-overlapping functions. The RPL9 family in Arabidopsis thaliana comprises two nearly identical members, RPL9B and RPL9C, and a more divergent member, RPL9D. Mutations in RPL9C and RPL9D genes lead to delayed growth early in development, and loss of both genes is embryo lethal, indicating that these are dosage-sensitive and redundant genes. Phylogenetic analysis of RPL9 as well as RPL4, RPL5, RPL27a, RPL36a, and RPS6 family genes in the Brassicaceae indicated that multicopy ribosomal protein genes have been largely retained following whole genome duplication. However, these gene families also show instances of tandem duplication, small scale deletion, and evidence of gene conversion. Furthermore, phylogenetic analysis of RPL9 genes in angiosperm species showed that genes within a species are more closely related to each other than to RPL9 genes in other species, suggesting ribosomal protein genes undergo convergent evolution. Our analysis indicates that ribosomal protein gene retention following whole genome duplication contributes to the number of genes in a family. However, small scale rearrangements influence copy number and likely drive concerted evolution of these dosage-sensitive genes.
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Berríos S, Manieu C, López-Fenner J, Ayarza E, Page J, González M, Manterola M, Fernández-Donoso R. Robertsonian chromosomes and the nuclear architecture of mouse meiotic prophase spermatocytes. Biol Res 2014; 47:16. [PMID: 25027603 PMCID: PMC4101721 DOI: 10.1186/0717-6287-47-16] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 04/21/2014] [Indexed: 11/06/2022] Open
Abstract
Background The nuclear architecture of meiotic prophase spermatocytes is based on higher-order patterns of spatial associations among chromosomal domains from different bivalents. The meiotic nuclear architecture depends on the chromosome characteristics and consequently is prone to modification by chromosomal rearrangements. In this work, we consider Mus domesticus spermatocytes with diploid chromosome number 2n = 40, all telocentric, and investigate a possible modification of the ancestral nuclear architecture due to the emergence of derived Rb chromosomes, which may be present in the homozygous or heterozygous condition. Results In the 2n = 40 spermatocyte nuclei random associations mediated by pericentromeric heterochromatin among the 19 telocentric bivalents ocurr at the nuclear periphery. The observed frequency of associations among them, made distinguishable by specific probes and FISH, seems to be the same for pairs that may or may not form Rb chromosomes. In the homozygote Rb 2n = 24 spermatocytes, associations also mediated by pericentromeric heterochromatin occur mainly between the three telocentric or the eight metacentric bivalents themselves. In heterozygote Rb 2n = 32 spermatocytes all heterochromatin is localized at the nuclear periphery, yet associations are mainly observed among the three telocentric bivalents and between the asynaptic axes of the trivalents. Conclusions The Rb chromosomes pose sharp restrictions for interactions in the 2n = 24 and 2n = 32 spermatocytes, as compared to the ample possibilities for interactions between bivalents in the 2n = 40 spermatocytes. Undoubtedly the emergence of Rb chromosomes changes the ancestral nuclear architecture of 2n = 40 spermatocytes since they establish new types of interactions among chromosomal domains, particularly through centromeric and heterochromatic regions at the nuclear periphery among telocentric and at the nuclear center among Rb metacentric ones.
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Disparate molecular evolution of two types of repetitive DNAs in the genome of the grasshopper Eyprepocnemis plorans. Heredity (Edinb) 2013; 112:531-42. [PMID: 24346496 DOI: 10.1038/hdy.2013.135] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 11/14/2013] [Indexed: 11/09/2022] Open
Abstract
Wide arrays of repetitive DNA sequences form an important part of eukaryotic genomes. These repeats appear to evolve as coherent families, where repeats within a family are more similar to each other than to other orthologous representatives in related species. The continuous homogenization of repeats, through selective and non-selective processes, is termed concerted evolution. Ascertaining the level of variation between repeats is crucial to determining which evolutionary model best explains the homogenization observed for these sequences. Here, for the grasshopper Eyprepocnemis plorans, we present the analysis of intragenomic diversity for two repetitive DNA sequences (a satellite DNA (satDNA) and the 45S rDNA) resulting from the independent microdissection of several chromosomes. Our results show different homogenization patterns for these two kinds of paralogous DNA sequences, with a high between-chromosome structure for rDNA but no structure at all for the satDNA. This difference is puzzling, considering the adjacent localization of the two repetitive DNAs on paracentromeric regions in most chromosomes. The disparate homogenization patterns detected for these two repetitive DNA sequences suggest that several processes participate in the concerted evolution in E. plorans, and that these mechanisms might not work as genome-wide processes but rather as sequence-specific ones.
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Karlep L, Reintamm T, Kelve M. Intragenomic Profiling Using Multicopy Genes: The rDNA Internal Transcribed Spacer Sequences of the Freshwater Sponge Ephydatia fluviatilis. PLoS One 2013; 8:e66601. [PMID: 23825547 PMCID: PMC3688955 DOI: 10.1371/journal.pone.0066601] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 05/07/2013] [Indexed: 11/18/2022] Open
Abstract
Multicopy genes, like ribosomal RNA genes (rDNA), are widely used to describe and distinguish individuals. Despite concerted evolution that homogenizes a large number of rDNA gene copies, the presence of different gene variants within a genome has been reported. Characterization of an organism by defining every single variant of tens to thousands of rDNA repeat units present in a eukaryotic genome would be quite unreasonable. Here we provide an alternative approach for the characterization of a set of internal transcribed spacer sequences found within every rDNA repeat unit by implementing direct sequencing methodology. The prominent allelic variants and their relative amounts characterizing an individual can be described by a single sequencing electropherogram of the mixed amplicon containing the variants present within the genome. We propose a method for rational analysis of heterogeneity of multicopy genes by compiling a profile based on quantification of different sequence variants of the internal transcribed spacers of the freshwater sponge Ephydatia fluviatilis as an example. In addition to using conventional substitution analysis, we have developed a mathematical method, the proportion model method, to quantify the relative amounts of allelic variants of different length using data from direct sequencing of the heterogeneous amplicon. This method is based on determining the expected signal intensity values (corresponding to peak heights from the sequencing electropherogram) by sequencing clones from the same or highly similar amplicon and comparing hypothesized combinations against the values obtained by direct sequencing of the heterogeneous amplicon. This method allowed to differentiate between all specimens analysed.
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Affiliation(s)
- Liisi Karlep
- Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | - Tõnu Reintamm
- Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | - Merike Kelve
- Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
- * E-mail:
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Mirete S, Patiño B, Jurado M, Vázquez C, González-Jaén MT. Structural variation and dynamics of the nuclear ribosomal intergenic spacer region in key members of the Gibberella fujikuroi species complex. Genome 2013; 56:205-13. [PMID: 23706073 DOI: 10.1139/gen-2013-0008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The intergenic spacer (IGS) region of the ribosomal DNA was cloned and sequenced in eight species within the Gibberella fujikuroi species complex with anamorphs in the genus Fusarium, a group that includes the most relevant toxigenic species. DNA sequence analyses revealed two categories of repeated elements: long repeats and short repeats of 125 and 8 bp, respectively. Long repeats were present in two copies and were conserved in all the species analyzed, whereas different numbers of short repeat elements were observed, leading to species-specific IGS sequences with different length. In Fusarium subglutinans and Fusarium nygamai, these differences seemed to be the result of duplication and deletion events. Here, we propose a model based on unequal crossing over that can explain these processes. The partial IGS sequence of 22 Fusarium proliferatum isolates was also obtained to study variation at the intraspecific level. The results revealed no differences in terms of number or pattern of repeated elements and detected frequent gene conversion events. These results suggest that the homogenization observed at the intraspecific level might not be achieved primarily by unequal crossing-over events but rather by processes associated with recombination such as gene conversion events.
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Affiliation(s)
- Salvador Mirete
- Department of Molecular Evolution, Centro de Astrobiología, CSIC-INTA, Torrejón de Ardoz, 28850 Madrid, Spain.
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Bompfünewerer AF, Flamm C, Fried C, Fritzsch G, Hofacker IL, Lehmann J, Missal K, Mosig A, Müller B, Prohaska SJ, Stadler BMR, Stadler PF, Tanzer A, Washietl S, Witwer C. Evolutionary patterns of non-coding RNAs. Theory Biosci 2012; 123:301-69. [PMID: 18202870 DOI: 10.1016/j.thbio.2005.01.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2004] [Accepted: 01/24/2005] [Indexed: 01/04/2023]
Abstract
A plethora of new functions of non-coding RNAs (ncRNAs) have been discovered in past few years. In fact, RNA is emerging as the central player in cellular regulation, taking on active roles in multiple regulatory layers from transcription, RNA maturation, and RNA modification to translational regulation. Nevertheless, very little is known about the evolution of this "Modern RNA World" and its components. In this contribution, we attempt to provide at least a cursory overview of the diversity of ncRNAs and functional RNA motifs in non-translated regions of regular messenger RNAs (mRNAs) with an emphasis on evolutionary questions. This survey is complemented by an in-depth analysis of examples from different classes of RNAs focusing mostly on their evolution in the vertebrate lineage. We present a survey of Y RNA genes in vertebrates and study the molecular evolution of the U7 snRNA, the snoRNAs E1/U17, E2, and E3, the Y RNA family, the let-7 microRNA (miRNA) family, and the mRNA-like evf-1 gene. We furthermore discuss the statistical distribution of miRNAs in metazoans, which suggests an explosive increase in the miRNA repertoire in vertebrates. The analysis of the transcription of ncRNAs suggests that small RNAs in general are genetically mobile in the sense that their association with a hostgene (e.g. when transcribed from introns of a mRNA) can change on evolutionary time scales. The let-7 family demonstrates, that even the mode of transcription (as intron or as exon) can change among paralogous ncRNA.
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25
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UbC gene allele frequency in Korean population and novel UbC mosaic repeat unit formation. Genes Genomics 2012. [DOI: 10.1007/s13258-011-0237-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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26
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Wang Y, Hao B, Zhang Q, Tuo E, Sun G, Zhang R, Jin S, Zhu M, Wang Y, Hsiang T. Discovery of multiple IGS haplotypes within genotypes of Puccinia striiformis. Fungal Biol 2012; 116:522-8. [PMID: 22483050 DOI: 10.1016/j.funbio.2012.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Revised: 02/02/2012] [Accepted: 02/05/2012] [Indexed: 10/28/2022]
Abstract
In a search for specific molecular markers for population analysis of Puccinia striiformis f. sp. tritici, the ribosomal DNA (rDNA) intergenic spacer (IGS) 1 region (rDNA-IGS1, between the 28S and the 5S rDNA genes) was amplified, cloned, and sequenced. It was found to exhibit multiple bands and length polymorphism. Surprisingly, single isolates were found to possess between three to five different IGS1 haplotypes. Bands were cloned and sequenced, and two highly variable regions (α and β) were found between conserved regions, with repeat units interspersed in both types of regions. There were 14 different repeat units, and these were sometimes grouped further into four combinations of repeat units, with a few individual nucleotides (A or C) inserted between the repeats. Among three geographically dispersed isolates, the variable region α was divided into eight types, and the variable region β was divided into two types based on repeat units. Most of the 14 repeat units were shared by the variable and the conserved regions. Among the three isolates, there were a total of 12 IGS1 haplotypes, but some of these were shared between isolates such that there were only eight unique haplotypes. The occurrence of multiple haplotypes within single isolates may be useful for analyzing the population structure, tracking the origin of annual epidemics and providing insights into evolutionary biology of this pathogen.
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Affiliation(s)
- Yanchun Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, PR China
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Britton-Davidian J, Cazaux B, Catalan J. Chromosomal dynamics of nucleolar organizer regions (NORs) in the house mouse: micro-evolutionary insights. Heredity (Edinb) 2011; 108:68-74. [PMID: 22086078 DOI: 10.1038/hdy.2011.105] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Variation in the number and chromosomal location of nucleolar organizer regions (NORs) was studied in the house mouse, Mus musculus (2n=40). From an origin in Western Asia, this species colonized the Middle East, Europe and Asia. This expansion was accompanied by diversification into five subspecies. NOR diversity was revealed by fluorescence in situ hybridization using 18S and 28S probes on specimens spanning Asia to Western Europe. The results showed that the house mouse genome possessed a large number of NOR-bearing autosomes and a surprisingly high rate of polymorphism for the presence/absence of rRNA genes on all these chromosomes. All NOR sites were adjacent to the centromere except for two that were telomeric. Subspecific differentiation established from the NOR frequency data was concordant with the overall pattern of radiation proposed from molecular studies, but highlighted several discrepancies that need to be further addressed. NOR diversity in M. musculus consisted of a large number of polymorphic NORs that were common to at least two subspecies, and a smaller number of NORs that were unique to one subspecies. The most parsimonious scenario argues in favor of a subspecific differentiation by lineage sorting of ancestral NOR polymorphisms; only the unique NORs would have appeared by inter-chromosomal transposition, except for the two telomeric ones that may have originated by hybridization with another species. Such a scenario provides an alternative view from the one prevailing in most systematic and phylogenetic analyses that NORs have a high transposition rate due to concerted evolution of rRNA genes.
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Affiliation(s)
- J Britton-Davidian
- Institut des Sciences de l'Evolution, Université Montpellier 2, Montpellier cedex, France.
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28
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Cazaux B, Catalan J, Veyrunes F, Douzery EJ, Britton-Davidian J. Are ribosomal DNA clusters rearrangement hotspots?: a case study in the genus Mus (Rodentia, Muridae). BMC Evol Biol 2011; 11:124. [PMID: 21569527 PMCID: PMC3112088 DOI: 10.1186/1471-2148-11-124] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 05/13/2011] [Indexed: 11/10/2022] Open
Abstract
Background Recent advances in comparative genomics have considerably improved our knowledge of the evolution of mammalian karyotype architecture. One of the breakthroughs was the preferential localization of evolutionary breakpoints in regions enriched in repetitive sequences (segmental duplications, telomeres and centromeres). In this context, we investigated the contribution of ribosomal genes to genome reshuffling since they are generally located in pericentromeric or subtelomeric regions, and form repeat clusters on different chromosomes. The target model was the genus Mus which exhibits a high rate of karyotypic change, a large fraction of which involves centromeres. Results The chromosomal distribution of rDNA clusters was determined by in situ hybridization of mouse probes in 19 species. Using a molecular-based reference tree, the phylogenetic distribution of clusters within the genus was reconstructed, and the temporal association between rDNA clusters, breakpoints and centromeres was tested by maximum likelihood analyses. Our results highlighted the following features of rDNA cluster dynamics in the genus Mus: i) rDNA clusters showed extensive diversity in number between species and an almost exclusive pericentromeric location, ii) a strong association between rDNA sites and centromeres was retrieved which may be related to their shared constraint of concerted evolution, iii) 24% of the observed breakpoints mapped near an rDNA cluster, and iv) a substantial rate of rDNA cluster change (insertion, deletion) also occurred in the absence of chromosomal rearrangements. Conclusions This study on the dynamics of rDNA clusters within the genus Mus has revealed a strong evolutionary relationship between rDNA clusters and centromeres. Both of these genomic structures coincide with breakpoints in the genus Mus, suggesting that the accumulation of a large number of repeats in the centromeric region may contribute to the high level of chromosome repatterning observed in this group. However, the elevated rate of rDNA change observed in the chromosomally invariant clade indicates that the presence of these sequences is insufficient to lead to genome instability. In agreement with recent studies, these results suggest that additional factors such as modifications of the epigenetic state of DNA may be required to trigger evolutionary plasticity.
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Affiliation(s)
- Benoîte Cazaux
- Institut des Sciences de l'Evolution, UMR5554 CNRS/Université Montpellier II, France.
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Escobar JS, Glémin S, Galtier N. GC-Biased Gene Conversion Impacts Ribosomal DNA Evolution in Vertebrates, Angiosperms, and Other Eukaryotes. Mol Biol Evol 2011; 28:2561-75. [DOI: 10.1093/molbev/msr079] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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Chang KD, Fang SA, Chang FC, Chung MC. Chromosomal conservation and sequence diversity of ribosomal RNA genes of two distant Oryza species. Genomics 2010; 96:181-90. [PMID: 20580815 DOI: 10.1016/j.ygeno.2010.05.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2009] [Revised: 04/30/2010] [Accepted: 05/18/2010] [Indexed: 01/31/2023]
Abstract
Contrary to the chromosomal polymorphism of 45S ribosomal genes (45S rDNA) loci in other Oryza species, each of Oryza australiensis and Oryza brachyantha has only one 45S rDNA locus at the most conserved position of 45S rDNAs in Oryza. O. australiensis and O. brachyantha are known phylogenetically distant and have extremely different genome sizes among diploid Oryza species. This study reveals that the sequences and organizations of intergenic spacer (IGS) for 45S rDNA of both O. australiensis and O. brachyantha are different from other Oryza species. The IGS of O. australiensis contains 13 tandem repeats and only one transcriptional initiation site, while there are four tandem repeats and three transcriptional initiation sites in the IGS of O. brachyantha. Our results suggest different evolution processes of orthologous rDNA loci in the genus Oryza. Here we also demonstrate an efficient strategy to study locus-specific IGS before whole genome sequences data are available.
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Affiliation(s)
- Kwei-Duan Chang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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Ambrose CD, Crease TJ. Evolution of Repeated Sequences in the Ribosomal DNA Intergenic Spacer of 32 Arthropod Species. J Mol Evol 2010; 70:247-59. [DOI: 10.1007/s00239-010-9324-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Accepted: 02/02/2010] [Indexed: 11/25/2022]
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Wang S, Zhang L, Hu J, Bao Z, Liu Z. Molecular and cellular evidence for biased mitotic gene conversion in hybrid scallop. BMC Evol Biol 2010; 10:6. [PMID: 20064268 PMCID: PMC2818637 DOI: 10.1186/1471-2148-10-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2009] [Accepted: 01/11/2010] [Indexed: 11/10/2022] Open
Abstract
Background Concerted evolution has been believed to account for homogenization of genes within multigene families. However, the exact mechanisms involved in the homogenization have been under debate. Use of interspecific hybrid system allows detection of greater level of sequence variation, and therefore, provide advantage for tracing the sequence changes. In this work, we have used an interspecific hybrid system of scallop to study the sequence homogenization processes of rRNA genes. Results Through the use of a hybrid scallop system (Chlamys farreri ♀ × Argopecten irradians ♂), here we provide solid molecular and cellular evidence for homogenization of the rDNA sequences into maternal genotypes. The ITS regions of the rDNA of the two scallop species exhibit distinct sequences and thereby restriction fragment length polymorphism (RFLP) patterns, and such a difference was exploited to follow the parental ITS contributions in the F1 hybrid during early development using PCR-RFLP. The representation of the paternal ITS decreased gradually in the hybrid during the development of the hybrid, and almost diminished at the 14th day after fertilization while the representation of the maternal ITS gradually increased. Chromosomal-specific fluorescence in situ hybridization (FISH) analysis in the hybrid revealed the presence of maternal ITS sequences on the paternal ITS-bearing chromosomes, but not vice versa. Sequence analysis of the ITS region in the hybrid not only confirmed the maternally biased conversion, but also allowed the detection of six recombinant variants in the hybrid involving short recombination regions, suggesting that site-specific recombination may be involved in the maternally biased gene conversion. Conclusion Taken together, these molecular and cellular evidences support rapid concerted gene evolution via maternally biased gene conversion. As such a process would lead to the expression of only one parental genotype, and have the opportunities to generate recombinant intermediates; this work may also have implications in novel hybrid zone alleles and genetic imprinting, as well as in concerted gene evolution. In the course of evolution, many species may have evolved involving some levels of hybridization, intra- or interspecific, the sex-biased sequence homogenization could have led to a greater role of one sex than the other in some species.
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Affiliation(s)
- Shi Wang
- Key Laboratory of Marine Genetics and Breeding of Ministry of Education, Ocean University of China, Qingdao 266003, China
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Stage DE, Eickbush TH. Origin of nascent lineages and the mechanisms used to prime second-strand DNA synthesis in the R1 and R2 retrotransposons of Drosophila. Genome Biol 2009; 10:R49. [PMID: 19416522 PMCID: PMC2718515 DOI: 10.1186/gb-2009-10-5-r49] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Revised: 03/27/2009] [Accepted: 05/05/2009] [Indexed: 01/31/2023] Open
Abstract
Comparative analysis of 12 Drosophila genomes reveals insights into the evolution and mechanism of integration of R1 and R2 retrotransposons. Background Most arthropods contain R1 and R2 retrotransposons that specifically insert into the 28S rRNA genes. Here, the sequencing reads from 12 Drosophila genomes have been used to address two questions concerning these elements. First, to what extent is the evolution of these elements subject to the concerted evolution process that is responsible for sequence homogeneity among the different copies of rRNA genes? Second, how precise are the target DNA cleavages and priming of DNA synthesis used by these elements? Results Most copies of R1 and R2 in each species were found to exhibit less than 0.2% sequence divergence. However, in many species evidence was obtained for the formation of distinct sublineages of elements, particularly in the case of R1. Analysis of the hundreds of R1 and R2 junctions with the 28S gene revealed that cleavage of the first DNA strand was precise both in location and the priming of reverse transcription. Cleavage of the second DNA strand was less precise within a species, differed between species, and gave rise to variable priming mechanisms for second strand synthesis. Conclusions These findings suggest that the high sequence identity amongst R1 and R2 copies is because all copies are relatively new. However, each active element generates its own independent lineage that can eventually populate the locus. Independent lineages occur more often with R1, possibly because these elements contain their own promoter. Finally, both R1 and R2 use imprecise, rapidly evolving mechanisms to cleave the second strand and prime second strand synthesis.
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Affiliation(s)
- Deborah E Stage
- Biology Department, University of Rochester, Rochester NY 14627-0211, USA.
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Marz M, Kirsten T, Stadler PF. Evolution of spliceosomal snRNA genes in metazoan animals. J Mol Evol 2009; 67:594-607. [PMID: 19030770 DOI: 10.1007/s00239-008-9149-6] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2008] [Accepted: 07/14/2008] [Indexed: 11/28/2022]
Abstract
While studies of the evolutionary histories of protein families are commonplace, little is known on noncoding RNAs beyond microRNAs and some snoRNAs. Here we investigate in detail the evolutionary history of the nine spliceosomal snRNA families (U1, U2, U4, U5, U6, U11, U12, U4atac, and U6atac) across the completely or partially sequenced genomes of metazoan animals. Representatives of the five major spliceosomal snRNAs were found in all genomes. None of the minor splicesomal snRNAs were detected in nematodes or in the shotgun traces of Oikopleura dioica, while in all other animal genomes at most one of them is missing. Although snRNAs are present in multiple copies in most genomes, distinguishable paralogue groups are not stable over long evolutionary times, although they appear independently in several clades. In general, animal snRNA secondary structures are highly conserved, albeit, in particular, U11 and U12 in insects exhibit dramatic variations. An analysis of genomic context of snRNAs reveals that they behave like mobile elements, exhibiting very little syntenic conservation.
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Affiliation(s)
- Manuela Marz
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Härtelstrasse 16-18, 04107 Leipzig, Germany.
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Internal repetition and intraindividual variation in the rDNA ITS1 of the anopheles punctulatus group (Diptera: Culicidae): multiple units and rates of turnover. J Mol Evol 2009; 68:66-79. [PMID: 19123014 PMCID: PMC9935728 DOI: 10.1007/s00239-008-9188-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2007] [Revised: 11/05/2008] [Accepted: 12/01/2008] [Indexed: 10/21/2022]
Abstract
The rapid divergence of repetitive sequences makes them desirable markers for phylogenetic studies of closely related groups, provided that a high level of sequence homogeneity has been maintained within species. Intraspecific polymorphisms are found in an increasing number of studies now, and this highlights the need to determine why these occur. In this study we examined intraindividual variation present in the first ribosomal internal transcribed spacer (ITS1) from a group of cryptic mosquito species. Individuals of the Anopheles punctulatus group contained multiple ITS1 length variants that ranged from 1.2 to 8.0 kb. Nucleotide and copy number variation for several homologous internal repeats is common, yet the intraspecific sequence divergence of cloned PCR isolates is comparable to that of other mosquito species (~0.2-1.5%). Most of the length variation is comprised of a 5'-ITS1 repeat that was identified as a duplication of a conserved ITS2 region. Secondary structure conservation for this repeat is pronounced and several repeat types that are highly homogenized have formed. Significant interspecific divergence indicates a high rate of evolutionary change for this spacer. A maximum likelihood tree constructed here was congruent with previous phylogenetic hypotheses and suggests that concerted evolution is also accompanied by interpopulation divergence. The lack of interindividual differences and the presence of homogenized internal repeats suggest that a high rate of turnover has reduced the overall level of variation. However, the intraindividual variation also appears to be maintained by the absence of a single turnover rate and the complex dynamics of ongoing recombination within the spacer.
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Kupriyanova N, Shibalev D, Voronov A, Ryskov A. Enhanced heterogeneity of the LR2 segment in the human ribosomal intergenic spacer. Gene X 2008; 425:44-7. [DOI: 10.1016/j.gene.2008.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2008] [Revised: 08/06/2008] [Accepted: 08/07/2008] [Indexed: 10/21/2022] Open
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Role of recombination in the long-term retention of transposable elements in rRNA gene loci. Genetics 2008; 180:1617-26. [PMID: 18791229 DOI: 10.1534/genetics.108.093716] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Multiple theoretical studies have focused on the concerted evolution of the tandemly repeated rRNA genes of eukaryotes; however, these studies did not consider the transposable elements that interrupt the rRNA genes in many organisms. For example, in insects, R1 and R2 have been stable components of the rDNA locus for hundreds of millions of years, suggesting either that they have minimal effects on fitness or that they are unable to be eliminated. We constructed a simulation model of recombination and retrotransposition within the rDNA locus that addresses the population dynamics and fitness consequences associated with R1 and R2 insertions. The simulations suggest that even without R1 and R2 retrotransposition the frequent sister chromatid exchanges postulated from various empirical studies will, in combination with selection, generate rDNA loci that are much larger than those needed for transcription. These large loci enable the host to tolerate high levels of R1 and R2 insertions with little fitness consequences. Changes in retrotransposition rates are likely to be accommodated by adjustments in sister chromatid exchange (SCE) rate, rather than by direct selection on the number of uninserted rDNA units. These simulations suggest that the rDNA locus serves as an ideal niche for the long-term survival of transposable elements.
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Tseng H, Chou W, Wang J, Zhang X, Zhang S, Schultz RM. Mouse ribosomal RNA genes contain multiple differentially regulated variants. PLoS One 2008; 3:e1843. [PMID: 18365001 PMCID: PMC2266999 DOI: 10.1371/journal.pone.0001843] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Accepted: 02/12/2008] [Indexed: 11/22/2022] Open
Abstract
Previous cytogenetic studies suggest that various rDNA chromosomal loci are not equally active in different cell types. Consistent with this variability, rDNA polymorphism is well documented in human and mouse. However, attempts to identify molecularly rDNA variant types, which are regulated individually (i.e., independent of other rDNA variants) and tissue-specifically, have not been successful. We report here the molecular cloning and characterization of seven mouse rDNA variants (v-rDNA). The identification of these v-rDNAs was based on restriction fragment length polymorphisms (RFLPs), which are conserved among individuals and mouse strains. The total copy number of the identified variants is less than 100 and the copy number of each individual variant ranges from 4 to 15. Sequence analysis of the cloned v-rDNA identified variant-specific single nucleotide polymorphisms (SNPs) in the transcribed region. These SNPs were used to develop a set of variant-specific PCR assays, which permitted analysis of the v-rDNAs' expression profiles in various tissues. These profiles show that three v-rDNAs are expressed in all tissues (constitutively active), two are expressed in some tissues (selectively active), and two are not expressed (silent). These expression profiles were observed in six individuals from three mouse strains, suggesting the pattern is not randomly determined. Thus, the mouse rDNA array likely consists of genetically distinct variants, and some are regulated tissue-specifically. Our results provide the first molecular evidence for cell-type-specific regulation of a subset of rDNA.
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Affiliation(s)
- Hung Tseng
- Department of Dermatology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
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Moran Y, Weinberger H, Sullivan JC, Reitzel AM, Finnerty JR, Gurevitz M. Concerted Evolution of Sea Anemone Neurotoxin Genes Is Revealed through Analysis of the Nematostella vectensis Genome. Mol Biol Evol 2008; 25:737-47. [DOI: 10.1093/molbev/msn021] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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40
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Novozhilov AS, Karev GP, Koonin EV. Biological applications of the theory of birth-and-death processes. Brief Bioinform 2008; 7:70-85. [PMID: 16761366 DOI: 10.1093/bib/bbk006] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In this review, we discuss applications of the theory of birth-and-death processes to problems in biology, primarily, those of evolutionary genomics. The mathematical principles of the theory of these processes are briefly described. Birth-and-death processes, with some straightforward additions such as innovation, are a simple, natural and formal framework for modeling a vast variety of biological processes such as population dynamics, speciation, genome evolution, including growth of paralogous gene families and horizontal gene transfer and somatic evolution of cancers. We further describe how empirical data, e.g. distributions of paralogous gene family size, can be used to choose the model that best reflects the actual course of evolution among different versions of birth-death-and-innovation models. We conclude that birth-and-death processes, thanks to their mathematical transparency, flexibility and relevance to fundamental biological processes, are going to be an indispensable mathematical tool for the burgeoning field of systems biology.
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Affiliation(s)
- Artem S Novozhilov
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Besthesda, MD 20894, USA
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Intraspecific concerted evolution of the rDNA ITS1 in Anopheles farauti sensu stricto (Diptera: Culicidae) reveals recent patterns of population structure. J Mol Evol 2008; 67:397-411. [PMID: 18818859 PMCID: PMC9931795 DOI: 10.1007/s00239-008-9161-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2007] [Revised: 06/18/2008] [Accepted: 08/28/2008] [Indexed: 10/21/2022]
Abstract
We examined the intraindividual variation present in the first ribosomal internal transcribed spacer (ITS1) of Anopheles farauti to determine the level of divergence among populations for this important malarial vector. We isolated 187 clones from 70 individuals and found regional variation among four internal tandem repeats. The data were partitioned prior to analysis given the presence of a paralogous ITS2 sequence, called the 5'-subrepeat, inserted in the ITS1 of most clones. A high level of homogenization and population differentiation was observed for this repeat, which indicates a higher rate of turnover relative to the adjacent 'core' region. Bayesian analysis was performed using several substitutional models on both a combined and a partitioned data set. On the whole, the ITS1 phylogeny and geographic origin of the samples appear to be congruent. Some interesting exceptions indicate the spread of variant repeats between populations and the retention of ancestral polymorphism. Our data clearly demonstrate concerted evolution at the intraspecific level despite intraindividual variation and a complex internal repeat structure from a species that occupies a continuous coastal distribution. A high rate of genomic turnover in combination with a high level of sequence divergence appears to be a major factor leading to its concerted evolution within these populations.
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Stults DM, Killen MW, Pierce HH, Pierce AJ. Genomic architecture and inheritance of human ribosomal RNA gene clusters. Genes Dev 2008; 18:13-8. [PMID: 18025267 PMCID: PMC2134781 DOI: 10.1101/gr.6858507] [Citation(s) in RCA: 214] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2007] [Accepted: 09/17/2007] [Indexed: 01/21/2023]
Abstract
The finishing of the Human Genome Project largely completed the detailing of human euchromatic sequences; however, the most highly repetitive regions of the genome still could not be assembled. The 12 gene clusters producing the structural RNA components of the ribosome are critically important for cellular viability, yet fall into this unassembled region of the Human Genome Project. To determine the extent of human variation in ribosomal RNA gene content (rDNA) and patterns of rDNA cluster inheritance, we have determined the physical lengths of the rDNA clusters in peripheral blood white cells of healthy human volunteers. The cluster lengths exhibit striking variability between and within human individuals, ranging from 50 kb to >6 Mb, manifest essentially complete heterozygosity, and provide each person with their own unique rDNA electrophoretic karyotype. Analysis of these rDNA fingerprints in multigenerational human families demonstrates that the rDNA clusters are subject to meiotic rearrangement at a frequency >10% per cluster, per meiosis. With this high intrinsic recombinational instability, the rDNA clusters may serve as a unique paradigm of potential human genomic plasticity.
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Affiliation(s)
- Dawn M. Stults
- Graduate Center for Toxicology, University of Kentucky, Lexington, Kentucky 40515, USA
| | - Michael W. Killen
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, Lexington, Kentucky 40515, USA
| | - Heather H. Pierce
- Department of Internal Medicine, Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40515, USA
| | - Andrew J. Pierce
- Department of Microbiology, Immunology and Molecular Genetics, Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40515, USA
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Stage DE, Eickbush TH. Sequence variation within the rRNA gene loci of 12 Drosophila species. Genome Res 2007; 17:1888-97. [PMID: 17989256 DOI: 10.1101/gr.6376807] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Concerted evolution maintains at near identity the hundreds of tandemly arrayed ribosomal RNA (rRNA) genes and their spacers present in any eukaryote. Few comprehensive attempts have been made to directly measure the identity between the rDNA units. We used the original sequencing reads (trace archives) available through the whole-genome shotgun sequencing projects of 12 Drosophila species to locate the sequence variants within the 7.8-8.2 kb transcribed portions of the rDNA units. Three to 18 variants were identified in >3% of the total rDNA units from 11 species. Species where the rDNA units are present on multiple chromosomes exhibited only minor increases in sequence variation. Variants were 10-20 times more abundant in the noncoding compared with the coding regions of the rDNA unit. Within the coding regions, variants were three to eight times more abundant in the expansion compared with the conserved core regions. The distribution of variants was largely consistent with models of concerted evolution in which there is uniform recombination across the transcribed portion of the unit with the frequency of standing variants dependent upon the selection pressure to preserve that sequence. However, the 28S gene was found to contain fewer variants than the 18S gene despite evolving 2.5-fold faster. We postulate that the fewer variants in the 28S gene is due to localized gene conversion or DNA repair triggered by the activity of retrotransposable elements that are specialized for insertion into the 28S genes of these species.
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Affiliation(s)
- Deborah E Stage
- University of Rochester, Department of Biology, Rochester, New York 14627, USA
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Wang S, Zhang L, Zhan A, Wang X, Liu Z, Hu J, Bao Z. Patterns of Concerted Evolution of the rDNA Family in a Natural Population of Zhikong Scallop, Chlamys farreri. J Mol Evol 2007; 65:660-7. [DOI: 10.1007/s00239-007-9039-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2007] [Revised: 06/24/2007] [Accepted: 09/18/2007] [Indexed: 10/22/2022]
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Abstract
Evolution of the tandemly repeated ribosomal RNA (rRNA) genes is intriguing because in each species all units within the array are highly uniform in sequence but that sequence differs between species. In this review we summarize the origins of the current models to explain this process of concerted evolution, emphasizing early studies of recombination in yeast and more recent studies in Drosophila and mammalian systems. These studies suggest that unequal crossover is the major driving force in the evolution of the rRNA genes with sister chromatid exchange occurring more often than exchange between homologs. Gene conversion is also believed to play a role; however, direct evidence for its involvement has not been obtained. Remarkably, concerted evolution is so well orchestrated that even transposable elements that insert into a large fraction of the rRNA genes appear to have little effect on the process. Finally, we summarize data that suggest that recombination in the rDNA locus of higher eukaryotes is sufficiently frequent to monitor changes within a few generations.
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Affiliation(s)
- Thomas H Eickbush
- Department of Biology, University of Rochester, Rochester, New York 14627, USA.
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Netchvolodov KK, Boiko AV, Ryskov AP, Kupriyanova NS. Evolutionary divergence of the pre-promotor region of ribosomal DNA in the great apes. ACTA ACUST UNITED AC 2007; 17:378-91. [PMID: 17343212 DOI: 10.1080/10425170600752643] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The human ribosomal intergenic spacer (rIGS) differs considerably on nucleotide sequence and regulatory elements positioning from their counterparts in the mouse, rat and Xenopus laevis. In the present study, we have PCR amplified, cloned and sequenced the rIGS fragments of about 4.5 kb length, located approximately 2 kb upstream of the rRNA transcription start point for the great apes, Pan paniscus, Pan troglodytes, Gorilla gorilla and Pongo pygmaeus. Alignment of the primates' orthologic nucleotide sequences reveals high extent of similarity, with the exception of highly repetitious region between the two Alu repeats, nearest to the onset of transcription. Data obtained have been analyzed for further understanding of the evolution of repetitive sequences. We have also shown, that MARs/SARs distribution patterns in the pre-promoter rIGSs of the great apes and the mouse are surprisingly similar in spite of an absence of similarity in the primary structure and regulatory elements organization in the region under study.
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Jackson AP. Tandem gene arrays in Trypanosoma brucei: comparative phylogenomic analysis of duplicate sequence variation. BMC Evol Biol 2007; 7:54. [PMID: 17408475 PMCID: PMC1855330 DOI: 10.1186/1471-2148-7-54] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2006] [Accepted: 04/04/2007] [Indexed: 11/23/2022] Open
Abstract
Background The genome sequence of the protistan parasite Trypanosoma brucei contains many tandem gene arrays. Gene duplicates are created through tandem duplication and are expressed through polycistronic transcription, suggesting that the primary purpose of long, tandem arrays is to increase gene dosage in an environment where individual gene promoters are absent. This report presents the first account of the tandem gene arrays in the T. brucei genome, employing several related genome sequences to establish how variation is created and removed. Results A systematic survey of tandem gene arrays showed that substantial sequence variation existed across the genome; variation from different regions of an array often produced inconsistent phylogenetic affinities. Phylogenetic relationships of gene duplicates were consistent with concerted evolution being a widespread homogenising force. However, tandem duplicates were not usually identical; therefore, any homogenising effect was coincident with divergence among duplicates. Allelic gene conversion was detected using various criteria and was apparently able to both remove and introduce sequence variation. Tandem arrays containing structural heterogeneity demonstrated how sequence homogenisation and differentiation can occur within a single locus. Conclusion The use of multiple genome sequences in a comparative analysis of tandem gene arrays identified substantial sequence variation among gene duplicates. The distribution of sequence variation is determined by a dynamic balance of conservative and innovative evolutionary forces. Gene trees from various species showed that intraspecific duplicates evolve in concert, perhaps through frequent gene conversion, although this does not prevent sequence divergence, especially where structural heterogeneity physically separates a duplicate from its neighbours. In describing dynamics of sequence variation that have consequences beyond gene dosage, this survey provides a basis for uncovering the hidden functionality within tandem gene arrays in trypanosomatids.
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Affiliation(s)
- Andrew P Jackson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK.
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Jarmuz M, Glotzbach CD, Bailey KA, Bandyopadhyay R, Shaffer LG. The Evolution of satellite III DNA subfamilies among primates. Am J Hum Genet 2007; 80:495-501. [PMID: 17273970 PMCID: PMC1821104 DOI: 10.1086/512132] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2006] [Accepted: 12/16/2006] [Indexed: 01/30/2023] Open
Abstract
We demonstrate that satellite III (SatIII) DNA subfamilies cloned from human acrocentric chromosomes arose in the Hominoidea superfamily. Two groups, distinguished by sequence composition, evolved nonconcurrently, with group 2 evolving 16-23 million years ago (MYA) and the more recent group 1 sequences emerging approximately 4.5 MYA. We also show the relative order of emergence of each group 2 subfamily in the various primate species. Our results show that each SatIII subfamily is an independent evolutionary unit, that the rate of evolution is not uniform between species, and that the evolution within a species is not uniform between chromosomes.
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Affiliation(s)
- Malgorzata Jarmuz
- Health Research and Education Center, Washington State University, Spokane 99210, USA
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Young DW, Hassan MQ, Pratap J, Galindo M, Zaidi SK, Lee SH, Yang X, Xie R, Javed A, Underwood JM, Furcinitti P, Imbalzano AN, Penman S, Nickerson JA, Montecino MA, Lian JB, Stein JL, van Wijnen AJ, Stein GS. Mitotic occupancy and lineage-specific transcriptional control of rRNA genes by Runx2. Nature 2007; 445:442-6. [PMID: 17251981 DOI: 10.1038/nature05473] [Citation(s) in RCA: 184] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2006] [Accepted: 11/20/2006] [Indexed: 11/09/2022]
Abstract
Regulation of ribosomal RNA genes is a fundamental process that supports the growth of cells and is tightly coupled with cell differentiation. Although rRNA transcriptional control by RNA polymerase I (Pol I) and associated factors is well studied, the lineage-specific mechanisms governing rRNA expression remain elusive. Runt-related transcription factors Runx1, Runx2 and Runx3 establish and maintain cell identity, and convey phenotypic information through successive cell divisions for regulatory events that determine cell cycle progression or exit in progeny cells. Here we establish that mammalian Runx2 not only controls lineage commitment and cell proliferation by regulating genes transcribed by RNA Pol II, but also acts as a repressor of RNA Pol I mediated rRNA synthesis. Within the condensed mitotic chromosomes we find that Runx2 is retained in large discrete foci at nucleolar organizing regions where rRNA genes reside. These Runx2 chromosomal foci are associated with open chromatin, co-localize with the RNA Pol I transcription factor UBF1, and undergo transition into nucleoli at sites of rRNA synthesis during interphase. Ribosomal RNA transcription and protein synthesis are enhanced by Runx2 deficiency that results from gene ablation or RNA interference, whereas induction of Runx2 specifically and directly represses rDNA promoter activity. Runx2 forms complexes containing the RNA Pol I transcription factors UBF1 and SL1, co-occupies the rRNA gene promoter with these factors in vivo, and affects local chromatin histone modifications at rDNA regulatory regions. Thus Runx2 is a critical mechanistic link between cell fate, proliferation and growth control. Our results suggest that lineage-specific control of ribosomal biogenesis may be a fundamental function of transcription factors that govern cell fate.
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Affiliation(s)
- Daniel W Young
- Department of Cell Biology and Cancer Center, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
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50
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Ganley ARD, Kobayashi T. Highly efficient concerted evolution in the ribosomal DNA repeats: total rDNA repeat variation revealed by whole-genome shotgun sequence data. Genome Res 2007; 17:184-91. [PMID: 17200233 PMCID: PMC1781350 DOI: 10.1101/gr.5457707] [Citation(s) in RCA: 243] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Repeat families within genomes are often maintained with similar sequences. Traditionally, this has been explained by concerted evolution, where repeats in an array evolve "in concert" with the same sequence via continual turnover of repeats by recombination. Another form of evolution, birth-and-death evolution, can also explain this pattern, although in this case selection is the critical force maintaining the repeats. The level of intragenomic variation is the key difference between these two forms of evolution. The prohibitive size and repetitive nature of large repeat arrays have made determination of the absolute level of intragenomic repeat variability difficult, thus there is little evidence to support concerted evolution over birth-and-death evolution for many large repeat arrays. Here we use whole-genome shotgun sequence data from the genome projects of five fungal species to reveal absolute levels of sequence variation within the ribosomal RNA gene repeats (rDNA). The level of sequence variation is remarkably low. Furthermore, the polymorphisms that are detected are not functionally constrained and seem to exist beneath the level of selection. These results suggest the rDNA is evolving via concerted evolution. Comparisons with a repeat array undergoing birth-and-death evolution provide a clear contrast in the level of repeat array variation between these two forms of evolution, confirming that the rDNA indeed does evolve via concerted evolution. These low levels of intra-genomic variation are consistent with a model of concerted evolution in which homogenization is very rapid and efficiently maintains highly similar repeat arrays.
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