Genomes and Genes
Summary: Ribonucleic acid in fungi having regulatory and catalytic roles as well as involvement in protein synthesis.
Publications275 found, 100 shown here
- The transcriptional landscape of the yeast genome defined by RNA sequencingUgrappa Nagalakshmi
Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
Science 320:1344-9. 2008..We also found unexpected 3'-end heterogeneity and the presence of many overlapping genes. These results indicate that the yeast transcriptome is more complex than previously appreciated...
- Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noiseJohn R S Newman
Howard Hughes Medical Institute, San Francisco, California, USA
Nature 441:840-6. 2006..Thus, these studies reveal a remarkable structure to biological noise and suggest that protein noise levels have been selected to reflect the costs and potential benefits of this variation...
- Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolutionBrian T Wilhelm
Cancer Research UK Fission Yeast Functional Genomics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
Nature 453:1239-43. 2008..Splicing efficiency was largely coordinated with transcript levels, and increased transcription led to increased splicing in test genes. Hundreds of introns showed such regulated splicing during cellular proliferation or differentiation...
- Movement of eukaryotic mRNAs between polysomes and cytoplasmic processing bodiesMuriel Brengues
Department of Molecular and Cellular Biology and Howard Hughes Medical Institute, University of Arizona, Tucson, AZ 85721 0106, USA
Science 310:486-9. 2005..Moreover, the presence of related proteins in P-bodies and maternal mRNA storage granules suggests this mechanism is widely adapted for mRNA storage...
- Yeast exosome mutants accumulate 3'-extended polyadenylated forms of U4 small nuclear RNA and small nucleolar RNAsA van Hoof
Department of Molecular Biology, Howard Hughes Medical Institute, University of Arizona, Tucson, Arizona 85721, USA
Mol Cell Biol 20:441-52. 2000..This finding suggests that the cytoplasmic and nuclear forms of the exosome represent two functionally different complexes involved in distinct 3'-to-5' processing and degradation reactions...
- rRNA modifications and ribosome functionWayne A Decatur
Trends Biochem Sci 27:344-51. 2002..The correlations suggest that many ribosome functions benefit from nucleotide modification...
- Exploring the metabolic and genetic control of gene expression on a genomic scaleJ L DeRisi
Department of Biochemistry, Stanford University School of Medicine, Howard Hughes Medical Institute, Stanford, CA 94305 5428, USA
Science 278:680-6. 1997..These results demonstrate the feasibility and utility of this approach to genomewide exploration of gene expression patterns...
- S. pombe mei2+ encodes an RNA-binding protein essential for premeiotic DNA synthesis and meiosis I, which cooperates with a novel RNA species meiRNAY Watanabe
Department of Biophysics and Biochemistry School of Science, University of Tokyo, Japan
Cell 78:487-98. 1994..Mutations that apparently block the RNA binding ability of Mei2 inhibit premeiotic DNA synthesis. Mei2 is thus likely to couple with another RNA species to promote premeiotic DNA synthesis...
- Gametogenesis in yeast is regulated by a transcriptional cascade dependent on Ndt80S Chu
Department of Biochemistry and Biophysics, University of California, San Francisco 94143 0448, USA
Mol Cell 1:685-96. 1998..Thus Ndt80 is a pivotal component of a transcriptional cascade programming yeast gametogenesis and may also be a target of meiotic checkpoint control...
- Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiaeYoav Arava
Department of Biochemistry, Stanford University, Stanford, CA 94305 5307, USA
Proc Natl Acad Sci U S A 100:3889-94. 2003..Global analysis revealed an unexpected correlation: Ribosome density decreases with increasing ORF length. Models to account for this surprising observation are discussed...
- Global analysis of protein expression in yeastSina Ghaemmaghami
Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California 94143 2240, USA
Nature 425:737-41. 2003..Many of these molecules, including essential proteins and most transcription factors, are present at levels that are not readily detectable by other proteomic techniques nor predictable by mRNA levels or codon bias measurements...
- Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 geneJoseph A Martens
Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
Nature 429:571-4. 2004..This work identifies a previously unknown class of transcriptional regulatory genes...
- The splicing ATPase prp43p is a component of multiple preribosomal particlesSimon Lebaron
Laboratoire de Biologie Moleculaire Eucaryote, UMR5099 CNRS Université Paul Sabatier, IFR109, 118 route de Narbonne, 31062 Toulouse Cedex 09, France
Mol Cell Biol 25:9269-82. 2005..Our data also suggest that the ATPase activity of Prp43p is required for early steps of pre-rRNA processing and normal accumulation of mature rRNAs...
- Deadenylation of the unstable mRNA encoded by the yeast MFA2 gene leads to decapping followed by 5'-->3' digestion of the transcriptD Muhlrad
Department of Molecular and Cellular Biology, University of Arizona, Tucson 85721
Genes Dev 8:855-66. 1994..Because the poly(A) tail and the cap structure are found on essentially all mRNAs, this pathway could be a general mechanism for the decay of many eukaryotic transcripts...
- RNAi-mediated targeting of heterochromatin by the RITS complexAndre Verdel
Department of Cell Biology, Harvard Medical School, Boston, MA02115, USA
Science 303:672-6. 2004..The results suggest a mechanism for the role of the RNAi machinery and small RNAs in targeting of heterochromatin complexes and epigenetic gene silencing at specific chromosomal loci...
- Global analysis of Pub1p targets reveals a coordinate control of gene expression through modulation of binding and stabilityRadharani Duttagupta
Department of Molecular Genetics, Microbiology, and Immunology, UMDNJ Robert Wood Johnson Medical School, 675 Hoes Ln, Piscataway, New Jersey 08854 5627, USA
Mol Cell Biol 25:5499-513. 2005..These results suggest that Pub1p binds to discrete subsets of cellular transcripts and posttranscriptionally regulates their expression at multiple levels...
- Differential gene expression by Paracoccidioides brasiliensis in host interaction conditions: representational difference analysis identifies candidate genes associated with fungal pathogenesisAlexandre Melo Bailão
Laboratorio de Biologia Molecular, Instituto de Ciencias Biologicas, Universidade Federal de Goias, 74001 970 Goiania, Goias, Brazil
Microbes Infect 8:2686-97. 2006..This work can facilitate functional studies of novel regulated genes that may be important for the survival and growth strategies of P. brasiliensis in humans...
- Genome-wide transcription profiling of the early phase of biofilm formation by Candida albicansLuis A Murillo
Department of Cell and Tissue Biology, University of California, San Francisco, 521 Parnassus Ave, San Francisco, CA 94143 0422, USA
Eukaryot Cell 4:1562-73. 2005..We identify here a potential alternative pathway for cysteine metabolism and the biofilm-associated expression of genes involved in glutathione production in C. albicans...
- Characterization of the Ustilago maydis sid2 gene, encoding a multidomain peptide synthetase in the ferrichrome biosynthetic gene clusterW M Yuan
Department of Plant Pathology, University of Wisconsin, Madison, Wisconsin 53706, USA
J Bacteriol 183:4040-51. 2001..Indeed, mutation of two of these motifs, known to be important to regulation of sid1, altered the differential regulation of sid2 by iron...
- Molecular mechanisms underlying the mitosis-meiosis decisionYuriko Harigaya
Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo, 113 0033, Japan
Chromosome Res 15:523-37. 2007....
- Decapping and decay of messenger RNA occur in cytoplasmic processing bodiesUjwal Sheth
Department of Molecular and Cellular Biology and Howard Hughes Medical Institute, University of Arizona, Tucson, AZ 85721, USA
Science 300:805-8. 2003..These results define the flux of mRNAs between polysomes and P bodies as a critical aspect of cytoplasmic mRNA metabolism and a possible site for regulation of mRNA degradation...
- Mating type switching in yeast controlled by asymmetric localization of ASH1 mRNAR M Long
Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
Science 277:383-7. 1997..A cis-acting element in the 3'-untranslated region of ASH1 mRNA is sufficient to localize a chimeric RNA to daughter cells. These results suggest that localization of mRNA may have been an early property of the eukaryotic lineage...
- Genomic organization of the structural genes controlling the astaxanthin biosynthesis pathway of Xanthophyllomyces dendrorhousMauricio Niklitschek
Departamento de Ciencias Ecologicas, Facultad de Ciencias, Universidad de Chile, Chile
Biol Res 41:93-108. 2008....
- The yeast hnRNP-like protein Hrp1/Nab4 marks a transcript for nonsense-mediated mRNA decayC I Gonzalez
Department of Molecular Genetics and Microbiology, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway 08854, USA
Mol Cell 5:489-99. 2000..A mutation in HRP1 that stabilizes nonsense-containing mRNAs abolishes its affinity for the DSE and fails to interact with Upf1p. We present a model describing how Hrp1p marks a transcript for rapid decay...
- Pat1 contains distinct functional domains that promote P-body assembly and activation of decappingGuy R Pilkington
Department of Molecular and Cellular Biology and Howard Hughes Medical Institute, University of Arizona, 1007 E Lowell St, Tucson, AZ 85721 0206, USA
Mol Cell Biol 28:1298-312. 2008..These results indicate that Pat1 is an RNA binding protein and a multidomain protein that functions at multiple stages in the process of translation repression and mRNA decapping...
- tRNA transfers to the limelightAnita K Hopper
Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, USA
Genes Dev 17:162-80. 2003
- Yeast Sm-like proteins function in mRNA decapping and decayS Tharun
Department of Molecular and Cellular Biology and Howard Hughes Medical Institute, University of Arizona, Tucson 85721, USA
Nature 404:515-8. 2000..In addition, the Lsm complex that functions in mRNA decay appears to be distinct from the U6-associated Lsm complex, indicating that Lsm proteins form specific complexes that affect different aspects of mRNA metabolism...
- Genetic dissection of transcriptional regulation in budding yeastRachel B Brem
Fred Hutchinson Cancer Research Center FHCRC, 1100 Fairview Avenue North, D4 100, Seattle, WA 98109, USA and Howard Hughes Medical Institute
Science 296:752-5. 2002..We found eight such trans-acting loci, each affecting the expression of a group of 7 to 94 genes of related function...
- Widespread bidirectional promoters are the major source of cryptic transcripts in yeastHelen Neil
Institut Pasteur, Unité de Génétique des Interactions Macromoléculaires, CNRS, URA2171, 75015 Paris, France
Nature 457:1038-42. 2009....
- A complex gene regulatory mechanism that operates at the nexus of multiple RNA processing decisionsDavid S McPheeters
Center for RNA Molecular Biology and Department of Molecular Biology and Microbiology, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106 4960, USA
Nat Struct Mol Biol 16:255-64. 2009..This highly integrated regulatory strategy may ensure a rapid response to adverse conditions, thereby guaranteeing survival...
- Actin-dependent localization of an RNA encoding a cell-fate determinant in yeastP A Takizawa
Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco 94143 0450, USA
Nature 389:90-3. 1997..Thus, as in higher eukaryotes, Saccharomyces cerevisiae employs RNA localization to generate an asymmetric distribution of proteins and hence to determine cell fate...
- Dual requirement for yeast hnRNP Nab2p in mRNA poly(A) tail length control and nuclear exportRonald E Hector
Department of Molecular Genetics and Microbiology, Powell Gene Therapy Center, University of Florida College of Medicine, Gainesville, FL 32610 0266, USA
EMBO J 21:1800-10. 2002..We propose that Nab2p provides an important link between the termination of mRNA polyadenylation and nuclear export...
- Processing of 20S pre-rRNA to 18S ribosomal RNA in yeast requires Rrp10p, an essential non-ribosomal cytoplasmic proteinE Vanrobays
LBME du CNRS, 118 route de Narbonne, 31062 Toulouse Cedex 04, France
EMBO J 20:4204-13. 2001..Thus, Rio1p has been renamed Rrp10p (ribosomal RNA processing #10). Rio1p/Rrp10p is the first non-ribosomal factor characterized specifically required for 20S pre-rRNA processing...
- Functional specificity of shuttling hnRNPs revealed by genome-wide analysis of their RNA binding profilesKaren Kim Guisbert
Department of Biochemistry and Biophysics, 600 16th Street, Genentech Hall, University of California at San Francisco, San Francisco, CA 94143, USA
RNA 11:383-93. 2005..These specialized associations of the hnRNP proteins of Saccharomyces cerevisiae suggest the opportunity to regulate the processing of particular transcripts between transcription and translation...
- A high-resolution map of transcription in the yeast genomeLior David
Stanford Genome Technology Center and Department of Biochemistry, Stanford University, Palo Alto, CA 94304, USA
Proc Natl Acad Sci U S A 103:5320-5. 2006..These findings may suggest a regulatory role of antisense transcription in S. cerevisiae. Moreover, the data show that even this well studied genome has transcriptional complexity far beyond current annotation...
- A large nucleolar U3 ribonucleoprotein required for 18S ribosomal RNA biogenesisFrançois Dragon
Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut 06520 8040, USA
Nature 417:967-70. 2002..We have termed this large RNP the small subunit (SSU) processome...
- Rng3, a member of the UCS family of myosin co-chaperones, associates with myosin heavy chains cotranslationallyMaria J Amorim
Hopkins Building, Department of Biochemistry, University of Cambridge, Building O, Downing Site, Cambridge CB2 1QW, UK
EMBO Rep 10:186-91. 2009..Furthermore, our data suggest that microarray-based approaches allow the genome-wide identification of cotranslational chaperone targets, and thus pave the way for the dissection of translation-linked chaperone networks...
- RNAi in budding yeastInes A Drinnenberg
Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
Science 326:544-50. 2009..These results identify a previously unknown class of Dicer proteins, bring the tool of RNAi to the study of budding yeasts, and bring the tools of budding yeast to the study of RNAi...
- Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 5' to 3' mRNA decay pathways in yeastFeng He
Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
Mol Cell 12:1439-52. 2003....
- SAGA interacting factors confine sub-diffusion of transcribed genes to the nuclear envelopeGhislain G Cabal
Unité de Biologie Cellulaire du Noyau, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris Cedex 15, France
Nature 441:770-3. 2006..The observed real-time dynamic mooring of active GAL genes to the inner side of the nuclear pore complex is in accordance with the 'gene gating' hypothesis...
- The transcriptional activator Cat8p provides a major contribution to the reprogramming of carbon metabolism during the diauxic shift in Saccharomyces cerevisiaeV Haurie
Institut de Biochimie et Génétique Cellulaires, UMR 5095, 33077 Bordeaux Cedex, France
J Biol Chem 276:76-85. 2001..Interestingly, no function involved in the tricarboxylic cycle and the oxidative phosphorylation seems to be controlled by Cat8p...
- A conserved element in the yeast RNase MRP RNA subunit can participate in a long-range base-pairing interactionScott C Walker
Department of Biomolecular Sciences, UMIST, P O Box 88, Manchester, M60 1QD, UK
J Mol Biol 341:375-88. 2004....
- csmA, a gene encoding a class V chitin synthase with a myosin motor-like domain of Aspergillus nidulans, is translated as a single polypeptide and regulated in response to osmotic conditionsNorio Takeshita
Department of Biotechnology, The University of Tokyo, 1 1 1 Yayoi, Bunkyo ku, Tokyo 113 8657, Japan
Biochem Biophys Res Commun 298:103-9. 2002....
- The Isw2 chromatin remodeling complex represses early meiotic genes upon recruitment by Ume6pJ P Goldmark
Division of Basic Sciences, Fred Hutchinson Cancer Research Institute, Fred Hutchinson Cancer Research Center and University of Washington, Seattle 98109, USA
Cell 103:423-33. 2000..Based on these findings, we propose a model for the mechanism of transcriptional repression by two distinct chromatin remodeling complexes...
- Transcriptional interactions between yeast tRNA genes, flanking genes and Ty elements: a genomic point of viewEric C Bolton
Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
Genome Res 13:254-63. 2003..Direct analysis of PTR3 transcription, promoted by sequences very close to a tRNA gene, shows that this tRNA position effect can operate on a native chromosomal gene...
- A single dicer gene is required for efficient gene silencing associated with two classes of small antisense RNAs in Mucor circinelloidesJuan P de Haro
Departamento de Genética y Microbiología, Facultad de Biologia, Universidad de Murcia, 30100 Murcia, Spain
Eukaryot Cell 8:1486-97. 2009....
- The yeast mitochondrial degradosome. Its composition, interplay between RNA helicase and RNase activities and the role in mitochondrial RNA metabolismAndrzej Dziembowski
Department of Genetics, Warsaw University and Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02 106 Warsaw, Poland
J Biol Chem 278:1603-11. 2003..We suggest that the degradosome is a central part of a mitochondrial RNA surveillance system responsible for degradation of aberrant and unprocessed RNAs...
- Time course global gene expression analysis of an in vivo Candida biofilmJeniel E Nett
Department of Medicine, University of Wisconsin, Madison, Wisconsin, USA
J Infect Dis 200:307-13. 2009....
- Molecular dissection of mRNA poly(A) tail length control in yeastNicolas Viphakone
Universite Victor Segalen Bordeaux 2, CNRS, Institut de Biochimie et Génétique Cellulaires, Bordeaux, France
Nucleic Acids Res 36:2418-33. 2008....
- YRA1 autoregulation requires nuclear export and cytoplasmic Edc3p-mediated degradation of its pre-mRNAShuyun Dong
Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
Mol Cell 25:559-73. 2007....
- nmt1 of fission yeast. A highly transcribed gene completely repressed by thiamineK Maundrell
Sclavo Research Centre, Siena, Italy
J Biol Chem 265:10857-64. 1990..The nmt1 promotor has been subcloned, and thiamine-mediated transcriptional control has been transferred to the bacterial reporter gene chloramphenicol acetyltransferase...
- The Khd1 protein, which has three KH RNA-binding motifs, is required for proper localization of ASH1 mRNA in yeastKenji Irie
Department of Molecular Biology, Graduate School of Science, Nagoya University, Chikusa ku, Nagoya 464 8602, Japan
EMBO J 21:1158-67. 2002..These results suggest that Khd1 may function in the linkage between ASH1 mRNA localization and its translation...
- The Rat1p 5' to 3' exonuclease degrades telomeric repeat-containing RNA and promotes telomere elongation in Saccharomyces cerevisiaeBrian Luke
Ecole Polytechnique Federale de Lausanne, Swiss Institute for Experimental Cancer Research ISREC, CH 1066 Epalinges, Switzerland
Mol Cell 32:465-77. 2008..Thus, telomeric transcription combined with Rat1p-dependent TERRA degradation is important for regulating telomerase in yeast. Telomere transcription is conserved in different kingdoms of the eukaryotic domain...
- Endonucleolytic cleavage of eukaryotic mRNAs with stalls in translation elongationMeenakshi K Doma
Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA
Nature 440:561-4. 2006..No-go decay provides a mechanism for clearing the cell of stalled translation elongation complexes, which could occur as a result of damaged mRNAs or ribosomes, or as a mechanism of post-transcriptional control...
- RNP localization and transport in yeastP Chartrand
Department of Anatomy, Albert Einstein College of Medicine, Bronx, New York 10461, USA
Annu Rev Cell Dev Biol 17:297-310. 2001..This review summarizes the current knowledge on RNP transport and localization in yeast...
- Multiple RNA surveillance pathways limit aberrant expression of iron uptake mRNAs and prevent iron toxicity in S. cerevisiaeAlbert Lee
Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, Box 951569, Los Angeles, California 90095, USA
Mol Cell 19:39-51. 2005....
- Aspergillus nidulans wetA activates spore-specific gene expressionM A Marshall
Departments of Genetics, University of Georgia, Athens 30602
Mol Cell Biol 11:55-62. 1991..We propose that wetA is responsible for activating a set of genes whose products make up the final two conidial wall layers or direct their assembly and through this activity is responsible for acquisition of spore dormancy...
- Rapid, transcript-specific changes in splicing in response to environmental stressJeffrey A Pleiss
Department of Biochemistry and Biophysics, University of California, San Francisco, 600 16th Street, Genentech Hall, Room N 374, San Francisco, CA 94143 2200, USA
Mol Cell 27:928-37. 2007..We propose that regulation of splicing, like transcription, can afford rapid and specific changes in gene expression in response to the environment...
- A faux 3'-UTR promotes aberrant termination and triggers nonsense-mediated mRNA decayNadia Amrani
Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester, Massachusetts 01655 0122, USA
Nature 432:112-8. 2004..These findings indicate that efficient termination and mRNA stability are dependent on a properly configured 3'-UTR...
- The yeast ribosome synthesis factor Emg1 is a novel member of the superfamily of alpha/beta knot fold methyltransferasesNicolas Leulliot
Institut de Biochimie et de Biophysique Moleculaire et Cellulaire, UMR8619, Bat 430, Universite de Paris Sud, 91405 Orsay Cedex, France
Nucleic Acids Res 36:629-39. 2008..We conclude that the catalytic activity of Emg1 is not essential and that the presence of the protein is both necessary and sufficient for ribosome biogenesis...
- P bodies promote stress granule assembly in Saccharomyces cerevisiaeJ Ross Buchan
Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, University of Arizona, Tucson, AZ 85721, USA
J Cell Biol 183:441-55. 2008..These observations argue that P bodies are important sites for decisions of mRNA fate and that stress granules, at least in yeast, primarily represent pools of mRNAs stalled in the process of reentry into translation from P bodies...
- Absolute quantification of the budding yeast transcriptome by means of competitive PCR between genomic and complementary DNAsFumihito Miura
Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277 8561, Japan
BMC Genomics 9:574. 2008..It would help not only to precisely grasp the structure of the transcriptome but also to accelerate data exchange and integration...
- Composition and functional characterization of yeast 66S ribosome assembly intermediatesP Harnpicharnchai
Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
Mol Cell 8:505-15. 2001..These results demonstrate that proteomic approaches in concert with genetic tools provide powerful means to purify and characterize ribosome assembly intermediates...
- Ribosome synthesis in Saccharomyces cerevisiaeJ Venema
Department of Biochemistry and Molecular Biology, BioCentrum Amsterdam, Vrije Universiteit, The Netherlands
Annu Rev Genet 33:261-311. 1999..Here, we will discuss the recent, and often surprising, advances in our understanding of ribosome synthesis in the yeast Saccharomyces cerevisiae. These will underscore the unexpected complexity of eukaryotic ribosome synthesis...
- Mutations in yeast mt tRNAs: specific and general suppression by nuclear encoded tRNA interactorsC De Luca
Department of Cell and Developmental Biology, Pasteur Institute Cenci Bolognetti Foundation, University of Rome I, Italy
Gene 377:169-76. 2006..Finally, we demonstrated, using the RT-PCR method, the existence of significantly variable levels of the TUF1 transcript among strains with functional and dysfunctional mitochondria...
- 60S pre-ribosome formation viewed from assembly in the nucleolus until export to the cytoplasmTracy A Nissan
Biochemie Zentrum Heidelberg, Universitat Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
EMBO J 21:5539-47. 2002..As the 60S pre-ribosome reaches the cytoplasm, almost all of the factors are dissociated. These data provide an initial biochemical map of 60S ribosomal subunit formation on its path from the nucleolus to the cytoplasm...
- SHAPE analysis of long-range interactions reveals extensive and thermodynamically preferred misfolding in a fragile group I intron RNACaia D S Duncan
Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599 3290, USA
Biochemistry 47:8504-13. 2008....
- She2p is a novel RNA binding protein with a basic helical hairpin motifDierk Niessing
Laboratories of Molecular Biophysics and The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
Cell 119:491-502. 2004....
- Yeast Pescadillo is required for multiple activities during 60S ribosomal subunit synthesisMarlene Oeffinger
Wellcome Trust Centre for Cell Biology, University of Edinburgh, United Kingdom
RNA 8:626-36. 2002..Nop7p is a component of at least three different pre-60S particles, and we propose that it carries out distinct functions in each of these complexes...
- Interactions among the protein and RNA subunits of Saccharomyces cerevisiae nuclear RNase PFelicia Houser-Scott
Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109 0606, USA
Proc Natl Acad Sci U S A 99:2684-9. 2002..This study provides a low-resolution map of the multisubunit architecture of the ribonucleoprotein enzyme, nuclear RNase P from S. cerevisiae...
- Competition between the ATPase Prp5 and branch region-U2 snRNA pairing modulates the fidelity of spliceosome assemblyYong Zhen Xu
Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461 1975, USA
Mol Cell 28:838-49. 2007....
- Correlation between the secondary structure of pre-mRNA introns and the efficiency of splicing in Saccharomyces cerevisiaeSanja Rogic
Department of Computer Science, University of British Columbia, Vancouver, Canada
BMC Genomics 9:355. 2008..However, no attempts were made to compute a shortened, 'structural' branchpoint distance and thus the functional relationship between this distance and the splicing efficiency remains unknown...
- A novel mechanism for regulating activity of a transcription factor that controls the unfolded protein responseJ S Cox
Department of Biochemistry and Biophysics, University of California, School of Medicine, San Francisco 94143 0448, USA
Cell 87:391-404. 1996..We propose that the complex regulation of Hac1p expression serves to provide multiple levels at which the UPR can be controlled...
- Meiosis-specific RNA splicing in yeastJ A Engebrecht
Department of Biology, Yale University, New Haven, Connecticut 06511 8112
Cell 66:1257-68. 1991..Therefore, at least one of the functions of the MER1 protein is to mediate splicing of the MER2 transcript. Genetic data suggest that the MER1 gene may also be responsible for splicing the transcript of at least one other gene...
- A universal telomerase RNA core structure includes structured motifs required for binding the telomerase reverse transcriptase proteinJue Lin
Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA
Proc Natl Acad Sci U S A 101:14713-8. 2004..These results, combined with previous studies on telomerase RNAs from other budding yeasts, vertebrates, and ciliates, define a minimal universal core for telomerase RNAs...
- An RNA switch at the 5' splice site requires ATP and the DEAD box protein Prp28pJ P Staley
Department of Biochemistry and Biophysics, University of California, San Francisco 94143, USA
Mol Cell 3:55-64. 1999..In vitro, the switch requires both Prp28p and ATP. We propose that Prp28p directs isomerization of RNA at the 5' splice site and promotes fidelity in splicing...
- Nuclear pore association confers optimal expression levels for an inducible yeast geneAngela Taddei
Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH 4058 Basel, Switzerland
Nature 441:774-8. 2006..From this we conclude that nuclear position has an active role in determining optimal gene expression levels...
- The Putative RNA Helicase Dbp4p Is Required for Release of the U14 snoRNA from Preribosomes in Saccharomyces cerevisiaeMartin Kos
Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
Mol Cell 20:53-64. 2005..Point mutations in helicase motifs I and III of Dbp4p blocked release of U14 from preribosomes. We conclude that the helicase activity of Dbp4p is required to unwind U14 and snR41 from the pre-rRNA...
- A bulged stem tethers Est1p to telomerase RNA in budding yeastAnita G Seto
Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309 0215, USA
Genes Dev 16:2800-12. 2002..We propose that this RNA structure links the enzymatic core of telomerase with Est1p, thereby allowing Est1p to recruit or activate telomerase at the telomere...
- Purification and characterization of the nuclear RNase P holoenzyme complex reveals extensive subunit overlap with RNase MRPJ R Chamberlain
Program in Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, Michigan 48109 0606 USA
Genes Dev 12:1678-90. 1998..The degree of structural similarity between nuclear RNase P and RNase MRP suggests that some aspects of their functions in pre-tRNA and pre-rRNA processing pathways might overlap or be coordinated...
- Identification of the yeast gene encoding the tRNA m1G methyltransferase responsible for modification at position 9Jane E Jackman
Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York 14642, USA
RNA 9:574-85. 2003..Trm10p homologs are found widely in eukaryotes and many archaea, with multiple homologs in several metazoans, including at least three in humans...
- Unwinding RNA in Saccharomyces cerevisiae: DEAD-box proteins and related familiesJ De la Cruz
Instituto de Bioqu mica Vegetal y Fotos ntesis, Centro Isla de la Cartuja, Universidad de Sevilla CSIC, Americo Vespucio s n, 41092 Sevilla, Spain
Trends Biochem Sci 24:192-8. 1999..Recent progress in the functional analysis of various family members has given new insights into, and confirmed the significance of these proteins for, most cellular RNA metabolic processes...
- Involvement of DEAD-box proteins in group I and group II intron splicing. Biochemical characterization of Mss116p, ATP hydrolysis-dependent and -independent mechanisms, and general RNA chaperone activityCoralie Halls
Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, School of Biological Sciences, University of Texas at Austin, Austin, TX 78712, USA
J Mol Biol 365:835-55. 2007....
- Metabolic specialization associated with phenotypic switching in CandidaalbicansChung Yu Lan
Department of Stomatology, University of California, San Francisco 94143, USA
Proc Natl Acad Sci U S A 99:14907-12. 2002..These results extend our understanding of strategies used in microbial phase variation and pathogenesis and further characterize the unanticipated diversity of genes expressed in phenotypic switching...
- rRNA modifications in an intersubunit bridge of the ribosome strongly affect both ribosome biogenesis and activityXue 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...
- Phylogenetic analysis of the structure of RNase MRP RNA in yeastsXing Li
Department of Biological Sciences, University of Maryland, Baltimore 21250, USA
RNA 8:740-51. 2002..Two of these regions are part of a helix implicated in RNA catalysis in RNase P, suggesting that RNase MRP may cleave rRNA using a similar catalytic mechanism...
- The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase IIMinkyu Kim
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
Nature 432:517-22. 2004..These findings support a model in which poly(A) site cleavage and subsequent degradation of the 3'-downstream RNA by Rat1 trigger transcription termination...
- Plasma membrane compartmentalization in yeast by messenger RNA transport and a septin diffusion barrierP A Takizawa
Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, CA 94143, USA
Science 290:341-4. 2000..These results indicate that yeast creates distinct plasma membrane compartments, as has been described in neurons and epithelial cells...
- The Est3 protein is a subunit of yeast telomeraseT R Hughes
Program in Cellular and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
Curr Biol 10:809-12. 2000..Yeast telomerase therefore contains a minimum of three Est proteins for which there is both in vivo and in vitro evidence for their role in telomere replication as subunits of the telomerase complex...
- The DCP2 protein is required for mRNA decapping in Saccharomyces cerevisiae and contains a functional MutT motifT Dunckley
Department of Molecular and Cellular Biology and Howard Hughes Medical Institute, University of Arizona, Tucson, AZ 85721, USA
EMBO J 18:5411-22. 1999..These results suggest that direct or indirect interaction of Dcp1p with Dcp2p is required for the production of active decapping enzyme, perhaps in a process requiring the hydrolysis of a pyrophosphate bond...
- Quality control of mRNA 3'-end processing is linked to the nuclear exosomeP Hilleren
Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA
Nature 413:538-42. 2001..In exosome mutants, hypo- as well as hyperadenylated mRNAs are released and translated. These observations suggest that the exosome contributes to a checkpoint that monitors proper 3'-end formation of mRNA...
- An active retrotransposon in Candida albicansN J Holton
Department of Biochemistry, University of Otago, PO Box 56, Dunedin, New Zealand
Nucleic Acids Res 29:4014-24. 2001..This is the first report of transposition in C.albicans...
- The eukaryotic initiation factor (eIF) 4G HEAT domain promotes translation re-initiation in yeast both dependent on and independent of eIF4A mRNA helicaseRyosuke Watanabe
Molecular, Cellular, and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, Kansas 66506, USA
J Biol Chem 285:21922-33. 2010..Based on the RNA-binding activities identified within the unstructured segments flanking the eIF4G2 HEAT domain, we discuss the role of the HEAT domain in scanning beyond loading eIF4A onto the pre-initiation complex...
- Yeast mRNA Poly(A) tail length control can be reconstituted in vitro in the absence of Pab1p-dependent Poly(A) nuclease activitySonia Dheur
CNRS UMR 5095, Institut de Biochimie et Génétique Cellulaires, 1 rue Camille Saint Saens, F 33077 Bordeaux cedex, France
J Biol Chem 280:24532-8. 2005..Based on these findings, we propose that Nab2p is necessary and sufficient to regulate poly(A) tail length during de novo synthesis in yeast...
- Identification of Lhp1p-associated RNAs by microarray analysis in Saccharomyces cerevisiae reveals association with coding and noncoding RNAsMaki Inada
Department of Biochemistry and Biophysics, University of California, 600 16th Street, San Francisco, CA 94143 2200, USA
Proc Natl Acad Sci U S A 101:434-9. 2004..These results suggest that Lhp1p may play a novel role in the translation of one or more cellular mRNAs...
- Posttranscriptional control of gene expression in yeastJ E McCarthy
Posttranscriptional Control Group, Department of Biomolecular Sciences, University of Manchester Institute of Science and Technology UMIST, Manchester M60 1QD, United Kingdom
Microbiol Mol Biol Rev 62:1492-553. 1998....
- Two classes of small antisense RNAs in fungal RNA silencing triggered by non-integrative transgenesFrancisco E Nicolas
Departamento de Genética y Microbiología, Facultad de Biologia, Universidad de Murcia, 30071 Murcia, Spain
EMBO J 22:3983-91. 2003..These findings, together with the self-replicative nature of the triggering molecules, make M. circinelloides a suitable organism for investigating some unresolved questions in RNA silencing...
- Multiple protein/protein and protein/RNA interactions suggest roles for yeast DNA/RNA helicase Sen1p in transcription, transcription-coupled DNA repair and RNA processingDoris Ursic
Laboratories of Molecular Biology and Genetics, R M Bock Laboratories, 1525 Linden Drive, University of Wisconsin, Madison, WI 53706, USA
Nucleic Acids Res 32:2441-52. 2004..The protein-protein and protein-RNA interactions reported here suggest that the DNA/RNA helicase activity of Sen1p is utilized for several different purposes in multiple gene expression pathways...
- Circadian clock-controlled genes isolated from Neurospora crassa are late night- to early morning-specificD Bell-Pedersen
Department of Biochemistry, Darmouth Medical School, Hanover, NH 03755, USA
Proc Natl Acad Sci U S A 93:13096-101. 1996..These data suggest a major role for the clock in the regulation of biological processes distinct from development...
- Evidence that poly(A) binding protein has an evolutionarily conserved function in facilitating mRNA biogenesis and exportJulia A Chekanova
Department of Biological Sciences, State University of New York at Albany, Albany, New York 12222, USA
RNA 9:1476-90. 2003..We propose that eukaryotic PABPs have an evolutionarily conserved function in facilitating mRNA biogenesis and export...
- Functional equivalence of hairpins in the RNA subunits of RNase MRP and RNase P in Saccharomyces cerevisiaeL Lindahl
Department of Biological Sciences, University of Maryland Baltimore County, Baltimore 21250, USA
RNA 6:653-8. 2000..We propose that the MRP3 and P3 hairpins in S. cerevisiae perform similar functions and have coevolved to maintain common features that are different from those of MRP3 and P3 hairpins in other species...
- Role of RNA silencing as an antiviral defense mechanism in fungiDonald L Nuss; Fiscal Year: 2013..The influence of fungal RNA silencing antiviral pathways clearly needs to be considered in any current and future use of mycoviruses for ..
- COORDINATION OF BACTERIAL RIBOSOMAL PROTEIN SYNTHESISLasse Lindahl; Fiscal Year: 2001....
- Molecular Mechanisms of Global Represion in YeastKevin Struhl; Fiscal Year: 2008..We will use RNAi to identify genes affected by the various TLE proteins, and will address the mechanism of repression by TLE proteins by using derivatives of the well characterized B-interferon promoter. ..
- Compartmentalization of HIV within the genital tractDavid Smith; Fiscal Year: 2007..unreadable] [unreadable]..
- New Research Strategies in Osteogenesis ImperfectaPeter Byers; Fiscal Year: 2006..unreadable] [unreadable] [unreadable] [unreadable]..
- New Approaches for Development of PcP TherapyMelanie Cushion; Fiscal Year: 2006..Finally, they will select the most efficacious combinations of agents and evaluate their effects on gene expression again using the macroarray approach. ..
- Molecular Epidemiology of Human P. carinii PneumoniaLaurence Huang; Fiscal Year: 2006..abstract_text> ..
- High Throughput Assay:Topoisomerase Enzyme Targets (RMI)JAMES STIVERS; Fiscal Year: 2005..The utility of the assay has been validated, by screening a 2000 member small molecule library from which several novel lead compounds have been identified that specifically target a poxvirus family topoisomerase. ..
- Role of the OPI1 gene in controlling viability of Candida glabrataTODD REYNOLDS; Fiscal Year: 2008..unreadable] [unreadable] [unreadable]..
- The Role of Polyadenylation in RNA TurnoverSIDNEY KUSHNER; Fiscal Year: 2007..abstract_text> ..
- The Challenges of Autosomal Recessive and Other New Forms of OIPeter Byers; Fiscal Year: 2008..It also will facilitate identification of new OI genes, identify new paths of research to benefit patients, and increase progress of the Linked Clinical Research Centers. [unreadable] [unreadable] [unreadable] [unreadable]..
- Molecular Targets of Novel Antifungal CompoundsAmeeta Agarwal; Fiscal Year: 2008..This work will provide a starting point in the development of new antifungal therapies. [unreadable] [unreadable] [unreadable]..
- Biochemistry of recombination in gametogenesisWayne P Wahls; Fiscal Year: 2010....
- Characterization of the SARSCoV frameshift signalJonathan D Dinman; Fiscal Year: 2010....
- Regulation of translation initiation in eukaryotesVincent P Mauro; Fiscal Year: 2010..g. for the production of therapeutic proteins, and new avenues for analyzing the potential contributions of mis-regulation to disease. ..
- Mechanism of Eukaryotic Translation TerminationDavid M Bedwell; Fiscal Year: 2011..The third aim of this proposal will test various aspects of this model so we can better understand the important interplay between translation termination and mRNA stability. ..
- Targeted 2nd generation sequencing in phenotyped Framingham & PGP populations.George M Church; Fiscal Year: 2010..It will eventually also enable health providers to learn the genetic variations of their patients very inexpensively and thus help refine and improve their medical care. ..
- Structure and Function of a Eukaryotic CentromereKerry S Bloom; Fiscal Year: 2010....
- Nanostenting Hydrogels for Sinus SurgeryRICHARD ORLANDI; Fiscal Year: 2004..The results of these Phase I studies will determine the feasibility and the optimal chemical properties of a nanostenting HA gel for human trials. ..
- Internal Initiation in the Translation of Cellular mRNAsVincent Mauro; Fiscal Year: 2004....
- KTC: AN ACCURATE METHOD FOR TRANSCRIPTOME ANALYSISMichael Holland; Fiscal Year: 2002..The accuracy, high sensitivity, wide detection range, and flexibility of kinetic PCR assays enable this technology to address a wide range of genomics-based analyses. ..
- IDENTIFICATION AND EXPRESSION OF SKIN SPECIFIC GENESPeter Byers; Fiscal Year: 2002....
- Gordon Research Conferences: Collagen 2003, 2005, 2007Peter Byers; Fiscal Year: 2003..The funds will be used to partially defray conferee travel expenses and registration fees for invited speakers and for young members of the research community. ..
- Eighth International Workshops on Opportunistic ProtistsMelanie Cushion; Fiscal Year: 2003..Mead's and Cushion's ancestors include native Americans; Marciano-Cabral is Hispanic; Kaneshiro has Pacific-Asian ancestry; Lindsay, Weiss are white. Lindsay is a physically handicapped individual. ..
- REGULATION OF MEIOTIC DEVELOPMENT BY MTS1-MTS2 PROTEINWAYNE WAHLS; Fiscal Year: 2004..4) To test alternative hypotheses that the Mts1-Mts2-M26 complex either enhances the use of a pre-existing recombinational initiation site or creates a new initiation site. The PI request four years of support to carry out this study. ..
- RIBOSOMAL FRAMESHIFTING AS A PROBE OF 5S RRNA FUNCTIONJONATHAN DINMAN; Fiscal Year: 2004..The proposed research will serve to further our understanding of this ubiquitous yet little understood rRNA and will place us in the unique position to link functional aspects of 5S rRNA to its structure within the ribosome. ..
- Robustness and Genetic Variation in Gene NetworksStephen Proulx; Fiscal Year: 2004..This work will increase our understanding of the forces that structure gene networks and our ability to predict which genes are most likely to cause disease. ..
- MOLEC GENETICS OF COMPLEX I IN MAMMALIAN MITOCHONDRIAImmo Scheffler; Fiscal Year: 2004..Such mice promise to become model systems for mitochondrial diseases. 5) Known cDNAs will be tested to identify the defective gene in the other four complementation groups with complex I defects. ..
- Computation tools for analyzing gene expression dataNaama Barkai; Fiscal Year: 2004..Kinetic microarray experiments that highlight specific features of the transcriptional network will be designed, performed and analyzed. Methods for extracting regulatory relationships from these experiments will be developed. ..
- Combinatoial CREB/ATF dimers and cellular growth controlWAYNE WAHLS; Fiscal Year: 2004..Aim 3, To further characterize regulatory mechanisms for stress responses mediated by the Mts1 bZIP protein: elucidate the role of the MAP kinase Spcl in controlling an autoinhibitory function of Mts1. ..
- Mild Ol - Toward Better Understanding and TreatmentPeter Byers; Fiscal Year: 2004..abstract_text> ..
- PNEUMOCYSTIS GENOME PROJECTMelanie Cushion; Fiscal Year: 2004..Thus, there is but a single aim to this proposal: 1. To finish sequencing the genome of pneumocystis carinii and provide a completed assembly. ..
- Regulation of gene expression by ribosomal frameshiftingJONATHAN DINMAN; Fiscal Year: 2004....
- Role of Oxidative Mechanisms in the Toxicity of MetalsSIMON AVERY; Fiscal Year: 2007..unreadable] [unreadable]..
- The Mammalian Signal Recognition ParticleKEVIN WEEKS; Fiscal Year: 2006..Moreover, the work is designed to identify principles generalizable to other biologically and medically prominent ribonucleoprotein complexes. ..
- Aveolar Macrophage Apoptosis and PneumocystisChao Hung Lee; Fiscal Year: 2009..abstract_text> ..
- IDENTIFICATION OF HELICOBACTER PYLORI VIRULENCE GENESMichael Holland; Fiscal Year: 2004..Transcript profiles obtained under a variety of in vitro conditions will be organized into relational data sets and analyzed to reveal transcriptional paths and networks operative in H. pylori. ..
- Protein-Facilitated Group I Intron SplicingMark Caprara; Fiscal Year: 2006..A co-crystal of IAniI and its DNA target site diffracts to high resolution and the resulting structure will provide a powerful reference to establish structure-function relationships. ..
- STRUCTURAL STUDY OF EUKARYOTIC TRANSCRIPTION REGULATIONFrancisco Asturias; Fiscal Year: 2004..By identifying structural differences and similarities between the complexes we hope to contribute to the understanding of what increasingly appears as a universal mechanism for transcription control. ..
- MOLECULAR PATHOLOGY OF PNEUMOCYSTIS PNEUMONIAChao Hung Lee; Fiscal Year: 2004..carinii-infected lung will also be tested. Any P. carinii or host protein that is found to have the ability to down regulate GATA-2 expression will be identified by sequencing a portion of the protein. ..
- TRANSMISSION OF PNEUMOCYSTIS INFECTIONMelanie Cushion; Fiscal Year: 2001..These studies will result in a clearer understanding of the biology leading to infection with Pc and will provide a rational basis for clinical management and therapeutic intervention. ..
- Biochemical analysis of Pol II elongation complexes and mechanismCRAIG KAPLAN; Fiscal Year: 2007..Insights into Pol II function will allow a better understanding of how Pol II may be misregulated in disease states in other species, such as humans. [unreadable] [unreadable] [unreadable]..
- Mechanisms of 3' Splice Site Selection in S. cerevisiaeDAVID MCPHEETERS; Fiscal Year: 2005..Because these enzymes have important roles in all aspects of cellular RNA metabolism, the results of these studies will be relevant to the study of their functions in other biological contexts. ..
- STRUCTURE/FUNCTION OF YEAST DNA POLYMERASE DELTAPETER BURGERS; Fiscal Year: 2002..Improper regulation of these processes in humans may lead to cancer. ..
- Light-regulated genes affecting the pathogen potential of Cryptococcus neoformansAlexander Idnurm; Fiscal Year: 2008..unreadable] [unreadable] [unreadable] [unreadable]..
- Cellular & Molecular Fungal Biology 2008 Gordon Research ConferenceNancy Keller; Fiscal Year: 2008..unreadable] [unreadable] [unreadable]..
- Protein-Facilitates RNA CatalystsKEVIN WEEKS; Fiscal Year: 2007..5) To begin to explore the molecular mechanism by which Mrs1 facilitates catalysis of the bl3 group I intron. (6) To develop a high resolution model for the maturase-bl3 RNA complex. ..