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Young LA, Maughan PJ, Jarvis DE, Hunt SP, Warner HC, Durrant KK, Kohlert T, Curti RN, Bertero D, Filippi GA, Pospíšilíková T, Krak K, Mandák B, Jellen EN. A chromosome-scale reference of Chenopodium watsonii helps elucidate relationships within the North American A-genome Chenopodium species and with quinoa. THE PLANT GENOME 2023; 16:e20349. [PMID: 37195017 DOI: 10.1002/tpg2.20349] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/07/2023] [Accepted: 04/13/2023] [Indexed: 05/18/2023]
Abstract
Quinoa (Chenopodium quinoa), an Andean pseudocereal, attained global popularity beginning in the early 2000s due to its protein quality, glycemic index, and high fiber, vitamin, and mineral contents. Pitseed goosefoot (Chenopodium berlandieri), quinoa's North American free-living sister species, grows on disturbed and sandy substrates across the North America, including saline coastal sands, southwestern deserts, subtropical highlands, the Great Plains, and boreal forests. Together with South American avian goosefoot (Chenopodium hircinum) they comprise the American tetraploid goosefoot complex (ATGC). Superimposed on pitseed goosefoot's North American range are approximately 35 AA diploids, most of which are adapted to a diversity of niche environments. We chose to assemble a reference genome for Sonoran A-genome Chenopodium watsonii due to fruit morphological and high (>99.3%) preliminary sequence-match similarities with quinoa, along with its well-established taxonomic status. The genome was assembled into 1377 scaffolds spanning 547.76 Mb (N50 = 55.14 Mb, L50 = 5), with 94% comprised in nine chromosome-scale scaffolds and 93.9% Benchmarking Universal Single-Copy Orthologs genes identified as single copy and 3.4% as duplicated. A high degree of synteny, with minor and mostly telomeric rearrangements, was found when comparing this taxon with the previously reported genome of South American C. pallidicaule and the A-subgenome chromosomes of C. quinoa. Phylogenetic analysis was performed using 10,588 single-nucleotide polymorphisms generated by resequencing a panel of 41 New World AA diploid accessions and the Eurasian H-genome diploid Chenopodium vulvaria, along with three AABB tetraploids previously sequenced. Phylogenetic analysis of these 32 taxa positioned the psammophyte Chenopodium subglabrum on the branch containing A-genome sequences from the ATGC. We also present evidence for long-range dispersal of Chenopodium diploids between North and South America.
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Affiliation(s)
- Lauren A Young
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, Utah, USA
| | | | - David E Jarvis
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, Utah, USA
| | - Spencer P Hunt
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, Utah, USA
| | - Heather C Warner
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, Utah, USA
| | - Kristin K Durrant
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, Utah, USA
| | - Tyler Kohlert
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, Utah, USA
| | - Ramiro N Curti
- Facultad de Ciencias Naturales, Universidad Nacional de Salta, CCT-CONICET, Salta, Argentina
| | - Daniel Bertero
- Cátedra de Producción Vegetal, Facultad de Agronomía, Universidad de Buenos Aires and IFEVA-CONICET, Buenos Aires, Argentina
| | - Gabrielle A Filippi
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Tereza Pospíšilíková
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Karol Krak
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czech Republic
| | - Bohumil Mandák
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czech Republic
| | - Eric N Jellen
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, Utah, USA
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Xue Y, Chen R, Qu L, Cao X. Noncoding RNA: from dark matter to bright star. SCIENCE CHINA-LIFE SCIENCES 2020; 63:463-468. [DOI: 10.1007/s11427-020-1676-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Indexed: 12/16/2022]
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Li LX, Liao HZ, Jiang LX, Tan Q, Ye D, Zhang XQ. Arabidopsis thaliana NOP10 is required for gametophyte formation. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:723-736. [PMID: 29578643 DOI: 10.1111/jipb.12652] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/22/2018] [Indexed: 05/19/2023]
Abstract
The female gametophyte is crucial for sexual reproduction of higher plants, yet little is known about the molecular mechanisms underlying its development. Here, we report that Arabidopsis thaliana NOP10 (AtNOP10) is required for female gametophyte formation. AtNOP10 was expressed predominantly in the seedling and reproductive tissues, including anthers, pollen grains, and ovules. Mutations in AtNOP10 interrupted mitosis of the functional megaspore during early development and prevented polar nuclear fusion in the embryo sacs. AtNOP10 shares a high level of amino acid sequence similarity with Saccharomyces cerevisiae (yeast) NOP10 (ScNOP10), an important component of the H/ACA small nucleolar ribonucleoprotein particles (H/ACA snoRNPs) implicated in 18S rRNA synthesis and rRNA pseudouridylation. Heterologous expression of ScNOP10 complemented the mutant phenotype of Atnop10. Thus, AtNOP10 influences functional megaspore mitosis and polar nuclear fusion during gametophyte formation in Arabidopsis.
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Affiliation(s)
- Lin-Xiao Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Hong-Ze Liao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- State Key Laboratory of Non-Food Biomass Energy and Enzyme Technology, National Engineering Research Center for Non-Food Biorefinery and Guangxi Key Laboratory of Biorefinery, Guangxi Academy of Sciences, Nanning 530007, China
| | - Li-Xi Jiang
- College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Qing Tan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - De Ye
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xue-Qin Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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Tripp V, Martin R, Orell A, Alkhnbashi OS, Backofen R, Randau L. Plasticity of archaeal C/D box sRNA biogenesis. Mol Microbiol 2016; 103:151-164. [PMID: 27743417 DOI: 10.1111/mmi.13549] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2016] [Indexed: 01/11/2023]
Abstract
Archaeal and eukaryotic organisms contain sets of C/D box s(no)RNAs with guide sequences that determine ribose 2'-O-methylation sites of target RNAs. The composition of these C/D box sRNA sets is highly variable between organisms and results in varying RNA modification patterns which are important for ribosomal RNA folding and stability. Little is known about the genomic organization of C/D box sRNA genes in archaea. Here, we aimed to obtain first insights into the biogenesis of these archaeal C/D box sRNAs and analyzed the genetic context of more than 300 archaeal sRNA genes. We found that the majority of these genes do not possess independent promoters but are rather located at positions that allow for co-transcription with neighboring genes and their start or stop codons were frequently incorporated into the conserved boxC and D motifs. The biogenesis of plasmid-encoded C/D box sRNA variants was analyzed in vivo in Sulfolobus acidocaldarius. It was found that C/D box sRNA maturation occurs independent of their genetic context and relies solely on the presence of intact RNA kink-turn structures. The observed plasticity of C/D box sRNA biogenesis is suggested to enable their accelerated evolution and, consequently, allow for adjustments of the RNA modification landscape.
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Affiliation(s)
- Vanessa Tripp
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, Marburg, 35043, Germany.,LOEWE Center for Synthetic Microbiology, SYNMIKRO, Karl-von-Frisch-Strasse 16, Marburg, 35043, Germany
| | - Roman Martin
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, Marburg, 35043, Germany
| | - Alvaro Orell
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, Marburg, 35043, Germany
| | - Omer S Alkhnbashi
- Bioinformatics group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, Freiburg, 79110, Germany
| | - Rolf Backofen
- Bioinformatics group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, Freiburg, 79110, Germany.,BIOSS Centre for Biological Signalling Studies, Cluster of Excellence, University of Freiburg, Germany
| | - Lennart Randau
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, Marburg, 35043, Germany.,LOEWE Center for Synthetic Microbiology, SYNMIKRO, Karl-von-Frisch-Strasse 16, Marburg, 35043, Germany
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Poyntner C, Blasi B, Arcalis E, Mirastschijski U, Sterflinger K, Tafer H. The Transcriptome of Exophiala dermatitidis during Ex-vivo Skin Model Infection. Front Cell Infect Microbiol 2016; 6:136. [PMID: 27822460 PMCID: PMC5075926 DOI: 10.3389/fcimb.2016.00136] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 10/06/2016] [Indexed: 12/12/2022] Open
Abstract
The black yeast Exophiala dermatitidis is a widespread polyextremophile and human pathogen, that is found in extreme natural habitats and man-made environments such as dishwashers. It can cause various diseases ranging from phaeohyphomycosis and systemic infections, with fatality rates reaching 40%. While the number of cases in immunocompromised patients are increasing, knowledge of the infections, virulence factors and host response is still scarce. In this study, for the first time, an artificial infection of an ex-vivo skin model with Exophiala dermatitidis was monitored microscopically and transcriptomically. Results show that Exophiala dermatitidis is able to actively grow and penetrate the skin. The analysis of the genomic and RNA-sequencing data delivers a rich and complex transcriptome where circular RNAs, fusion transcripts, long non-coding RNAs and antisense transcripts are found. Changes in transcription strongly affect pathways related to nutrients acquisition, energy metabolism, cell wall, morphological switch, and known virulence factors. The L-Tyrosine melanin pathway is specifically upregulated during infection. Moreover the production of secondary metabolites, especially alkaloids, is increased. Our study is the first that gives an insight into the complexity of the transcriptome of Exophiala dermatitidis during artificial skin infections and reveals new virulence factors.
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Affiliation(s)
- Caroline Poyntner
- Department of Biotechnology, VIBT EQ Extremophile Center, University of Natural Resources and Life Sciences Vienna, Austria
| | - Barbara Blasi
- Department of Biotechnology, VIBT EQ Extremophile Center, University of Natural Resources and Life Sciences Vienna, Austria
| | - Elsa Arcalis
- Department for Applied Genetics and Cell Biology, Molecular Plant Physiology and Crop Biotechnology, University of Natural Resources and Life Sciences Vienna, Austria
| | - Ursula Mirastschijski
- Klinikum Bremen-Mitte, Department of Plastic, Reconstructive and Aesthetic Surgery, Faculty of Biology and Chemistry, Center for Biomolecular Interactions Bremen, University Bremen Bremen, Germany
| | - Katja Sterflinger
- Department of Biotechnology, VIBT EQ Extremophile Center, University of Natural Resources and Life Sciences Vienna, Austria
| | - Hakim Tafer
- Department of Biotechnology, VIBT EQ Extremophile Center, University of Natural Resources and Life Sciences Vienna, Austria
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Liu N, Xiao B, Ren HY, Tang ZL, Li K. Systematic identification and characterization of porcine snoRNAs: structural, functional and developmental insights. Anim Genet 2012; 44:24-33. [DOI: 10.1111/j.1365-2052.2012.02363.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2012] [Indexed: 11/28/2022]
Affiliation(s)
- Nan Liu
- State Key Laboratory for Animal Nutrition; Institute of Animal Science; Chinese Academy of Agricultural Sciences; Beijing; 100193; China
| | - Bang Xiao
- State Key Laboratory for Animal Nutrition; Institute of Animal Science; Chinese Academy of Agricultural Sciences; Beijing; 100193; China
| | - Hong-Yan Ren
- State Key Laboratory for Animal Nutrition; Institute of Animal Science; Chinese Academy of Agricultural Sciences; Beijing; 100193; China
| | - Zhong-Lin Tang
- State Key Laboratory for Animal Nutrition; Institute of Animal Science; Chinese Academy of Agricultural Sciences; Beijing; 100193; China
| | - Kui Li
- State Key Laboratory for Animal Nutrition; Institute of Animal Science; Chinese Academy of Agricultural Sciences; Beijing; 100193; China
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Li D, Wang Y, Zhang K, Jiao Z, Zhu X, Skogerboe G, Guo X, Chinnusamy V, Bi L, Huang Y, Dong S, Chen R, Kan Y. Experimental RNomics and genomic comparative analysis reveal a large group of species-specific small non-message RNAs in the silkworm Bombyx mori. Nucleic Acids Res 2011; 39:3792-805. [PMID: 21227919 PMCID: PMC3089462 DOI: 10.1093/nar/gkq1317] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Accumulating evidences show that small non-protein coding RNAs (ncRNAs) play important roles in development, stress response and other cellular processes. The silkworm is an important model for studies on insect genetics and control of lepidopterous pests. Here, we have performed the first systematic identification and analysis of intermediate size ncRNAs (50–500 nt) in the silkworm. We identified 189 novel ncRNAs, including 141 snoRNAs, six snRNAs, three tRNAs, one SRP and 38 unclassified ncRNAs. Forty ncRNAs showed significantly altered expression during silkworm development or across specific stage transitions. Genomic comparisons revealed that 123 of these ncRNAs are potentially silkworm-specific. Analysis of the genomic organization of the ncRNA loci showed that 32.62% of the novel snoRNA loci are intergenic, and that all the intronic snoRNAs follow the pattern of one-snoRNA-per-intron. Target site analysis predicted a total of 95 2′-O-methylation and pseudouridylation modification sites of rRNAs, snRNAs and tRNAs. Together, these findings provide new clues for future functional study of ncRNA during insect development and evolution.
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Affiliation(s)
- Dandan Li
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, Nanjing 210095, China
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Gaspin C, Rami JF, Lescure B. Distribution of short interstitial telomere motifs in two plant genomes: putative origin and function. BMC PLANT BIOLOGY 2010; 10:283. [PMID: 21171996 PMCID: PMC3022908 DOI: 10.1186/1471-2229-10-283] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Accepted: 12/20/2010] [Indexed: 05/05/2023]
Abstract
BACKGROUND Short interstitial telomere motifs (telo boxes) are short sequences identical to plant telomere repeat units. They are observed within the 5' region of several genes over-expressed in cycling cells. In synergy with various cis-acting elements, these motifs participate in the activation of expression. Here, we have analysed the distribution of telo boxes within Arabidopsis thaliana and Oryza sativa genomes and their association with genes involved in the biogenesis of the translational apparatus. RESULTS Our analysis showed that the distribution of the telo box (AAACCCTA) in different genomic regions of A. thaliana and O. sativa is not random. As is also the case for plant microsatellites, they are preferentially located in the 5' flanking regions of genes, mainly within the 5' UTR, and distributed as a gradient along the direction of transcription. As previously reported in Arabidopsis, a conserved topological association of telo boxes with site II or TEF cis-acting elements is observed in almost all promoters of genes encoding ribosomal proteins in O. sativa. Such a conserved promoter organization can be found in other genes involved in the biogenesis of the translational machinery including rRNA processing proteins and snoRNAs. Strikingly, the association of telo boxes with site II motifs or TEF boxes is conserved in promoters of genes harbouring snoRNA clusters nested within an intron as well as in the 5' flanking regions of non-intronic snoRNA genes. Thus, the search for associations between telo boxes and site II motifs or TEF box in plant genomes could provide a useful tool for characterizing new cryptic RNA pol II promoters. CONCLUSIONS The data reported in this work support the model previously proposed for the spreading of telo boxes within plant genomes and provide new insights into a putative process for the acquisition of microsatellites in plants. The association of telo boxes with site II or TEF cis-acting elements appears to be an essential feature of plant genes involved in the biogenesis of ribosomes and clearly indicates that most plant snoRNAs are RNA pol II products.
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Affiliation(s)
- Christine Gaspin
- INRA Toulouse, UBIA & Plateforme Bioinformatique, UR 875, Chemin de Borde Rouge, Auzeville BP 52627, 31326 Castanet-Tolosan, France
| | - Jean-François Rami
- Centre de coopération internationale en recherche agronomique pour le développement (CIRAD). UMR Développement et Amélioration des Plantes, TA A96/3, Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | - Bernard Lescure
- Laboratoire Interactions Plantes-Microorganismes (LIPM), UMR 441-2594 (INRA-CNRS), BP 52627, Chemin de Borde Rouge, Auzeville BP 52627, 31326 Castanet-Tolosan, France
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Liu N, Xiao ZD, Yu CH, Shao P, Liang YT, Guan DG, Yang JH, Chen CL, Qu LH, Zhou H. SnoRNAs from the filamentous fungus Neurospora crassa: structural, functional and evolutionary insights. BMC Genomics 2009; 10:515. [PMID: 19895704 PMCID: PMC2780460 DOI: 10.1186/1471-2164-10-515] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Accepted: 11/08/2009] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND SnoRNAs represent an excellent model for studying the structural and functional evolution of small non-coding RNAs involved in the post-transcriptional modification machinery for rRNAs and snRNAs in eukaryotic cells. Identification of snoRNAs from Neurospora crassa, an important model organism playing key roles in the development of modern genetics, biochemistry and molecular biology will provide insights into the evolution of snoRNA genes in the fungus kingdom. RESULTS Fifty five box C/D snoRNAs were identified and predicted to guide 71 2'-O-methylated sites including four sites on snRNAs and three sites on tRNAs. Additionally, twenty box H/ACA snoRNAs, which potentially guide 17 pseudouridylations on rRNAs, were also identified. Although not exhaustive, the study provides the first comprehensive list of two major families of snoRNAs from the filamentous fungus N. crassa. The independently transcribed strategy dominates in the expression of box H/ACA snoRNA genes, whereas most of the box C/D snoRNA genes are intron-encoded. This shows that different genomic organizations and expression modes have been adopted by the two major classes of snoRNA genes in N. crassa . Remarkably, five gene clusters represent an outstanding organization of box C/D snoRNA genes, which are well conserved among yeasts and multicellular fungi, implying their functional importance for the fungus cells. Interestingly, alternative splicing events were found in the expression of two polycistronic snoRNA gene hosts that resemble the UHG-like genes in mammals. Phylogenetic analysis further revealed that the extensive separation and recombination of two functional elements of snoRNA genes has occurred during fungus evolution. CONCLUSION This is the first genome-wide analysis of the filamentous fungus N. crassa snoRNAs that aids in understanding the differences between unicellular fungi and multicellular fungi. As compared with two yeasts, a more complex pattern of methylation guided by box C/D snoRNAs in multicellular fungus than in unicellular yeasts was revealed, indicating the high diversity of post-transcriptional modification guided by snoRNAs in the fungus kingdom.
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Affiliation(s)
- Na Liu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Zhen-Dong Xiao
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Chun-Hong Yu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Peng Shao
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Yin-Tong Liang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Dao-Gang Guan
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Jian-Hua Yang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Chun-Long Chen
- Centre National de la Recherche Scientifique (CNRS), UPR 2167, CGM, Gif sur Yvette, 91198, France
| | - Liang-Hu Qu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Hui Zhou
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
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Pai DA, Engelke DR. Spatial organization of genes as a component of regulated expression. Chromosoma 2009; 119:13-25. [PMID: 19727792 DOI: 10.1007/s00412-009-0236-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Revised: 08/05/2009] [Accepted: 08/06/2009] [Indexed: 12/15/2022]
Abstract
The DNA of living cells is highly compacted. Inherent in this spatial constraint is the need for cells to organize individual genetic loci so as to facilitate orderly retrieval of information. Complex genetic regulatory mechanisms are crucial to all organisms, and it is becoming increasingly evident that spatial organization of genes is one very important mode of regulation for many groups of genes. In eukaryotic nuclei, it appears not only that DNA is organized in three-dimensional space but also that this organization is dynamic and interactive with the transcriptional state of the genes. Spatial organization occurs throughout evolution and with genes transcribed by all classes of RNA polymerases in all eukaryotic nuclei, from yeast to human. There is an increasing body of work examining the ways in which this organization and consequent regulation are accomplished. In this review, we discuss the diverse strategies that cells use to preferentially localize various classes of genes.
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Affiliation(s)
- Dave A Pai
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Dr., Ann Arbor, MI, 48109-0606, USA
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Dieci G, Preti M, Montanini B. Eukaryotic snoRNAs: a paradigm for gene expression flexibility. Genomics 2009; 94:83-8. [PMID: 19446021 DOI: 10.1016/j.ygeno.2009.05.002] [Citation(s) in RCA: 221] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Revised: 04/30/2009] [Accepted: 05/07/2009] [Indexed: 11/26/2022]
Abstract
Small nucleolar RNAs (snoRNAs) are one of the most ancient and numerous families of non-protein-coding RNAs (ncRNAs). The main function of snoRNAs - to guide site-specific rRNA modification - is the same in Archaea and all eukaryotic lineages. In contrast, as revealed by recent genomic and RNomic studies, their genomic organization and expression strategies are the most varied. Seemingly snoRNA coding units have adopted, in the course of evolution, all the possible ways of being transcribed, thus providing a unique paradigm of gene expression flexibility. By focusing on representative fungal, plant and animal genomes, we review here all the documented types of snoRNA gene organization and expression, and we provide a comprehensive account of snoRNA expressional freedom by precisely estimating the frequency, in each genome, of each type of genomic organization. We finally discuss the relevance of snoRNA genomic studies for our general understanding of ncRNA family evolution and expression in eukaryotes.
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Affiliation(s)
- Giorgio Dieci
- Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, Parma, Italy.
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Mishra PC, Kumar A, Sharma A. Analysis of small nucleolar RNAs reveals unique genetic features in malaria parasites. BMC Genomics 2009; 10:68. [PMID: 19200392 PMCID: PMC2656528 DOI: 10.1186/1471-2164-10-68] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Accepted: 02/07/2009] [Indexed: 01/07/2023] Open
Abstract
Background Ribosome biogenesis is an energy consuming and stringently controlled process that involves hundreds of trans-acting factors. Small nucleolar RNAs (snoRNAs), important components of ribosome biogenesis are non-coding guide RNAs involved in rRNA processing, nucleotide modifications like 2'-O-ribose methylation, pseudouridylation and possibly gene regulation. snoRNAs are ubiquitous and are diverse in their genomic organization, mechanism of transcription and process of maturation. In vertebrates, most snoRNAs are present in introns of protein coding genes and are processed by exonucleolytic cleavage, while in plants they are transcribed as polycistronic transcripts. Results This is a comprehensive analysis of malaria parasite snoRNA genes and proteins that have a role in ribosomal biogenesis. Computational and experimental approaches have been used to identify several box C/D snoRNAs from different species of Plasmodium and confirm their expression. Our analyses reveal that the gene for endoribonuclease Rnt1 is absent from Plasmodium falciparum genome, which indicates the existence of alternative pre-rRNA processing pathways. The structural features of box C/D snoRNAs are highly conserved in Plasmodium genus; however, unlike other organisms most parasite snoRNAs are present in single copy. The genomic localization of parasite snoRNAs shows mixed patterns of those observed in plants, yeast and vertebrates. We have localized parasite snoRNAs in untranslated regions (UTR) of mRNAs, and this is an unprecedented and novel genetic feature. Akin to mammalian snoRNAs, those in Plasmodium may also behave as mobile genetic elements. Conclusion This study provides a comprehensive overview on trans-acting genes involved in ribosome biogenesis and also a genetic insight into malaria parasite snoRNA genes.
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Affiliation(s)
- Prakash Chandra Mishra
- Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology Aruna Asaf Ali Road, New Delhi, 110067, India.
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Xiong H, Qian J, He T, Li F. Independent transcription of miR-281 in the intron of ODA in Drosophila melanogaster. Biochem Biophys Res Commun 2008; 378:883-9. [PMID: 19073139 DOI: 10.1016/j.bbrc.2008.12.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Accepted: 12/03/2008] [Indexed: 02/09/2023]
Abstract
MicroRNAs (miRNAs) have recently received much interest for their role in post-transcriptional regulation. However, the study of miRNA transcription lags behind that of gene cloning and functional analysis. The MiR-281 in Drosophila melanogaster is located in the first intron of isoform RA of the ornithine decarboxylase antizyme (ODA) gene. ODA has three isoforms because of alternative transcription start sites (TSSs). Expression profile analysis indicated that miR-281 is not co-expressed with any ODA isoform. We amplified the primary transcripts of miR-281 using the RACE technique. The pri-miRNA is 2149bp with a poly (A) tail and a canonical polyadenylation signal (AATAAA). Chromatin immunoprecipitation analysis confirmed the binding of hypophosphorylated Pol-II and the transcription factor Myc at the core miR-281 promoter region. The abundance of miR-281 does not correlate, either positively or negatively, with the expression of any ODA isoform, indicating that ODA has little influence on the transcription of miR-281.
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Affiliation(s)
- Huiping Xiong
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
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14
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Genomewide analysis of box C/D and box H/ACA snoRNAs in Chlamydomonas reinhardtii reveals an extensive organization into intronic gene clusters. Genetics 2008; 179:21-30. [PMID: 18493037 DOI: 10.1534/genetics.107.086025] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Chlamydomonas reinhardtii is a unicellular green alga, the lineage of which diverged from that of land plants >1 billion years ago. Using the powerful small nucleolar RNA (snoRNA) mining platform to screen the C. reinhardtii genome, we identified 322 snoRNA genes grouped into 118 families. The 74 box C/D families can potentially guide methylation at 96 sites of ribosomal RNAs (rRNAs) and snRNAs, and the 44 box H/ACA families can potentially guide pseudouridylation at 62 sites. Remarkably, 242 of the snoRNA genes are arranged into 76 clusters, of which 77% consist of homologous genes produced by small local tandem duplications. At least 70 snoRNA gene clusters are found within introns of protein-coding genes. Although not exhaustive, this analysis reveals that C. reinhardtii has the highest number of intronic snoRNA gene clusters among eukaryotes. The prevalence of intronic snoRNA gene clusters in C. reinhardtii is similar to that of rice but in contrast with the one-snoRNA-per-intron organization of vertebrates and fungi and with that of Arabidopsis thaliana in which only a few intronic snoRNA gene clusters were identified. This analysis of C. reinhardtii snoRNA gene organization shows the functional importance of introns in a single-celled organism and provides evolutionary insight into the origin of intron-encoded RNAs in the plant lineage.
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15
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Jöchl C, Rederstorff M, Hertel J, Stadler PF, Hofacker IL, Schrettl M, Haas H, Hüttenhofer A. Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis. Nucleic Acids Res 2008; 36:2677-89. [PMID: 18346967 PMCID: PMC2377427 DOI: 10.1093/nar/gkn123] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Small non-protein-coding RNAs (ncRNAs) have systematically been studied in various model organisms from Escherichia coli to Homo sapiens. Here, we analyse the small ncRNA transcriptome from the pathogenic filamentous fungus Aspergillus fumigatus. To that aim, we experimentally screened for ncRNAs, expressed under various growth conditions or during specific developmental stages, by generating a specialized cDNA library from size-selected small RNA species. Our screen revealed 30 novel ncRNA candidates from known ncRNA classes such as small nuclear RNAs (snRNAs) and C/D box-type small nucleolar RNAs (C/D box snoRNAs). Additionally, several candidates for H/ACA box snoRNAs could be predicted by a bioinformatical screen. We also identified 15 candidates for ncRNAs, which could not be assigned to any known ncRNA class. Some of these ncRNA species are developmentally regulated implying a possible novel function in A. fumigatus development. Surprisingly, in addition to full-length tRNAs, we also identified 5′- or 3′-halves of tRNAs, only, which are likely generated by tRNA cleavage within the anti-codon loop. We show that conidiation induces tRNA cleavage resulting in tRNA depletion within conidia. Since conidia represent the resting state of A. fumigatus we propose that conidial tRNA depletion might be a novel mechanism to down-regulate protein synthesis in a filamentous fungus.
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Affiliation(s)
- Christoph Jöchl
- Innsbruck Biocenter, Division of Genomics and RNomics - Innsbruck Medical University, Fritz-Pregl-Strasse 3, 6020 Innsbruck, Austria
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16
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Yachie N, Numata K, Saito R, Kanai A, Tomita M. Prediction of non-coding and antisense RNA genes in Escherichia coli with Gapped Markov Model. Gene 2006; 372:171-81. [PMID: 16564143 DOI: 10.1016/j.gene.2005.12.034] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2005] [Revised: 12/02/2005] [Accepted: 12/28/2005] [Indexed: 11/27/2022]
Abstract
A new mathematical index was developed to identify and characterize non-coding RNA (ncRNA) genes encoded within the Escherichia coli (E. coli) genome. It was designated the GMMI (Gapped Markov Model Index) and used to evaluate sequence patterns located at the separate positions of consensus sequences, codon biases and/or possible RNA structures on the basis of the Markov model. The GMMI was able to separate a set of known mRNA sequences from a mixture of ncRNAs including tRNAs and rRNAs. Consequently, the GMMI was employed to predict novel ncRNA candidates. At the beginning, possible transcription units were extracted from the E. coli genome using consensus sequences for the sigma70 promoter and the rho-independent terminator. Then, these units were evaluated by using the GMMI. This identified 133 candidate ncRNAs, which contain 29 previously annotated small RNA genes and 46 possible antisense ncRNAs. Furthermore 12 transcripts (including five antisense RNAs) were confirmed according to the expression analysis. These data suggests that the expression of small antisense RNAs might be more common than previously thought in the E. coli genome.
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Affiliation(s)
- Nozomu Yachie
- Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0035, Japan
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17
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Gu AD, Zhou H, Yu CH, Qu LH. A novel experimental approach for systematic identification of box H/ACA snoRNAs from eukaryotes. Nucleic Acids Res 2005; 33:e194. [PMID: 16361266 PMCID: PMC1316117 DOI: 10.1093/nar/gni185] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Box H/ACA snoRNAs represent an abundant group of small non-coding RNAs mainly involved in the pseudouridylation of rRNAs and/or snRNAs in eukaryotes and Archaea. In this study, we describe a novel experimental method for systematic identification of box H/ACA snoRNAs from eukaryotes. In the specialized cDNA libraries constructed by this method with total cellular RNAs from human blood cells, the high efficiency of cloning for diverse box H/ACA snoRNAs was achieved and seven novel species of this snoRNA family were identified from human for the first time. Furthermore, the novel method has been successfully applied for the identification of the box H/ACA snoRNAs from Drosophila and the fission yeast, demonstrating a powerful ability for systematic analysis of box H/ACA snoRNAs in a broad spectrum of eukaryotes.
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Affiliation(s)
| | | | | | - Liang-Hu Qu
- To whom correspondence should be addressed. Tel: +86 20 84112399; Fax: +86 20 84036551;
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18
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Huang ZP, Zhou H, He HL, Chen CL, Liang D, Qu LH. Genome-wide analyses of two families of snoRNA genes from Drosophila melanogaster, demonstrating the extensive utilization of introns for coding of snoRNAs. RNA (NEW YORK, N.Y.) 2005; 11:1303-16. [PMID: 15987805 PMCID: PMC1370813 DOI: 10.1261/rna.2380905] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Small nucleolar RNAs (snoRNAs) are an abundant group of noncoding RNAs mainly involved in the post-transcriptional modifications of rRNAs in eukaryotes. In this study, a large-scale genome-wide analysis of the two major families of snoRNA genes in the fruit fly Drosophila melanogaster has been performed using experimental and computational RNomics methods. Two hundred and twelve gene variants, encoding 56 box H/ACA and 63 box C/D snoRNAs, were identified, of which 57 novel snoRNAs have been reported for the first time. These snoRNAs were predicted to guide a total of 147 methylations and pseudouridylations on rRNAs and snRNAs, showing a more comprehensive pattern of rRNA modification in the fruit fly. With the exception of nine, all the snoRNAs identified to date in D. melanogaster are intron encoded. Remarkably, the genomic organization of the snoRNAs is characteristic of 8 dUhg genes and 17 intronic gene clusters, demonstrating that distinct organizations dominate the expression of the two families of snoRNAs in the fruit fly. Of the 267 introns in the host genes, more than half have been identified as host introns for coding of snoRNAs. In contrast to mammals, the variation in size of the host introns is mainly due to differences in the number of snoRNAs they contain. These results demonstrate the extensive utilization of introns for coding of snoRNAs in the host genes and shed light on further research of other noncoding RNA genes in the large introns of the Drosophila genome.
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Affiliation(s)
- Zhan-Peng Huang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, Zhongshan University, Guangzhou 510275, Republic of China
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19
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Huang ZP, Zhou H, Liang D, Qu LH. Different expression strategy: multiple intronic gene clusters of box H/ACA snoRNA in Drosophila melanogaster. J Mol Biol 2004; 341:669-83. [PMID: 15288778 DOI: 10.1016/j.jmb.2004.06.041] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2004] [Revised: 05/24/2004] [Accepted: 06/14/2004] [Indexed: 11/30/2022]
Abstract
The high degree of rRNA pseudouridylation in Drosophila melanogaster provides a good model for studying the genomic organization, structural and functional diversity of box H/ACA small nucleolar RNAs (snoRNAs). Accounting for both conserved sequence motifs and secondary structures, we have developed a computer-assisted method for box H/ACA snoRNA searching. Ten snoRNA clusters containing 42 box H/ACA snoRNAs were identified from D.melanogaster. Strikingly, they are located in the introns of eight protein-coding genes. In contrast to the mode of one snoRNA per intron so far observed in all animals, our results demonstrate for the first time a novel polycistronic organization that implies a different expression strategy for a box H/ACA snoRNA gene when compared to box C/D snoRNAs in D.melanogaster. Mutiple isoforms of the box H/ACA snoRNAs, from which most clusters are made up, were observed in D.melanogaster. The degree of sequence similarity between the isoforms varies from 99% to 70%, implying duplication events in different periods and a trend of enlarging the intronic snoRNA clusters. The variation in the functional elements of the isoforms could lead to partial alternation of snoRNA's function in loss or gain of rRNA complementary sequences and probably contributes to the great diversity of rRNA pseudouridylation in D.melanogaster.
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Affiliation(s)
- Zhan-Peng Huang
- Key Laboratory of Gene Engineering of the Ministry of Education, Biotechnology Research Center, Zhongshan University, Guangzhou, 510275, People's Republic of China
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20
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Luo Y, Zhuo H, Li S, Qu L. Identification and functional analysis of a novel box C/D snoRNA fromSchizosaccharomyces pombe. CHINESE SCIENCE BULLETIN-CHINESE 2004. [DOI: 10.1007/bf03184284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Russell AG, Schnare MN, Gray MW. Pseudouridine-guide RNAs and other Cbf5p-associated RNAs in Euglena gracilis. RNA (NEW YORK, N.Y.) 2004; 10:1034-46. [PMID: 15208440 PMCID: PMC1370595 DOI: 10.1261/rna.7300804] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
In eukaryotes, box H/ACA small nucleolar RNAs (snoRNAs) guide sites of pseudouridine (Psi) formation in rRNA. These snoRNAs reside in RNP complexes containing the putative Psi synthase, Cbf5p. In this study we have identified Cbf5p-associated RNAs in Euglena gracilis, an early diverging eukaryote, by immunoprecipitating Cbf5p-containing complexes from cellular extracts. We characterized one box H/ACA-like RNA which, however, does not appear to guide Psi formation in rRNA. We also identified four single Psi-guide box AGA RNAs. We determined target sites for these putative Psi-guide RNAs and confirmed that the predicted Psi modifications do, in fact, occur at these positions in Euglena rRNA. The Cbf5p-associated snoRNAs appear to be encoded by multicopy genes, some of which are clustered in the genome together with methylation-guide snoRNA genes. These modification-guide snoRNAs and snoRNA genes are the first ones to be reported in euglenid protists, the evolutionary sister group to the kinetoplastid protozoa. Unexpectedly, we also found and have partially characterized a selenocysteine tRNA homolog in the anti-Cbf5p-immunoprecipitated sample.
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Affiliation(s)
- Anthony G Russell
- Department of Biochemistry and Molecular Biology, Sir Charles Tupper Medical Building, Room 8F-2, Dal-housie University, 5850 College Street, Halifax, Nova Scotia B3H 1X5, Canada
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22
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Liang XH, Ochaion A, Xu YX, Liu Q, Michaeli S. Small nucleolar RNA clusters in trypanosomatid Leptomonas collosoma. Genome organization, expression studies, and the potential role of sequences present upstream from the first repeated cluster. J Biol Chem 2003; 279:5100-9. [PMID: 14645367 DOI: 10.1074/jbc.m308264200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Trypanosomatid small nucleolar RNA (snoRNA) genes are clustered in the genome. snoRNAs are transcribed polycistronically and processed into mature RNAs. In this study, we characterized four snoRNA clusters in Leptomonas collosoma. All of the clusters analyzed carry both C/D and H/ACA RNAs. The H/ACA RNAs are composed of a single hairpin, a structure typical to trypanosome and archaea guide RNAs. Using deletion and mutational analysis of a tagged C/D snoRNA situated within the snoRNA cluster, we identified 10-nucleotide flanking sequences that are essential for processing snoRNA from its precursor. Chromosome walk was performed on a snoRNA cluster, and a sequence of 700 bp was identified between the first repeat and the upstream open reading frame. Cloning of this sequence in an episome vector enhanced the expression of a tagged snoRNA gene in an orientation-dependent manner. However, continuous transcript spanning of this region was detected in steady-state RNA, suggesting that snoRNA transcription also originates from an upstream-long polycistronic transcriptional unit. The 700-bp fragment may therefore represent an example of many more elements to be discovered that enhance transcription along the chromosome, especially when transcription from the upstream gene is reduced or when enhanced transcription is needed.
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Affiliation(s)
- Xue-hai Liang
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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23
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Massardo DR, Esposito B, Veneziano A, Wolf K, Alifano P, Del Giudice L. Hyper-expression of small nucleolar RNAs (snoRNAs) in female inflorescences of hazelnut (Corylus avellana L.) supports rRNA aggregation in vitro. PLANT & CELL PHYSIOLOGY 2003; 44:884-892. [PMID: 14519769 DOI: 10.1093/pcp/pcg111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Under certain in vitro (salt and temperature) conditions rRNA aggregation occurs in female inflorescences but not in leaves or pollen RNA preparations from hazelnut (Corylus avellana L.), a species of economic interest. This paper describes experiments addressing an explanation of this phenomenon. The experiments demonstrate that: (i) trans-acting factors induce rRNA aggregate formation in female inflorescences RNA preparations; (ii) these factors support aggregation also of heterologous rRNA; (iii) aggregation is a function of temperature pre-treatment of rRNA and not of source 18S rRNA; (iv) the factors inducing rRNA aggregates are sensitive to RNase; (v) antisense small nucleolar RNAs (snoRNAs) participate in rRNA aggregate formation. snoRNAs are involved in pre-rRNA spacer cleavages, and are required for the two most common types of rRNA modifications: 2'-O-ribose methylation and pseudouridylation. Even though it is questionable whether rRNA aggregation really happens in female inflorescence in vivo, the phenomenon observed in vitro may reflect the abundance of snoRNAs in these reproductive structures. In fact the level of accumulation of three tested snoRNAs, R1, U14 and U3, is much higher in female inflorescence than in leaves or pollen of hazelnut. This finding opens the possibility of studying the role of snoRNAs in tissue development in plants.
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Affiliation(s)
- Domenica Rita Massardo
- Istituto di Genetica e Biofisica Adriano Buzzati-Traverso--C.N.R., Via G. Marconi 10, I-80125 Napoli, Italy
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24
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Abstract
Small nucleolar RNAs (snoRNAs) are involved in precursor ribosomal RNA (pre-rRNA) processing and rRNA base modifications (2'-O-ribose methylation and pseudouridylation). Their genomic organization show great flexibility: some are individually or polycistronically transcribed, while others are encoded within introns of other genes. Here, we present an evolutionary analysis of the U49 gene in seven species. In all species analyzed, U49 contains the typical hallmarks of C and D box motifs, and a conserved 12-15 nt sequence complementary to rRNA that define them as homologs. In mouse, human, and Drosophila U49 is found encoded within introns of different genes, and in plants it is transcribed polycistronically from four different locations. In addition, U49 has two copies in two different introns of the RpL14 gene in Drosophila. The results indicate a substantial degree of duplication and translocation of the U49 gene in evolution. In light of its variable organization we discuss which of the two proposed mechanisms of rearrangement has acted upon the U49 snoRNA gene: chromosomal duplication or transposition through an RNA intermediate.
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Affiliation(s)
- Espen Enerly
- Division of Molecular Biology, Institute of Biology, University of Oslo, Blindern, Oslo, Norway
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25
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Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH. The high diversity of snoRNAs in plants: identification and comparative study of 120 snoRNA genes from Oryza sativa. Nucleic Acids Res 2003; 31:2601-13. [PMID: 12736310 PMCID: PMC156054 DOI: 10.1093/nar/gkg373] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2003] [Revised: 02/18/2003] [Accepted: 03/25/2003] [Indexed: 11/14/2022] Open
Abstract
Using a powerful computer-assisted analysis strategy, a large-scale search of small nucleolar RNA (snoRNA) genes in the recently released draft sequence of the rice genome was carried out. This analysis identified 120 different box C/D snoRNA genes with a total of 346 gene variants, which were predicted to guide 135 2'-O-ribose methylation sites in rice rRNAs. Though not exhaustive, this analysis has revealed that rice has the highest number of known box C/D snoRNAs among eukaryotes. Interestingly, although many snoRNA genes are conserved between rice and Arabidopsis, almost half of the identified snoRNA genes are rice specific, which may highlight further the differences in rRNA methylation patterns between monocotyledons and dicotyledons. In addition to 76 singletons, 70 clusters involving 270 snoRNA genes were also found in rice. The large number of the novel snoRNA polycistrons found in the introns of rice protein-coding genes is in contrast to the one-snoRNA-per-intron organization of vertebrates and yeast, and of Arabidopsis in which only a few intronic snoRNA gene clusters were identified. Furthermore, due to a high degree of gene duplication, rice snoRNA genes are clearly redundant and exhibit great sequence variation among isoforms, allowing generation of new snoRNAs for selection. Thus, the large snoRNA gene family in plants can serve as an excellent model for a rapid and functional evolution.
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MESH Headings
- Base Sequence
- Cloning, Molecular
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- Gene Library
- Genes, Plant/genetics
- Genetic Variation
- Genome, Plant
- Methylation
- Molecular Sequence Data
- Multigene Family/genetics
- Oryza/genetics
- Plants/genetics
- RNA, Ribosomal/metabolism
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- Ribose/metabolism
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Chun-Long Chen
- Key Laboratory of Gene Engineering of the Ministry of Education, Biotechnology Research Center, Zhoushan University, Guangzhou 510275, China
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26
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Kruszka K, Barneche F, Guyot R, Ailhas J, Meneau I, Schiffer S, Marchfelder A, Echeverría M. Plant dicistronic tRNA-snoRNA genes: a new mode of expression of the small nucleolar RNAs processed by RNase Z. EMBO J 2003; 22:621-32. [PMID: 12554662 PMCID: PMC140725 DOI: 10.1093/emboj/cdg040] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) guiding modifications of ribosomal RNAs and other RNAs display diverse modes of gene organization and expression depending on the eukaryotic system: in animals most are intron encoded, in yeast many are monocistronic genes and in plants most are polycistronic (independent or intronic) genes. Here we report an unprecedented organization: plant dicistronic tRNA-snoRNA genes. In Arabidopsis thaliana we identified a gene family encoding 12 novel box C/D snoRNAs (snoR43) located just downstream from tRNA(Gly) genes. We confirmed that they are transcribed, probably from the tRNA gene promoter, producing dicistronic tRNA(Gly)-snoR43 precursors. Using transgenic lines expressing a tagged tRNA-snoR43.1 gene we show that the dicistronic precursor is accurately processed to both snoR43.1 and tRNA(Gly). In addition, we show that a recombinant RNase Z, the plant tRNA 3' processing enzyme, efficiently cleaves the dicistronic precursor in vitro releasing the snoR43.1 from the tRNA(Gly). Finally, we describe a similar case in rice implicating a tRNA(Met-e) expressed in fusion with a novel C/D snoRNA, showing that this mode of snoRNA expression is found in distant plant species.
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Affiliation(s)
| | - Fredy Barneche
- Laboratoire Génome et Développement des Plantes, UMR CNRS 5096, Université de Perpignan, 66860 Perpignan cedex, France,
Molecular Biology Department, University of Geneva-Sciences II, 30 Quai Ernest Ansermet, 1211-Geneva, Institut of Plant Biology, University of Zurich, Zollikerstrasse 19, 8008-Zurich, Switzerland and Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany Corresponding author e-mail:
K.Kruszka, F.Barneche and R.Guyot contributed equally to this work
| | - Romain Guyot
- Laboratoire Génome et Développement des Plantes, UMR CNRS 5096, Université de Perpignan, 66860 Perpignan cedex, France,
Molecular Biology Department, University of Geneva-Sciences II, 30 Quai Ernest Ansermet, 1211-Geneva, Institut of Plant Biology, University of Zurich, Zollikerstrasse 19, 8008-Zurich, Switzerland and Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany Corresponding author e-mail:
K.Kruszka, F.Barneche and R.Guyot contributed equally to this work
| | | | | | - Steffen Schiffer
- Laboratoire Génome et Développement des Plantes, UMR CNRS 5096, Université de Perpignan, 66860 Perpignan cedex, France,
Molecular Biology Department, University of Geneva-Sciences II, 30 Quai Ernest Ansermet, 1211-Geneva, Institut of Plant Biology, University of Zurich, Zollikerstrasse 19, 8008-Zurich, Switzerland and Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany Corresponding author e-mail:
K.Kruszka, F.Barneche and R.Guyot contributed equally to this work
| | - Anita Marchfelder
- Laboratoire Génome et Développement des Plantes, UMR CNRS 5096, Université de Perpignan, 66860 Perpignan cedex, France,
Molecular Biology Department, University of Geneva-Sciences II, 30 Quai Ernest Ansermet, 1211-Geneva, Institut of Plant Biology, University of Zurich, Zollikerstrasse 19, 8008-Zurich, Switzerland and Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany Corresponding author e-mail:
K.Kruszka, F.Barneche and R.Guyot contributed equally to this work
| | - Manuel Echeverría
- Laboratoire Génome et Développement des Plantes, UMR CNRS 5096, Université de Perpignan, 66860 Perpignan cedex, France,
Molecular Biology Department, University of Geneva-Sciences II, 30 Quai Ernest Ansermet, 1211-Geneva, Institut of Plant Biology, University of Zurich, Zollikerstrasse 19, 8008-Zurich, Switzerland and Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany Corresponding author e-mail:
K.Kruszka, F.Barneche and R.Guyot contributed equally to this work
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27
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Brown JWS, Echeverria M, Qu LH, Lowe TM, Bachellerie JP, Hüttenhofer A, Kastenmayer JP, Green PJ, Shaw P, Marshall DF. Plant snoRNA database. Nucleic Acids Res 2003; 31:432-5. [PMID: 12520043 PMCID: PMC165456 DOI: 10.1093/nar/gkg009] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Plant snoRNA database (http://www.scri.sari.ac.uk/plant_snoRNA/) provides information on small nucleolar RNAs from Arabidopsis and eighteen other plant species. Information includes sequences, expression data, methylation and pseudouridylation target modification sites, initial gene organization (polycistronic, single gene and intronic) and the number of gene variants. The Arabidopsis information is divided into box C/D and box H/ACA snoRNAs, and within each of these groups, by target sites in rRNA, snRNA or unknown. Alignments of orthologous genes and gene variants from different plant species are available for many snoRNA genes. Plant snoRNA genes have been given a standard nomenclature, designed wherever possible, to provide a consistent identity with yeast and human orthologues.
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Affiliation(s)
- John W S Brown
- Gene Expression Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK.
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28
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Brown JWS, Echeverria M, Qu LH. Plant snoRNAs: functional evolution and new modes of gene expression. TRENDS IN PLANT SCIENCE 2003; 8:42-9. [PMID: 12523999 DOI: 10.1016/s1360-1385(02)00007-9] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Small nucleolar RNAs (snoRNAs) are a well-characterized family of non-coding RNAs whose main function is rRNA modification. The diversity and complexity of this gene family continues to expand with the discovery of snoRNAs with non-rRNA or unknown targets. Plants contain more snoRNAs than other eukaryotes and have developed novel expression and processing strategies. The increased number of modifications, which will influence ribosome function, and the novel modes of expression might reflect the environmental conditions to which plants are exposed. Polyploidy and chromosomal rearrangements have generated multiple copies of snoRNA genes, allowing the generation of new snoRNAs for selection. The large snoRNA family in plants is an ideal model for investigation of mechanisms of evolution of gene families in plants.
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MESH Headings
- Base Sequence
- Evolution, Molecular
- Gene Expression Regulation, Plant
- Molecular Sequence Data
- Plants/genetics
- Plants/metabolism
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- Ribonucleoproteins, Small Nucleolar/chemistry
- Ribonucleoproteins, Small Nucleolar/genetics
- Ribonucleoproteins, Small Nucleolar/physiology
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- John W S Brown
- Gene Expression Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK.
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Hüttenhofer A, Brosius J, Bachellerie JP. RNomics: identification and function of small, non-messenger RNAs. Curr Opin Chem Biol 2002; 6:835-43. [PMID: 12470739 DOI: 10.1016/s1367-5931(02)00397-6] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
In the past few years, our knowledge about small non-mRNAs (snmRNAs) has grown exponentially. Approaches including computational and experimental RNomics have led to a plethora of novel snmRNAs, especially small nucleolar RNAs (snoRNAs). Members of this RNA class guide modification of ribosomal and spliceosomal RNAs. Novel targets for snoRNAs were identified such as tRNAs and potentially mRNAs, and several snoRNAs were shown to be tissue-specifically expressed. In addition, previously unknown classes of snmRNAs have been discovered. MicroRNAs and small interfering RNAs of about 21-23 nt, were shown to regulate gene expression by binding to mRNAs via antisense elements. Regulation of gene expression is exerted by degradation of mRNAs or translational regulation. snmRNAs play a variety of roles during regulation of gene expression. Moreover, the function of some snmRNAs known for decades, has been finally elucidated. Many other RNAs were identified by RNomics studies lacking known sequence and structure motifs. Future challenges in the field of RNomics include identification of the novel snmRNA's biological roles in the cell.
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Affiliation(s)
- Alexander Hüttenhofer
- Institute of Experimental Pathology, ZMBE, Von-Esmarch-Str. 56, 48149, Münster, Germany.
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