ribosomal rna

Summary

Summary: The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)

Top Publications

  1. pmc Mutation in TRMU related to transfer RNA modification modulates the phenotypic expression of the deafness-associated mitochondrial 12S ribosomal RNA mutations
    Min Xin Guan
    Division and Program in Human Genetics, Cincinnati Children s Hospital Medical Center, Cincinnati, Ohio 45229 3039, USA
    Am J Hum Genet 79:291-302. 2006
  2. pmc Genomic architecture and inheritance of human ribosomal RNA gene clusters
    Dawn M Stults
    Graduate Center for Toxicology, University of Kentucky, Lexington, Kentucky 40515, USA
    Genome Res 18:13-8. 2008
  3. pmc SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
    Elmar Pruesse
    Microbial Genomics Group, Max Planck Institute for Marine Microbiology
    Nucleic Acids Res 35:7188-96. 2007
  4. ncbi The post-transcriptional steps of eukaryotic ribosome biogenesis
    A K Henras
    Laboratoire de Biologie Moleculaire Eucaryote, CNRS, Universite de Toulouse, UPS, 118 route de Narbonne, 31062 Toulouse Cedex 09, France
    Cell Mol Life Sci 65:2334-59. 2008
  5. ncbi A molecular view of microbial diversity and the biosphere
    N R Pace
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 3102, USA
    Science 276:734-40. 1997
  6. ncbi Loss of human ribosomal gene CpG methylation enhances cryptic RNA polymerase II transcription and disrupts ribosomal RNA processing
    Thérèse Gagnon-Kugler
    Cancer Research Centre, CHUQ HDQ Research Centre, Pavillon St Patrick, 9 rue McMahon, Quebec, QC G1R 3S3, Canada
    Mol Cell 35:414-25. 2009
  7. ncbi The complete mitochondrial genome of the tobacco hornworm, Manduca sexta, (Insecta: Lepidoptera: Sphingidae), and an examination of mitochondrial gene variability within butterflies and moths
    Stephen L Cameron
    Australian National Insect Collection and CSIRO Entomology, Black Mountain Laboratories, Canberra, ACT, Australia
    Gene 408:112-23. 2008
  8. ncbi rRNA modifications and ribosome function
    Wayne A Decatur
    Trends Biochem Sci 27:344-51. 2002
  9. pmc Powering through ribosome assembly
    Bethany S Strunk
    Chemical Biology Doctoral Program, University of Michigan, Ann Arbor, Michigan 48109 1055, USA
    RNA 15:2083-104. 2009
  10. ncbi c-Myc binds to human ribosomal DNA and stimulates transcription of rRNA genes by RNA polymerase I
    Carla Grandori
    Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 1024, USA
    Nat Cell Biol 7:311-8. 2005

Detail Information

Publications373 found, 100 shown here

  1. pmc Mutation in TRMU related to transfer RNA modification modulates the phenotypic expression of the deafness-associated mitochondrial 12S ribosomal RNA mutations
    Min Xin Guan
    Division and Program in Human Genetics, Cincinnati Children s Hospital Medical Center, Cincinnati, Ohio 45229 3039, USA
    Am J Hum Genet 79:291-302. 2006
    The human mitochondrial 12S ribosomal RNA (rRNA) A1555G mutation has been associated with aminoglycoside-induced and nonsyndromic deafness in many families worldwide...
  2. pmc Genomic architecture and inheritance of human ribosomal RNA gene clusters
    Dawn M Stults
    Graduate Center for Toxicology, University of Kentucky, Lexington, Kentucky 40515, USA
    Genome Res 18:13-8. 2008
    ..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 ..
  3. pmc SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
    Elmar Pruesse
    Microbial Genomics Group, Max Planck Institute for Marine Microbiology
    Nucleic Acids Res 35:7188-96. 2007
    Sequencing ribosomal RNA (rRNA) genes is currently the method of choice for phylogenetic reconstruction, nucleic acid based detection and quantification of microbial diversity...
  4. ncbi The post-transcriptional steps of eukaryotic ribosome biogenesis
    A K Henras
    Laboratoire de Biologie Moleculaire Eucaryote, CNRS, Universite de Toulouse, UPS, 118 route de Narbonne, 31062 Toulouse Cedex 09, France
    Cell Mol Life Sci 65:2334-59. 2008
    ..Moreover, quality control mechanisms are being discovered that monitor ribosome synthesis and degrade the RNA components of defective pre-ribosomal particles...
  5. ncbi A molecular view of microbial diversity and the biosphere
    N R Pace
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 3102, USA
    Science 276:734-40. 1997
    ....
  6. ncbi Loss of human ribosomal gene CpG methylation enhances cryptic RNA polymerase II transcription and disrupts ribosomal RNA processing
    Thérèse Gagnon-Kugler
    Cancer Research Centre, CHUQ HDQ Research Centre, Pavillon St Patrick, 9 rue McMahon, Quebec, QC G1R 3S3, Canada
    Mol Cell 35:414-25. 2009
    Epigenetic methyl-CpG silencing of the ribosomal RNA (rRNA) genes is thought to downregulate rRNA synthesis in mammals. In contrast, we now show that CpG methylation in fact positively influences rRNA synthesis and processing...
  7. ncbi The complete mitochondrial genome of the tobacco hornworm, Manduca sexta, (Insecta: Lepidoptera: Sphingidae), and an examination of mitochondrial gene variability within butterflies and moths
    Stephen L Cameron
    Australian National Insect Collection and CSIRO Entomology, Black Mountain Laboratories, Canberra, ACT, Australia
    Gene 408:112-23. 2008
    ..Secondary structure models of the ribosomal RNA genes of Manduca are presented and are similar to those proposed for other insect orders...
  8. ncbi rRNA modifications and ribosome function
    Wayne A Decatur
    Trends Biochem Sci 27:344-51. 2002
    ..The correlations suggest that many ribosome functions benefit from nucleotide modification...
  9. pmc Powering through ribosome assembly
    Bethany S Strunk
    Chemical Biology Doctoral Program, University of Michigan, Ann Arbor, Michigan 48109 1055, USA
    RNA 15:2083-104. 2009
    ..biophysical, thermodynamic, and structural basis for the ordered and correct assembly of ribosomal proteins on ribosomal RNA. Furthermore, it has enabled reconstitution of active subunits from ribosomal RNA and proteins in vitro...
  10. ncbi c-Myc binds to human ribosomal DNA and stimulates transcription of rRNA genes by RNA polymerase I
    Carla Grandori
    Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 1024, USA
    Nat Cell Biol 7:311-8. 2005
    ..Here, we demonstrate that human c-Myc also directly enhances Pol I transcription of ribosomal RNA (rRNA) genes...
  11. pmc A genomic-library based discovery of a novel, possibly synthetic, acid-tolerance mechanism in Clostridium acetobutylicum involving non-coding RNAs and ribosomal RNA processing
    Jacob R Borden
    Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
    Metab Eng 12:268-81. 2010
    ..Our data suggest that by hybridizing against unprocessed rRNA precursors, ncRNA(RD7) alters rRNA processing, and these alterations result in acid tolerance, possibly through a mechanism involving the Ffh protein...
  12. pmc The mitochondrial genome of the honeybee Apis mellifera: complete sequence and genome organization
    R H Crozier
    Department of Genetics and Human Variation, La Trobe University, Bundoora, Victoria, Australia
    Genetics 133:97-117. 1993
    ..expectation are seen for the third positions of protein-coding genes and for the gene for the small subunit of ribosomal RNA. For the third codon positions the excess of transitions is adequately explained as due to the restriction of ..
  13. ncbi 90S pre-ribosomes include the 35S pre-rRNA, the U3 snoRNP, and 40S subunit processing factors but predominantly lack 60S synthesis factors
    Paola Grandi
    Cellzome AG, Meyerhofstrasse 1, 69117, Heidelberg, Germany
    Mol Cell 10:105-15. 2002
    ..We conclude that the 40S synthesis machinery predominately associates with the 35S pre-rRNA factors, whereas factors required for 60S subunit synthesis largely bind later, showing an unexpected dichotomy in binding...
  14. ncbi A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont
    Harald Huber
    Lehrstuhl fur Mikrobiologie und Archaeenzentrum, Universitat Regensburg, Universitatsstrasse 31, D 93053 Regensburg, Germany
    Nature 417:63-7. 2002
    According to small subunit ribosomal RNA (ss rRNA) sequence comparisons all known Archaea belong to the phyla Crenarchaeota, Euryarchaeota, and--indicated only by environmental DNA sequences--to the 'Korarchaeota'...
  15. ncbi Microbial population structures in the deep marine biosphere
    Julie A Huber
    Josephine Bay Paul Center, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA
    Science 318:97-100. 2007
    ..at two neighboring hydrothermal vents by examining the sequences of more than 900,000 microbial small-subunit ribosomal RNA amplicons...
  16. pmc rRNA maturation in yeast cells depleted of large ribosomal subunit proteins
    Gisela Pöll
    Institut für Biochemie III, Universitat Regensburg, Regensburg, Germany
    PLoS ONE 4:e8249. 2009
    ....
  17. pmc Many ribosomal protein genes are cancer genes in zebrafish
    Adam Amsterdam
    Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    PLoS Biol 2:E139. 2004
    ..Our findings suggest that many RP genes may act as haploinsufficient tumor suppressors in fish. Many RP genes might also be cancer genes in humans, where their role in tumorigenesis could easily have escaped detection up to now...
  18. pmc Evidence that ternary complex (eIF2-GTP-tRNA(i)(Met))-deficient preinitiation complexes are core constituents of mammalian stress granules
    Nancy Kedersha
    Division of Rheumatology and Immunology, Brigham and Women s Hospital, Boston, Massachusetts 02115, USA
    Mol Biol Cell 13:195-210. 2002
    ..We discuss these results in the context of a translational checkpoint model wherein TIA and eIF2 are functional antagonists of translational initiation, and in which lack of ternary complex drives SG assembly...
  19. ncbi Chromophore-assisted light inactivation of pKi-67 leads to inhibition of ribosomal RNA synthesis
    R Rahmanzadeh
    Research Center Borstel, Department of Immunology and Cell Biology, Division of Tumour Biology, Borstel, Germany
    Cell Prolif 40:422-30. 2007
    ..Recently, we proposed a function of pKi-67 in the early steps of ribosomal RNA (rRNA) synthesis...
  20. ncbi Mapping to nucleotide resolution of pseudouridine residues in large subunit ribosomal RNAs from representative eukaryotes, prokaryotes, archaebacteria, mitochondria and chloroplasts
    J Ofengand
    Department of Biochemistry and Molecular Biology, University of Miami School of Medicine, FL 33101, USA
    J Mol Biol 266:246-68. 1997
    ..mays chloroplasts and D. melanogaster LSU RNA, correlate the secondary structural context for all known psi residues in ribosomal RNA, and compare the sites for psi with those known for methylated nucleosides in H. sapiens.
  21. pmc The mitochondrial genomes of two nematodes, Caenorhabditis elegans and Ascaris suum
    R Okimoto
    Department of Biology, University of Utah, Salt Lake City 84112
    Genetics 130:471-98. 1992
    ..elegans and A. suum ancestral lines diverged close to the time of divergence of the cow and human ancestral lines, about 80 million years ago...
  22. pmc The complete mitochondrial genome of the bag-shelter moth Ochrogaster lunifer (Lepidoptera, Notodontidae)
    Paola Salvato
    Department of Public Health, Comparative Pathology and Veterinary Hygiene, University of Padova, Agripolis, Viale dell Universita 16, 35020 Legnaro, Italy
    BMC Genomics 9:331. 2008
    ..Thus advance of lepidopteran mitogenomics deeply requires new genomes derived from a broad taxon sampling. In present work we describe the mitochondrial genome of the moth Ochrogaster lunifer...
  23. pmc A role for c-Myc in the regulation of ribosomal RNA processing
    Isabel Schlosser
    GSF National Research Centre for Environment and Health, Institute of Clinical Molecular Biology and Tumor Genetics, Marchioninistrasse 25, 81377 Munich, Germany
    Nucleic Acids Res 31:6148-56. 2003
    ..identification of 38 new c-Myc target genes with nucleolar function, prompted us to investigate processing of ribosomal RNA (rRNA). Using pulse-chase labelling experiments we show that c-Myc regulates the efficiency of rRNA maturation...
  24. ncbi Drosophila melanogaster mitochondrial DNA: completion of the nucleotide sequence and evolutionary comparisons
    D L Lewis
    Department of Biochemistry, Michigan State University, East Lansing, USA
    Insect Mol Biol 4:263-78. 1995
    ..Included are the genes encoding the transfer RNAs for valine, isoleucine, glutamine and methionine, the small ribosomal RNA and the 5'-coding sequences of the large ribosomal RNA and NADH dehydrogenase subunit II...
  25. ncbi Drosophila mitochondrial DNA: conserved sequences in the A + T-rich region and supporting evidence for a secondary structure model of the small ribosomal RNA
    D O Clary
    Department of Biology, University of Utah, Salt Lake City 84112
    J Mol Evol 25:116-25. 1987
    ..virilis and D. yakuba strongly support the secondary structure model for the Drosophila small mt-rRNA that we previously proposed...
  26. ncbi Functional characterization of Pwp2, a WD family protein essential for the assembly of the 90 S pre-ribosomal particle
    Mercedes Dosil
    Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, University of Salamanca CSIC, Campus Unamuno, E 37007 Salamanca, Spain
    J Biol Chem 279:37385-97. 2004
    ..Taken together, these results indicate that Pwp2 forms part of a stable particle subunit independent of the U3 small nucleolar ribonucleoprotein that is essential for the initial assembly steps of the 90 S pre-ribosome...
  27. ncbi Crystal structure of the ribosome at 5.5 A resolution
    M M Yusupov
    Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
    Science 292:883-96. 2001
    ..5 angstrom resolution. All of the 16S, 23S, and 5S ribosomal RNA (rRNA) chains, the A-, P-, and E-site tRNAs, and most of the ribosomal proteins can be fitted to the electron ..
  28. ncbi Ki-67 protein is associated with ribosomal RNA transcription in quiescent and proliferating cells
    Jörn Bullwinkel
    Division of Tumour Biology, Research Center Borstel, Borstel, Germany
    J Cell Physiol 206:624-35. 2006
    ..of pKi-67 expression in non-proliferating cells, the protein can nevertheless be detected at sites linked to ribosomal RNA (rRNA) synthesis...
  29. ncbi Validation of two ribosomal RNA removal methods for microbial metatranscriptomics
    Shaomei He
    Department of Energy Joint Genome Institute, Walnut Creek, California, USA
    Nat Methods 7:807-12. 2010
    ..Illumina sequencing itself also can compromise quantitative data analysis by introducing a G+C bias between runs...
  30. ncbi The mitochondrial genome of the mosquito Anopheles gambiae: DNA sequence, genome organization, and comparisons with mitochondrial sequences of other insects
    C B Beard
    Centers for Disease Control and Prevention, Public Health Service, US Department of Health and Human Services, Atlanta, GA 30314 3724, USA
    Insect Mol Biol 2:103-24. 1993
    ..Comparisons were made with the mitochondrial genomes of other insects on the basis genome size and organization, DNA and putative amino acid sequence data, nucleotide substitutions, codon usage and bias, and patterns of AT enrichment...
  31. pmc The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis
    J R Cole
    Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824 4320, USA
    Nucleic Acids Res 33:D294-6. 2005
    ..The RDP-II email address for questions or comments is rdpstaff@msu.edu...
  32. ncbi Ribosomal RNA pseudouridines and pseudouridine synthases
    James Ofengand
    Department of Biochemistry and Molecular Biology, University of Miami School of Medicine, P O Box 016129, Miami, FL 33101, USA
    FEBS Lett 514:17-25. 2002
    ..No unique specific role for ribosomal pseudouridines has been identified. We propose that pseudouridine's function is as a molecular glue to stabilize required RNA conformations that would otherwise be too flexible...
  33. pmc mTOR-dependent activation of the transcription factor TIF-IA links rRNA synthesis to nutrient availability
    Christine Mayer
    Division of Molecular Biology of the Cell II, German Cancer Research Center, D 69120 Heidelberg, Germany
    Genes Dev 18:423-34. 2004
    In cycling cells, transcription of ribosomal RNA genes by RNA polymerase I (Pol I) is tightly coordinated with cell growth...
  34. ncbi Intergenic transcripts regulate the epigenetic state of rRNA genes
    Christine Mayer
    German Cancer Research Center, Division of Molecular Biology of the Cell II, D 69120 Heidelberg, Germany
    Mol Cell 22:351-61. 2006
    ..The results reveal an important contribution of processed IGS transcripts in chromatin structure and epigenetic control of the rDNA locus...
  35. pmc Nucleolar dominance and ribosomal RNA gene silencing
    Sarah Tucker
    Department of Biology, Washington University, St Louis, MO 63130, USA
    Curr Opin Cell Biol 22:351-6. 2010
    ..b>Ribosomal RNA gene silencing involves changes in DNA methylation and histone modifications, but the molecular basis for ..
  36. ncbi Two different chromatin structures coexist in ribosomal RNA genes throughout the cell cycle
    A Conconi
    Institute for Cell Biology, Swiss Federal Institute of Technology, Zurich
    Cell 57:753-61. 1989
    ..This suggests that the two states of chromatin are maintained independently of the transcriptional process and that they are stably propagated through the cell cycle...
  37. ncbi Evaluation of ribosomal RNA and actin gene sequences for the identification of ascomycetous yeasts
    H M Daniel
    Centre for Infectious Diseases and Microbiology, Molecular Mycology Laboratory, Westmead Hospital, ICPMR, Level 3, Room 3114A, Darcy Road, Westmead, NSW 2145, Australia
    Int J Food Microbiol 86:61-78. 2003
    ..The actin gene is a better marker in these cases. However, because of the availability of a large database of fungal D1/D2 LSU sequences, this gene region is currently still the preferred target for sequence-based identification...
  38. pmc Translational feedback regulation of the gene for L35 in Escherichia coli requires binding of ribosomal protein L20 to two sites in its leader mRNA: a possible case of ribosomal RNA-messenger RNA molecular mimicry
    Maude Guillier
    Institut de Biologie Physico Chimique, Unité Propre de Recherche 9073 du Centre National de la Recherche Scientifique, Paris, France
    RNA 8:878-89. 2002
    ..However L20 can bind to each site independently in vitro. One site is similar to the L20-binding site on 23S rRNA. Here we propose that L20 recognizes its mRNA and its rRNA in similar way...
  39. pmc The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data
    J R Cole
    Center for Microbial Ecology, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824 4320, USA
    Nucleic Acids Res 35:D169-72. 2007
    ..In addition, new video tutorials describe how to use RDP features. Details about RDP data and analytical functions can be found at the RDP-II website (http://rdp.cme.msu.edu/)...
  40. ncbi rRNA modifications in an intersubunit bridge of the ribosome strongly affect both ribosome biogenesis and activity
    Xue Hai Liang
    Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
    Mol Cell 28:965-77. 2007
    ..Taken together, the results indicate that this subset of rRNA modifications can influence both ribosome synthesis and function and in synergistic ways...
  41. pmc Benthic eukaryotic diversity in the Guaymas Basin hydrothermal vent environment
    Virginia P Edgcomb
    The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
    Proc Natl Acad Sci U S A 99:7658-62. 2002
    ..g., phototrophs) are simply deposited by sedimentary processes. In contrast, bacterial populations in these sediments are primarily characteristic of anoxic, reduced, hydrocarbon-rich sedimentary habitats...
  42. ncbi Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs
    Z Kiss-László
    Laboratorie de Biologie Moléculaire Eucaryote du CNRS, Toulouse, France
    Cell 85:1077-88. 1996
    ..The conclusion that sno-RNAs function in covalent modification of the sugar moieties of ribonucleotides demonstrates that eukaryotic small nuclear RNAs have a more versatile cellular function than earlier anticipated...
  43. ncbi Quantitative analysis of nucleic acid three-dimensional structures
    P Gendron
    , , C.P. 6128, Succ. Centre-Ville, , , H3C 3J7, Canada
    J Mol Biol 308:919-36. 2001
    ..It was applied to the ribosomal RNA fragment that binds to protein L11, which annotations revealed peculiar nucleotide conformations and base-base ..
  44. ncbi The multifunctional nucleolus
    Francois Michel Boisvert
    Wellcome Trust Biocentre, University of Dundee, Dundee DD1 5EH, UK
    Nat Rev Mol Cell Biol 8:574-85. 2007
    ....
  45. ncbi The mitochondrial genome of the smaller tea tortrix Adoxophyes honmai (Lepidoptera: Tortricidae)
    Eun Seung Lee
    Department of Plant Medicine, Chungbuk National University, Cheongju, Republic of Korea
    Gene 373:52-7. 2006
    ..honmai, an apoditrysian tortricid moth joined basally within the monophyly of Lepidoptera, supporting its relationship with other more derived species including obtectomeran Ostrinia species...
  46. ncbi At the crossroads of growth control; making ribosomal RNA
    Tom Moss
    Cancer Research Centre and Department of Medical Biology, Laval University, Hotel Dieu de Quebec, 9 rue McMahon, G1R 2J6 Québec, Canada
    Curr Opin Genet Dev 14:210-7. 2004
    ..In the past few years we have begun to penetrate the network linking rRNA gene transcription to growth...
  47. pmc The kink-turn: a new RNA secondary structure motif
    D J Klein
    Department of Molecular Biophysics and Biochemistry, Yale University and Howard Hughes Medical Institute, New Haven, CT 06520 8114, USA
    EMBO J 20:4214-21. 2001
    ..Five K-turns in 23S rRNA interact with nine proteins. While the observed K-turns interact with proteins of unrelated structures in different ways, they interact with L7Ae and two homologous proteins in the same way...
  48. ncbi The mitochondrial DNA molecular of Drosophila yakuba: nucleotide sequence, gene organization, and genetic code
    D O Clary
    J Mol Evol 22:252-71. 1985
    ..Evidence is summarized that supports the hypothesis that A and T nucleotides are favored at all locations in the D. yakuba mtDNA molecule where these nucleotides are compatible with function...
  49. ncbi Maturation and degradation of ribosomal RNA in bacteria
    Murray P Deutscher
    Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida, USA
    Prog Mol Biol Transl Sci 85:369-91. 2009
    ..The second focus of this review is to describe these degradative reactions, the RNases that carry them out, and the conditions that initiate the turnover process...
  50. ncbi Mitotic occupancy and lineage-specific transcriptional control of rRNA genes by Runx2
    Daniel W Young
    Department of Cell Biology and Cancer Center, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
    Nature 445:442-6. 2007
    Regulation of ribosomal RNA genes is a fundamental process that supports the growth of cells and is tightly coupled with cell differentiation...
  51. ncbi Ribosome assembly in eukaryotes
    Micheline Fromont-Racine
    Genetique des Interactions Macromoleculaires, Institut Pasteur, 75724 Cedex 15, Paris, France
    Gene 313:17-42. 2003
    ..Proteomic approaches have provided the first indications for a ribosome assembly pathway in eukaryotes and confirmed the dynamic character of the whole process...
  52. ncbi The mitochondrial 12S gene is a suitable marker of populations of Sarcoptes scabiei from wombats, dogs and humans in Australia
    L F Skerratt
    School of Veterinary Science, The University of Melbourne, Werribee, Victoria, Australia
    Parasitol Res 88:376-9. 2002
    We sequenced part of the mitochondrial 12S ribosomal RNA gene of 23 specimens of Sarcoptes scabiei from eight wombats, one dog and three humans...
  53. ncbi Archaeal phylogeny based on ribosomal proteins
    Oriane Matte-Tailliez
    Institut de Genetique et Microbiologie, Universite Paris Sud, Orsay, France
    Mol Biol Evol 19:631-9. 2002
    Until recently, phylogenetic analyses of Archaea have mainly been based on ribosomal RNA (rRNA) sequence comparisons, leading to the distinction of the two major archaeal phyla: the Euryarchaeota and the Crenarchaeota...
  54. pmc Bop1 is a mouse WD40 repeat nucleolar protein involved in 28S and 5. 8S RRNA processing and 60S ribosome biogenesis
    Z Strezoska
    Department of Molecular Genetics, University of Illinois at Chicago College of Medicine, Chicago, Illinois 60607 7170, USA
    Mol Cell Biol 20:5516-28. 2000
    ..These studies thus identify Bop1 as a novel, nonribosomal mammalian protein that plays a key role in the formation of the mature 28S and 5.8S rRNAs and in the biogenesis of the 60S ribosomal subunit...
  55. ncbi Ribosomal RNA-targeted nucleic acid probes for studies in microbial ecology
    R Amann
    Max Planck Institut für Marine Mikrobiologie, Bremen, Germany
    FEMS Microbiol Rev 24:555-65. 2000
    ..In order to speed up the transformation of microbial ecology from a mostly descriptive to a hypothesis-driven, experimental science more intense use must be made of the taxonomic precision and quantitativeness of rRNA-targeted probes...
  56. pmc Functions of the exosome in rRNA, snoRNA and snRNA synthesis
    C Allmang
    Institute of Cell and Molecular Biology, University of Edinburgh, Swann Building, King s Buildings, Edinburgh EH9 3JR, UK
    EMBO J 18:5399-410. 1999
    ..We conclude that the exosome is involved in the processing of many RNA substrates and that different components can have distinct functions...
  57. pmc Alterations of the dominant faecal bacterial groups in patients with Crohn's disease of the colon
    P Seksik
    INRA, CR de Jouy en Josas, 78352 Jouy en Josas, France
    Gut 52:237-42. 2003
    ..We investigated potential differences in the faecal microflora between patients with colonic CD in remission (n=9), patients with active colonic CD (n=8), and healthy volunteers (n=16) using culture independent techniques...
  58. pmc Ribosomal RNA and protein mutants resistant to spectinomycin
    N Bilgin
    Department of Molecular Biology, Uppsala University, Sweden
    EMBO J 9:735-9. 1990
    ..All of these ribosomal mutants confer a degree of Spc resistance for the EF-G cycle in vitro that is correlated with the degree of growth rate resistance to the antibiotic in culture...
  59. ncbi Structure and organization of the mitochondrial genome of the canine heartworm, Dirofilaria immitis
    M Hu
    Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria 3030, Australia
    Parasitology 127:37-51. 2003
    ..Also, the secondary structures of the 2 ribosomal RNA (rrn) genes are similar to the models for other nematodes. Overall, the availability of the complete D...
  60. pmc Characterization of AtNUC-L1 reveals a central role of nucleolin in nucleolus organization and silencing of AtNUC-L2 gene in Arabidopsis
    Frederic Pontvianne
    Unité Mixte de Recherche Centre National de la Recherche Scientifique 5096, Universite de Perpignan, Perpignan, 66860 Perpignan, France
    Mol Biol Cell 18:369-79. 2007
    ..This work is the first description of a higher eukaryotic organism with a disrupted nucleolin-like gene and defines a new role for nucleolin in nucleolus structure and rDNA chromatin organization...
  61. pmc Arabidopsis thaliana XRN2 is required for primary cleavage in the pre-ribosomal RNA
    Monika Zakrzewska-Placzek
    Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
    Nucleic Acids Res 38:4487-502. 2010
    ..Here we show that, similar to yeast nuclear Rat1, AtXRN2 has a role in ribosomal RNA processing...
  62. ncbi Gene rearrangements in snake mitochondrial genomes: highly concerted evolution of control-region-like sequences duplicated and inserted into a tRNA gene cluster
    Y Kumazawa
    Department of Earth and Planetary Sciences, Nagoya University, Japan
    Mol Biol Evol 13:1242-54. 1996
    ..The secondary structures of the determined tRNA genes point to the operation of simplification pressure on the T psi C arm of snake mitochondrial tRNAs...
  63. pmc Methylation of histone H3 and H4 by PRMT5 regulates ribosomal RNA gene transcription
    Sarmila Majumder
    Department of Molecular and Cellular Biochemistry, Ohio State University, Columbus, Ohio 43210, USA
    J Cell Biochem 109:553-63. 2010
    In an effort to understand the epigenetic regulation of ribosomal RNA gene (rDNA) expression we have previously demonstrated the role of DNA methyltransferases and methyl CpG binding proteins in rRNA synthesis...
  64. ncbi The mitochondrial genome of Xiphinema americanum sensu stricto (Nematoda: Enoplea): considerable economization in the length and structural features of encoded genes
    Y He
    Gewasbescherming CLO, Burg Van Gansberghelaan 96, Merelbeke, 9820, Belgium
    J Mol Evol 61:819-33. 2005
    ..In addition, five tRNAs genes are absent, lengthy noncoding regions are not present in the mtDNA, and several gene overlaps are present...
  65. ncbi Evolution of the secondary structure of the rRNA internal transcribed spacer 2 (ITS2) in hard ticks (Ixodidae, Arthropoda)
    O Hlinka
    Department of Microbiology and Parasitology, and Institute for Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia
    Heredity (Edinb) 88:275-9. 2002
    ....
  66. pmc Nucleolar assembly of the rRNA processing machinery in living cells
    T M Savino
    Institut Jacques Monod, UMR 7592, 2 place Jussieu, 75251 Paris Cedex 05, France
    J Cell Biol 153:1097-110. 2001
    ..machineries are targeted to accurate locations during nuclear assembly, we investigated the pathway of the ribosomal RNA (rRNA) processing machinery towards ribosomal genes (nucleolar organizer regions [NORs]) at exit of mitosis...
  67. ncbi Structures of the bacterial ribosome at 3.5 A resolution
    Barbara S Schuwirth
    Department of Chemistry, University of California, Berkeley, CA 94720, USA
    Science 310:827-34. 2005
    ....
  68. ncbi Sequence heterogeneity of the small subunit ribosomal RNA genes among blastocystis isolates
    N Arisue
    Department of Biosystems Science, Graduate University for Advanced Studies SOKENDAI, Hayama, Kanagawa 240 0193, Japan
    Parasitology 126:1-9. 2003
    Genes encoding small subunit ribosomal RNA (SSUrRNA) of 16 Blastocystis isolates from humans and other animals were amplified by the polymerase chain reaction, and the corresponding fragments were cloned and sequenced...
  69. pmc Synthetic lethality with conditional dbp6 alleles identifies rsa1p, a nucleoplasmic protein involved in the assembly of 60S ribosomal subunits
    D Kressler
    Departement de Biochimie Medicale, Centre Medical Universitaire, 1211 Geneva 4, Switzerland
    Mol Cell Biol 19:8633-45. 1999
    ..Finally, a hemagglutinin epitope-tagged Rsa1p localizes predominantly to the nucleoplasm. Together, these results point towards a function for Rsa1p in a late nucleoplasmic step of 60S-ribosomal-subunit assembly...
  70. ncbi Comparative RNomics and modomics in Mollicutes: prediction of gene function and evolutionary implications
    VALERIE DE CRECY-LAGARD
    Department of Microbiology, University of Florida, Gainesville 32611 0700, USA
    IUBMB Life 59:634-58. 2007
    ....
  71. ncbi The large subunit of the mammalian mitochondrial ribosome. Analysis of the complement of ribosomal proteins present
    E C Koc
    Department of Chemistry and Campus Box 3290, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
    J Biol Chem 276:43958-69. 2001
    ..elegans. Ten of the 20 mitochondrial specific 39 S proteins have homologs in S. cerevisiae. Homologs of 2 of these new classes of ribosomal proteins could be identified in the Arabidopsis thaliana genome...
  72. pmc Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil
    Noah Fierer
    Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309 0216, USA
    Appl Environ Microbiol 73:7059-66. 2007
    ..Within each of the four microbial groups, we observed minimal taxonomic overlap between sites, suggesting that soil archaea, bacteria, fungi, and viruses are globally as well as locally diverse...
  73. pmc Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements
    J J Gillespie
    Department of Entomology, Texas A and M University, College Station, TX, USA
    Insect Mol Biol 15:657-86. 2006
    ..8S, 28S and 5S) and mitochondrial (12S and 16S) ribosomal RNA (rRNA)-encoding gene sequences (rDNA) and related internally and externally transcribed spacer regions of Apis ..
  74. ncbi Structure of the 30S ribosomal subunit
    B T Wimberly
    MRC Laboratory of Molecular Biology, Cambridge, UK
    Nature 407:327-39. 2000
    ..The structure will facilitate the interpretation in molecular terms of lower resolution structural data on several functional states of the ribosome from electron microscopy and crystallography...
  75. pmc Proinsulin C-peptide regulates ribosomal RNA expression
    Emma Lindahl
    Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 171 77 Stockholm, Sweden
    J Biol Chem 285:3462-9. 2010
    ..cellular entry, C-peptide is localized to the nucleoli, where it promotes transcription of genes encoding for ribosomal RNA. We find that C-peptide binds to histones and enhances acetylation of lysine residue 16 of histone H4 at the ..
  76. pmc Non-coding RNA annotation of the genome of Trichoplax adhaerens
    Jana Hertel
    Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, D 04107 Leipzig, Germany
    Nucleic Acids Res 37:1602-15. 2009
    ..We did not find any microRNA candidates homologous to known eumetazoan sequences. Interestingly, most ncRNAs, including the pol-III transcripts, appear as single-copy genes or with very small copy numbers in the Trichoplax genome...
  77. ncbi SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny
    N Galtier
    CNRS UMR 5558, Biometrie, Génétique et Biologie des Populations, Universite Claude Bernard Lyon, Villeurbanne, France
    Comput Appl Biosci 12:543-8. 1996
    ..On-line help makes them easy to use. They are freely available by anonymous ftp at biom3.univ-lyon1.fr/pub/ mol_phylogeny or http:@acnuc.univ-lyon1.fr/, or by e-mail to galtier@biomserv.univ-lyon1.fr...
  78. ncbi Numerous gene rearrangements in the mitochondrial genome of the wallaby louse, Heterodoxus macropus (Phthiraptera)
    R Shao
    Department of Microbiology and Parasitology, and Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
    Mol Biol Evol 18:858-65. 2001
    ..The large number of gene rearrangements in the mt genome of H. macropus is unprecedented for an arthropod...
  79. ncbi Coordinate regulation of ribosome biogenesis and function by the ribosomal protein S6 kinase, a key mediator of mTOR function
    Katarzyna Jastrzebski
    Growth Control and Differentiation Program, Trescowthick Research Laboratories, Peter MacCallum Cancer Centre, Melbourne, Australia
    Growth Factors 25:209-26. 2007
    ..Finally, we will discuss the impact of S6K signaling and the consequent feedback regulation of the PI3K/Akt pathway on disease processes including cancer...
  80. pmc Role of human ribosomal RNA (rRNA) promoter methylation and of methyl-CpG-binding protein MBD2 in the suppression of rRNA gene expression
    Kalpana Ghoshal
    Department of Molecular and Cellular Biochemistry, College of Medicine, Ohio State University, Columbus, Ohio 43210, USA
    J Biol Chem 279:6783-93. 2004
    The methylation status of the CpG island located within the ribosomal RNA (rRNA) promoter in human hepatocellular carcinomas and pair-matched liver tissues was analyzed by bisulfite genomic sequencing...
  81. ncbi Tumor suppressor ARF degrades B23, a nucleolar protein involved in ribosome biogenesis and cell proliferation
    Koji Itahana
    Department of Molecular and Cellular Oncology, University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
    Mol Cell 12:1151-64. 2003
    ..Together, our results reveal a molecular mechanism of ARF in regulating ribosome biogenesis and cell proliferation via inhibiting B23, and suggest a nucleolar role of ARF in surveillance of oncogenic insults...
  82. pmc Analysis of nucleolar protein dynamics reveals the nuclear degradation of ribosomal proteins
    Yun Wah Lam
    Division of Gene Regulation and Expression, Wellcome Trust Biocentre, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
    Curr Biol 17:749-60. 2007
    ....
  83. ncbi Nucleolar Arf tumor suppressor inhibits ribosomal RNA processing
    Masataka Sugimoto
    Howard Hughes Medical Institute, St Jude Children s Research Hospital, 332 North Lauderdale, Memphis, TN 38105, USA
    Mol Cell 11:415-24. 2003
    ..We show that p19(Arf) inhibits production of ribosomal RNA, retarding processing of 47/45S and 32S precursors...
  84. ncbi Growth factor signaling regulates elongation of RNA polymerase I transcription in mammals via UBF phosphorylation and r-chromatin remodeling
    Victor Stefanovsky
    Cancer Research Centre and Department of Medical Biology, Laval University, Hotel Dieu de Quebec, 11 Cote du Palais, G1R 2J6 Québec, Canada
    Mol Cell 21:629-39. 2006
    ..The data suggest a mechanism for coordinating the cotranscriptional assembly of preribosomal particles...
  85. pmc A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes
    Linda A Amaral-Zettler
    The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
    PLoS ONE 4:e6372. 2009
    Massively parallel pyrosequencing of amplicons from the V6 hypervariable regions of small-subunit (SSU) ribosomal RNA (rRNA) genes is commonly used to assess diversity and richness in bacterial and archaeal populations...
  86. pmc The putative NTPase Fap7 mediates cytoplasmic 20S pre-rRNA processing through a direct interaction with Rps14
    Sander Granneman
    Yale University School of Medicine, Department of Molecular Biophysics and Biochemistry, 333 Cedar Street, SHM C 114, New Haven, CT 06520 8024, USA
    Mol Cell Biol 25:10352-64. 2005
    ..We propose that Fap7 mediates cleavage of the 20S pre-rRNA at site D by directly interacting with Rps14 and speculate that it is an enzyme that functions as an NTP-dependent molecular switch in 18S rRNA maturation...
  87. pmc Quality control of ribosomal RNA mediated by polynucleotide phosphorylase and RNase R
    Zhuan Fen Cheng
    Department of Biochemistry and Molecular Biology, University of Miami School of Medicine, FL 33101, USA
    Proc Natl Acad Sci U S A 100:6388-93. 2003
    ..In the absence of these RNases, rRNA fragments accumulate, leading to interference with ribosome maturation and ultimately to cell death...
  88. ncbi The phylogeny of Myxosporea (Myxozoa) based on small subunit ribosomal RNA gene analysis
    Ivan Fiala
    Institute of Parasitology and Faculty of Biological Sciences, Academy of Sciences of the Czech Republic, University of South Bohemia, Branisovska 31, 370 05 Ceske Budejovice, Czech Republic
    Int J Parasitol 36:1521-34. 2006
    The phylogeny of the Myxosporea was studied using the small-subunit ribosomal RNA gene sequences. Maximum parsimony and Bayesian inference were used to determine myxosporean phylogenetic relationships...
  89. pmc TOR regulates the subcellular distribution of DIM2, a KH domain protein required for cotranscriptional ribosome assembly and pre-40S ribosome export
    Emmanuel Vanrobays
    Fonds de la Recherche Scientifique FRS FNRS, Académie Wallonie Bruxelles, Institut de Biologie et de Médecine Moléculaires, Universite Libre de Bruxelles, Charleroi Gosselies, B 6041, Belgium
    RNA 14:2061-73. 2008
    ..Strikingly, DIM2 and RRP12 are both involved in the nucleocytoplasmic translocation of pre-ribosomes, suggesting that this step in the ribosome assembly pathway has been selected as a regulatory target for the TOR pathway...
  90. pmc The 3D rRNA modification maps database: with interactive tools for ribosome analysis
    Dorota Piekna-Przybylska
    Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
    Nucleic Acids Res 36:D178-83. 2008
    ..The database can be accessed at http://people.biochem.umass.edu/fournierlab/3dmodmap/..
  91. ncbi Twelve Group I introns in the same pre-rRNA transcript of the myxomycete Fuligo septica: RNA processing and evolution
    Eirik W Lundblad
    Department of Molecular Biotechnology, RNA Research Group, Institute of Medical Biology, University of Tromso, Tromso, Norway
    Mol Biol Evol 21:1283-93. 2004
    ..Phylogenetic analysis indicated that most Fuligo introns were distantly related to each other and were independently gained in ribosomal DNA during evolution...
  92. ncbi The complete nucleotide sequence of the mitochondrial genome of Phthonandria atrilineata (Lepidoptera: Geometridae)
    Ling Yang
    School of Life Sciences, University of Science and Technology of China, Hefei, 230027, People s Republic of China
    Mol Biol Rep 36:1441-9. 2009
    ..The phylogenetic relationships were reconstructed with the concatenated sequences of the 13 PCGs of the mitochondrial genome, which confirmed that P. atrilineata is most closely related to the superfamily Bombycoidea...
  93. pmc Distribution of substitution rates and location of insertion sites in the tertiary structure of ribosomal RNA
    J Wuyts
    Departement Biochemie, Universiteit Antwerpen (UIA, Universiteitsplein 1, B-2610 Antwerpen, Belgium
    Nucleic Acids Res 29:5017-28. 2001
    ..All these insertions occur at the ribosome surface. The taxon-specific insertions seem to arise randomly in the eukaryotic evolutionary tree, without any phylogenetic relatedness between the taxa possessing them...
  94. pmc The complete mitochondrial genome of the sexual oribatid mite Steganacarus magnus: genome rearrangements and loss of tRNAs
    Katja Domes
    Technische Universitat Darmstadt, Institut fur Zoologie, Darmstadt, Germany
    BMC Genomics 9:532. 2008
    ....
  95. pmc Polyadenylation of ribosomal RNA in human cells
    Shimyn Slomovic
    Department of Biology, Technion Israel Institute of Technology, Haifa 32000, Israel
    Nucleic Acids Res 34:2966-75. 2006
    ..Here we asked whether in human cells ribosomal RNA can undergo polyadenylation...
  96. pmc Two 5'-ETS regions implicated in interactions with U3 snoRNA are required for small subunit rRNA maturation in Trypanosoma brucei
    T Hartshorne
    Department of Biochemistry and Molecular Biology A 10, Albany Medical College, 47 New Scotland Avenue, Albany, NY 12208, USA
    Nucleic Acids Res 27:3300-9. 1999
    ..The distinctive positioning of putative trypanosomatid U3 binding sites with respect to A" and A0 cleavages suggests that different U3-dependent mechanisms may direct each processing event...
  97. pmc The complete nucleotide sequence of mouse 28S rRNA gene. Implications for the process of size increase of the large subunit rRNA in higher eukaryotes
    N Hassouna
    Nucleic Acids Res 12:3563-83. 1984
    ..These D domains appear closely related to the transcribed spacers of rRNA precursor but a sizable fraction displays a much slower rate of sequence variation...
  98. pmc The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy
    J R Cole
    Center for Microbial Ecology, 2225A Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824 4320, USA
    Nucleic Acids Res 31:442-3. 2003
    The Ribosomal Database Project-II (RDP-II) pro-vides data, tools and services related to ribosomal RNA sequences to the research community. Through its website (http://rdp.cme.msu...
  99. pmc In exponentially growing Saccharomyces cerevisiae cells, rRNA synthesis is determined by the summed RNA polymerase I loading rate rather than by the number of active genes
    Sarah L French
    Department of Microbiology, University of Virginia Health System, Charlottesville, Virginia 22908 0734, USA
    Mol Cell Biol 23:1558-68. 2003
    ..Results also allow an estimate of elongation rate of approximately 60 nucleotides/s for yeast Pol I and a reinitiation rate of less than 1 s on the most heavily transcribed genes...
  100. ncbi A story: unpaired adenosine bases in ribosomal RNAs
    R R Gutell
    Institute for Cellular and Molecular Biology, University of Texas, 2500 Speedway, Austin, TX, 78712 1095, USA
    J Mol Biol 304:335-54. 2000
    ..These sequence motifs were associated with several structural motifs, such as adenosine platforms, E and E-like loops, A:A and A:G pairings at the end of helices, G:A tandem base-pairs, GNRA tetraloop hairpins, and U-turns...
  101. pmc The primary open-angle glaucoma gene WDR36 functions in ribosomal RNA processing and interacts with the p53 stress-response pathway
    Jonathan M Skarie
    Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
    Hum Mol Genet 17:2474-85. 2008
    ..Although these results overall do not provide evidence for or against a role of WDR36 in POAG, they do provide important baseline information for future studies...

Research Grants74

  1. DNA REPAIR IN A HORMONE RESPONSIVE GENE
    Michael J Smerdon; Fiscal Year: 2013
    ..We will focus on removal of CPDs from each strand of active and inactive Pol II genes and ribosomal RNA genes (Pol I) of lrs mutants of repair proficient (wt) and repair deficient (rad) cells...
  2. Mucosal Immunity and Microbiota in Intestinal Graft-versus-Host Disease
    Marcel R m van den Brink; Fiscal Year: 2013
    ..The availability of a novel technology, 16s ribosomal RNA (rRNA) gene sequencing, to analyze the composition of the gut flora in much greater detail has resulted in ..
  3. The Role of Syntrophic Bacteria in Methanogenic Metabolism in the Human Gut
    Catherine Lozupone; Fiscal Year: 2013
    ..The goal of this work is to use both metagenomic (16S ribosomal RNA or shotgun) sequences from human stool samples and genome sequences from cultured gut isolates to predict ..
  4. Tb-FISH (Fluorescent in Situ Hybridization) Assay for Direct Detection of M. tube
    JYOTSNA S SHAH; Fiscal Year: 2010
    ..In-Situ Hybridization assay for detecting and differentiating Mycobacterium tuberculosis complex (MTB) ribosomal RNA (rRNA) and Mycobacterium species (rRNA) on a SINGLE methanol fixed smear, prepared either from a culture or ..
  5. INFLAMMATORY RESPONSES IN THE TOXICITY OF RICIN
    Bruce Magun; Fiscal Year: 2009
    ..toxins whose toxicity stems from the depurination of a single adenine within the "sarcin/ricin" loop of 28S ribosomal RNA (28S rRNA)...
  6. A family of novel mitochondrially-encoded peptides and their role in aging
    Pinchas Cohen; Fiscal Year: 2012
    ..In 2001, humanin;a novel 24-amino-acid peptide encoded from the 16S ribosomal RNA region of the mtDNA, was described to be a potent neurosurvival factor...
  7. Protein Kinase C Signaling Mechanisms in Cancer
    Alan P Fields; Fiscal Year: 2013
    ..a significant pool of cellular Ect2 localizes to the nucleolus in a PKC?- dependent manner where it regulates ribosomal RNA (rRNA) transcription;3) PKC? transcriptionally activates cell autonomous hedgehog (Hh) signaling in NSCLC ..
  8. Combinatorial Imaging of the Oral Microbiome
    Floyd E Dewhirst; Fiscal Year: 2010
    ..The technique of fluorescence in situ hybridization (FISH) targeting ribosomal RNA is widely used to identify microbes and can be specific and sensitive, but as commonly employed it allows the ..
  9. Regulation of repetitive chromatin structures during the human cell cycle
    Paul D Kaufman; Fiscal Year: 2013
    ..Microscopy detects a subset of cellular p150 associated with nucleoli, the sites of ribosomal RNA (rRNA) synthesis and ribosome assembly...
  10. MOLECULAR GENETICS OF NUCLEOLAR DOMINANCE
    CRAIG STUART PIKAARD; Fiscal Year: 2012
    ..is an epigenetic phenomenon that occurs in plant and animal genetic hybrids and describes the transcription of ribosomal RNA (rRNA) genes inherited from only one parent due to the selective silencing of the other progenitor's rRNA ..
  11. Microbiome in Chronic Obstructive Pulmonary Disease
    Rubin M Tuder; Fiscal Year: 2010
    ..Novel techniques aimed at amplification and sequencing of the gene encoding the bacterial small subunit ribosomal RNA (SSU-rRNA) allow for a molecular interrogation of species of bacteria present in lung diseases, such as ..
  12. polr1c and polr1d mutant zebrafish as new models for Treacher Collins syndrome
    KRISTIN EMILY NOACK WATT; Fiscal Year: 2013
    ..This work will examine how disruptions in global processes such as ribosomal RNA transcription and ribosome biogenesis can elicit very specific congenital defects...
  13. Shiga Toxin & Ricin: Mechanisms of Ribotoxic Stress
    Cheleste M Thorpe; Fiscal Year: 2010
    Ricin and Shiga toxin share a unique mode of action, causing irreversible damage to host ribosomal RNA. Our understanding of how these bioterror agents cause tissue damage is incomplete and no medications exist to prevent or treat ..
  14. Microbiome in COPD
    Rubin M Tuder; Fiscal Year: 2013
    ..To this end, we have relied on amplification and sequencing of the bacterial small subunit ribosomal RNA (SSU-rRNA) gene in a large number of phenotypically and clinically well-characterized COPD lung samples, ..
  15. Visualizing Genetic Activity in Normal &Mutant Yeast
    Ann L Beyer; Fiscal Year: 2013
    ..research is to better understand the molecular mechanisms that regulate RNA polymerase I transcription of ribosomal RNA. This rRNA becomes the major structural and functional component of ribosomes and its rate of synthesis ..
  16. Mechanism of angiogenin-induced angiogenesis
    Guo fu Hu; Fiscal Year: 2013
    ..Studies carried out in the previous funding period have demonstrated an important role of ANG in ribosomal RNA (rRNA) synthesis, which is essential for many fundamental biological processes including cell growth, ..
  17. Reversal of Spermatogonial Arrest in Mice
    Gunapala Shetty; Fiscal Year: 2012
    ..Jsd is a mutation in the Utp14b gene, which is involved in ribosomal RNA processing. Utp14b is a copy of the widely expressed (except spermatocytes) X linked Utp14a gene...
  18. High Performance Validation and Classification of Metagenomic Ribosomal-RNA Seque
    Daniel Frank; Fiscal Year: 2011
    ..1 ..
  19. Vertebrate Non-Coding RNPs: Integrating function, biogenesis and survival
    Joan A Steitz; Fiscal Year: 2013
    ..that the core RNA helicase component (eIF4AIII) of the exon junction complex has a second conserved role in ribosomal RNA biogenesis will be confirmed...
  20. The Pathogenesis of Dyskeratosis Congenita
    Philip J Mason; Fiscal Year: 2013
    ..of small nucleolar ribonucleoprotein particles (snoRNP), which function in modification and processing of ribosomal RNA (rRNA) and small nuclear RNAs (snRNA) as well as being important for the assembly and stability of the ..
  21. Structural Studies of epigenetic regulation of rRNA gene by TTF-I
    Carlos R Escalante; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Transcription and processing of ribosomal RNA genes (rRNA) are intimately linked to processes that control cell growth and proliferaton...
  22. NKT cells recognize and respond to microbes at mucosal surfaces
    Dale T Umetsu; Fiscal Year: 2010
    ..based 16S rRNA PhyloChip microarray method, which uses approximately 500,000 probes to detect the 16S ribosomal RNA signatures from 9,000 bacteria...
  23. The Role of Ribosomal RNA Modifications
    Christine S Chow; Fiscal Year: 2012
    A study of site-specific modifications in ribosomal RNA (rRNA) is proposed in which a combination of synthetic, biophysical, and biological approaches will be taken...
  24. Assay for Compounds that Elicit Misprocessing of Small Nuclear RNA
    Eric Wagner; Fiscal Year: 2009
    ..Included in this list are intron-containing polyadenylated messenger RNAs, histone mRNAs, and ribosomal RNA. It is quite surprising then how little is known about the biosynthesis of these noncoding RNAs...
  25. Novel Mitochondrially Encoded Peptides and Their Role in Health and Disease
    Pinchas Cohen; Fiscal Year: 2013
    ..In 2001, humanin, a 24-amino-acid peptide proposed to be encoded from the 16S ribosomal RNA of the mtDNA, was described as a potent neurosurvival factor, and we have recently shown it to be a centrally ..
  26. Plasmodium Genus and P. falciparum - P. vivax FISH Assays
    Jyotsna Shah; Fiscal Year: 2009
    ..provided by applicant): Plasmodium Genus Fluorescent In Situ Hybridization (P-Genus FISH) assay targeted to ribosomal RNA (rRNA) is a method that detects all the species of malaria on an air-dried blood smear...
  27. Mechanism &Function of Subnuclear Targeting of Transcription Factors in Bone
    Gary S Stein; Fiscal Year: 2011
    ..that Runx2 is bound to mitotic chromosomes to modulate both osteoblast specific gene expression and ribosomal RNA synthesis in osteoblasts immediately following mitosis...
  28. REPLICATION AND AMPLIFICATION OF TETRAHYMENA RDNA
    Geoffrey M Kapler; Fiscal Year: 2010
    ..Remarkably this RNA, designated 26T, corresponds to the extreme 3'terminus of 26S ribosomal RNA. We hypothesize that 26T RNA is processed from cytoplasmic ribosomes and functions as a physiological link ..
  29. TB Diagnostics at the Point of Care
    CHRISTOPHER GERARD COONEY; Fiscal Year: 2013
    ..mutations of TB, which have an associated 1000 polymorphisms that span 36 genes, two promoter regions, and one ribosomal RNA coding region [3]...
  30. RNA modification and antibiotic resistance
    GRAEME LESLIE CONN; Fiscal Year: 2013
    ..Two distinct families of aminoglycoside-resistance methyltransferases have been identified that modify 16S ribosomal RNA on nucleotide G1405 or A1408...
  31. Multidrug-Resistant Acinetobacter baumannii
    Yohei Doi; Fiscal Year: 2010
    ..baumannii. The hypotheses of the application are: (1) OXA-type carbapenemases (e.g., OXA-23) and ArmA 16S ribosomal RNA methylase are the primary mechanisms by which A...
  32. Sentinel Pol II RNAs for Measuring RNA Integrity in Biospecimens
    Curt H Hagedorn; Fiscal Year: 2012
    ..Current standard measures of RNA integrity focus on 28S and 18S ribosomal RNA. However, diagnostic and prognostic gene expression markers of cancer focus on changes in mRNAs which are RNA ..
  33. Rapid Microbial Identification by MALDI-TOF Mass Spectrometry of Ribosomal RNA
    George W Jackson; Fiscal Year: 2010
    ..and characterize a microbial identification platform using very rapid MALDI-TOF mass spectrometry of modified ribosomal RNA fragments...
  34. Retrotransposon expression within ribosomal gene loci
    Thomas H Eickbush; Fiscal Year: 2013
    ..This research also studies the regulated expression of the many ribosomal RNA genes, genes that play a key role in all aspects of cellular metabolism.
  35. Specialized ribosomes in control of gene expression and embryonic development
    Maria Barna; Fiscal Year: 2011
    ..Our studies will delineate how the 79 distinct ribosomal proteins (RPs) that associate with ribosomal RNA confer greater specificity to the RNA-based translational machinery as a mechanism to direct transcript-..
  36. Role of rRNA Modifications in Dyskeratosis Congenita and Translation Control
    Davide Ruggero; Fiscal Year: 2009
    ..Congenita 1 (DKC1), is a pseudouridine synthase that mediates post-transcriptional modification of ribosomal RNA (rRNA) of both large and small ribosomal subunits through conversion of the uridine nucleotide (U) to ..
  37. New mechanism of resistance to oxazolidinone antibiotics in Staphylococcus aureus
    Alexander S Mankin; Fiscal Year: 2010
    ..In almost all of the cases, the resistance was associated with mutations in domain V of 23S ribosomal RNA. This type of resistance appears rather rarely and develops slowly because of the presence of multiple copies ..
  38. Radical SAM Methytransferases
    Danica Galonic Fujimori; Fiscal Year: 2013
    ..Cfr encodes a methyltransferase enzyme which catalyses addition of a methyl group to adenosine 2503 (A2503) in ribosomal RNA. This nucleotide is positioned in the peptidyl transferase center of the large ribosomal subunit, a common ..
  39. Genomics, Biomarkers and Mechanisms of Healing in Chronic Wounds
    VICTORIA KATE SHANMUGAM; Fiscal Year: 2013
    ..To investigate this hypothesis we will: a. Use bacterial 16S ribosomal RNA gene profiles to compare wound biofilm bacterial diversity between healing and recalcitrant chronic wounds. b...
  40. Microbial community profiling of sewage contamination in the Great Lakes
    Sandra L McLellan; Fiscal Year: 2010
    ..Our experimental strategy will characterize rapidly evolving hypervariable regions in ribosomal RNA (rRNA) genes, each of which serves as a proxy for the occurrence of a microorganism in a sample...
  41. Supporting RNAstructure: Software for RNA Analysis
    David H Mathews; Fiscal Year: 2013
    ..such as hybridization in RNA interference, to catalyzing reactions, such as peptide bond formation by ribosomal RNA. To understand RNA function and to harness the power of RNA, with RNA interference, therapeutic RNA enzymes, ..
  42. Targeted genomic characterization of uncultured bacteria from the human microbiot
    Mircea Podar; Fiscal Year: 2011
    ..Our strategy utilizes the high phylogenetic resolution that the small subunit ribosomal RNA (SSU rRNA) provides in distinguishing microbial phylotypes...
  43. MECHANISM, ACTIVATION, AND CONTROL OF RRNA TRANSCRIPTION
    Richard L Gourse; Fiscal Year: 2013
    The machinery responsible for making proteins (e.g. ribosomal RNA, ribosomal proteins, translation factors, and tRNAs) is central to growth and development of all organisms...
  44. Translational Control by eIF3f in Pancreatic Cancer
    Eugene W Gerner; Fiscal Year: 2012
    ..Restoration of eIF3f expression in tumor cells induced ribosomal RNA degradation. Therefore, we hypothesize that eIF3f controls translation by regulating rRNA degradation...
  45. Role of ribosome impairments in X-linked Dyskeratosis Congenita pathogenesis
    Davide Ruggero; Fiscal Year: 2013
    ..X-DC), which is invariably associated with mutations in the DKC1 gene encoding for an enzyme that modifies ribosomal RNA (rRNA)...
  46. Structural and Biochemical Characterization of the S. cerevisiae RNA Exosome
    ELIZABETH VICTORINA WASMUTH; Fiscal Year: 2013
    ..Rrp6 activities are known to be important for processing structured substrates such as ribosomal RNA. The precise role of Exo9 in modulating the activities of its catalytic subunits, Rrp44 and Rrp6 is unknown...
  47. Structure and Regulation of snoRNP Interaction with rRNA
    Hong Li; Fiscal Year: 2012
    ..The foundation of ribosome biogenesis is the synthesis of ribosomal RNA. In this process, ribosomal RNA is captured, chemically modified, cleaved, and released by small nucleolar ..
  48. Mass Spectrometry of Ribosomal RNA:Protein Interactions
    Patrick A Limbach; Fiscal Year: 2013
    ..Importantly, this research plan will provide new tools and information of importance about protein synthesis, which is fundamentally significant and relevant to human health. ..
  49. GENETICS AND BIOCHEMISTRY OF RIBOSOME SYNTHESIS
    Masayasu Nomura; Fiscal Year: 2009
    ..Since transcription of ribosomal RNA (rRNA) is central in determining overall synthesis of ribosomes, our work focuses on regulation of rRNA ..
  50. Mass Spectrometry of Ribosomal RNA:Protein Interactions
    PATRICK LIMBACH; Fiscal Year: 2009
    ..Importantly, this research plan will provide new tools and information of importance about protein synthesis, which is fundamentally significant and relevant to human health. ..
  51. Comparative Analysis of RNA Helicases in E. coli
    Chaitanya Jain; Fiscal Year: 2012
    ..the cold-sensitive growth phenotype of srmB and deaD strains can be suppressed by over-expressing ribosomal RNA processing and modification factors;(iv) E...
  52. Structure and function of the U3 RNA-protein complex
    Carl C Correll; Fiscal Year: 2010
    ..Importantly, the effective chemotherapeutic agent 5-fluorouracil inhibits processing of the precursor ribosomal RNA (pre- rRNA), an essential step of ribosome biogenesis and hence of cellular growth...
  53. Cell growth control by cell and organelle size-dependent ribosome biogenesis
    Clifford P Brangwynne; Fiscal Year: 2012
    ..theoretical biophysical models for understanding these data based on the size dependence of the rate of ribosomal RNA processing within the dynamic liquid- like nucleolar material...
  54. A novel assay for RNA targeted drugs
    DEV PRIYA ARYA; Fiscal Year: 2011
    ..are a potent class of antibiotics that block bacterial protein synthesis by binding to a conserved site on ribosomal RNA. It is the purpose of the project to develop an innovative fluorescence-based screen for A-site targeted drugs ..
  55. The Role of Novel Bacteria in Male Urethritis
    Lisa E Manhart; Fiscal Year: 2012
    ..Broad range ribosomal RNA gene PCR is a powerful technique for bacterial pathogen discovery, but is less sensitive than targeted species-..
  56. INVESTIGATING NOVEL MECHANISMS OF TRANSCRIPTION INITIATION REGULATION IN MYCOBACT
    CHRISTINA LEIGH STALLINGS; Fiscal Year: 2013
    ..regulator that is necessary for Mtb pathogenesis, contributes to rifampicin resistance, regulates ribosomal RNA (rRNA) levels, and is not present in eukaryotes...
  57. FACTORS STABILIZING RNA STRUCTURES
    David E Draper; Fiscal Year: 2013
    ..processes relating to gene expression: the protein synthesis machinery depends on intricate transfer and ribosomal RNA structures, processing of messenger and other RNAs requires specific structures, and the regulation of ..
  58. African Collaborative Center for Microbiome and Genomics Research (ACCME)
    CLEMENT ADEBAYO ADEBAMOWO; Fiscal Year: 2013
    ..the investigative team, employing bacterial culture-independent, "clone and sequence approach" employing 16S ribosomal RNA (rRNA) gene technologies have documented the complexity of vaginal microbiome and classified consistent ..
  59. Probing the function of translational pausing in bacterial protein synthesis
    Gene Wei Li; Fiscal Year: 2013
    ..In fact, recent genome sequencing data have revealed that, although the antiSD region of ribosomal RNA is highly conserved throughout prokaryotes, many bacterial and archaeal species do not use it for translation ..
  60. Selection of Modified Ribosomes Using Novel Puromycins
    Sidney M Hecht; Fiscal Year: 2013
    ..coli following cell transformation with a (modified) plasmid-born 23S ribosomal RNA, for sensitivity to puromycin analogues containing a specific, structurally modified amino acid, it is ..
  61. Control of RNA polymerase I transcription initiation and elongation
    DAVID ALAN SCHNEIDER; Fiscal Year: 2013
    ..Thus, the mechanisms that control ribosomal RNA transcription by RNA polymerase I are directly relevant to the study of cell transformation and tumor cell ..
  62. TB- FISH Assay for Direct Detection of M. tuberculosis in unprocessed sputum
    Jyotsna Shah; Fiscal Year: 2007
    ..The TB- FISH test detects MTB ribosomal RNA. The test can be performed at room temperature, and does not require centrifugation or incubators...
  63. Multiplex TB-M.avium complex Fluorescent in Situ hybridization Assay, direct from
    Jyotsna Shah; Fiscal Year: 2009
    ..This assay uses fluorescent labeled MTB and MAC specific probes targeted to MTB and MAC ribosomal RNA (rRNA) respectively...
  64. DNA Probes for Acanthamoeba Genomics and Epidemiology
    Paul Fuerst; Fiscal Year: 2007
    ..Prior work used nucleotide sequences of the small subunit ribosomal RNA (ssu rDNA) genes from the nucleus and mitochondria to determine the phylogenetic relationships of Acanthamoeba ..
  65. Basonuclin and Ribosome Biogenesis in Mouse Oocyte and Embryo
    Richard M Schultz; Fiscal Year: 2010
    ..We showed recently that basonuclin (BNC1, Bnc1), a cell-type specific transcription factor for the ribosomal RNA genes (rDNA), is also a mammalian maternal effect gene...
  66. REPLICATION AND AMPLIFICATION OF TETRAHYMENA RDNA
    Geoffrey Kapler; Fiscal Year: 2000
    ..The rDNA minichromosome of T. thermophila, encoding the ribosomal RNA genes, has been used extensively as a model for DNA replication and gene amplification...
  67. 'RECODING: DYNAMIC REPROGRAMMING OF GENETIC READOUT'
    John Atkins; Fiscal Year: 2004
    ..to isolate down-mutants with screening rather than selection, and repeat in a strain with a single copy of ribosomal RNA genes...
  68. Role of ER-Localized Chaperones in Toxin Pathogenesis
    David Haslam; Fiscal Year: 2006
    ..From the ER lumen, the toxin must gain access to the cytoplasm, where it enzymatically inactivates the 28S ribosomal RNA, inhibiting protein synthesis...
  69. Pseudouridines, pseudouridine synthases, and ribosomes
    MURRAY DEUTSCHER; Fiscal Year: 2006
    Pseudouridine (psi), the most common modified nucleoside in RNA, occurs in ribosomal RNA (rRNA) ( transfer RNA (tRNA), and small nuclear (sn) and nucleolar (sno) RNAs, but not in messenger RNA...
  70. M. tuberculosis Fluorescent In-Situ Hybridization
    Jyotsna Shah; Fiscal Year: 2004
    ..TB-Dual Probe FISH) is a method of detecting and differentiating Mycobacterium tuberculosis complex (MTB) ribosomal RNA (rRNA) and Mycobacterium species (rRNA) on a SINGLE heat fixed smear, prepared either from a culture or ..
  71. GENETIC ANALYSIS OF RIBOSOMAL RNA FUNCTION
    Philip Cunningham; Fiscal Year: 2000
    Our long-term objective is to understand the role played by ribosomal RNA in protein synthesis...
  72. INTERACTION OF ANTIBIOTICS WITH RIBOSOMAL RNA
    Alexander Mankin; Fiscal Year: 1999
    ..He will map regions of rRNA located in the vicinity of the nascent peptide exit channel; a probable binding site of erythromycin resistance peptides. ..
  73. P.falciparum and P.vivax Fluorescent In Situ Hybridization
    Jyotsna Shah; Fiscal Year: 2006
    ..In-Situ Hybridization (PFV- FISH) is a method of detecting and differentiating Plasmodium falciparum (PF) ribosomal RNA (rRNA) and P. vivax (PV) rRNA on a SINGLE air- dried thin blood smear...
  74. STRUCTURE/FUNCTION OF THE 790 LOOP IN RIBOSOMAL RNA
    Philip Cunningham; Fiscal Year: 2001
    DESCRIPTION: The long term objective of this proposal is to understand the role played by ribosomal RNA in protein synthesis...