messenger rna

Summary

Summary: RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.

Top Publications

  1. pmc A new mathematical model for relative quantification in real-time RT-PCR
    M W Pfaffl
    Institute of Physiology, FML Weihenstephan, Center of Life and Food Sciences, Technical University of Munich, Germany
    Nucleic Acids Res 29:e45. 2001
  2. ncbi Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
    Benjamin P Lewis
    Cell 120:15-20. 2005
  3. ncbi The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
    R C Lee
    Harvard University, Department of Cellular and Developmental Biology, Cambridge, Massachusetts 02138
    Cell 75:843-54. 1993
  4. pmc BLAT--the BLAST-like alignment tool
    W James Kent
    Department of Biology and Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Genome Res 12:656-64. 2002
  5. pmc The human genome browser at UCSC
    W James Kent
    Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
    Genome Res 12:996-1006. 2002
  6. pmc Relative expression software tool (REST) for group-wise comparison and statistical analysis of relative expression results in real-time PCR
    Michael W Pfaffl
    Institute of Physiology, FML Weihenstephan, Center of Life and Food Sciences, Technical University of Munich, Germany
    Nucleic Acids Res 30:e36. 2002
  7. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
  8. ncbi Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets
    Claus Lindbjerg Andersen
    Molecular Diagnostic Laboratory, Department of Clinical Biochemistry, Aarhus University Hospital, Skejby, DK 8200 Aarhus N, Denmark
    Cancer Res 64:5245-50. 2004
  9. doi Mapping and quantifying mammalian transcriptomes by RNA-Seq
    Ali Mortazavi
    Division of Biology, MC 156 29, California Institute of Technology, Pasadena, California 91125, USA
    Nat Methods 5:621-8. 2008
  10. ncbi RNA maps reveal new RNA classes and a possible function for pervasive transcription
    Philipp Kapranov
    Affymetrix Laboratory, Affymetrix, Inc, 3420 Central Expressway, Santa Clara, CA, 95051, USA
    Science 316:1484-8. 2007

Research Grants

  1. Role of Polyamines in MYCN-Amplified Neuroblastoma
    ANDRE BACHMANN; Fiscal Year: 2009
  2. Epigenomic Events in Development of the Locus Coeruleus Noradrenergic Neurons
    Jan Krzysztof Blusztajn; Fiscal Year: 2012
  3. Regulation of Cardiac Kv Channel Expression
    Edwin S Levitan; Fiscal Year: 2013
  4. HORMONAL REGULATION OF MESSENGER RNA STABILITY
    Daniel R Schoenberg; Fiscal Year: 2013
  5. Coronavirus RNA Replication
    DAVID ALVIN BRIAN; Fiscal Year: 2012
  6. microRNA and Down Syndrome
    Karl H Obrietan; Fiscal Year: 2010
  7. Microbial regulation of intestinal gene expression through microRNA
    Sushila Dalal; Fiscal Year: 2012
  8. Nonsense Mediated RNA Decay Regulation in Erythropoiesis &Thalassemia
    LAWRENCE BENJAMIN GARDNER; Fiscal Year: 2012
  9. Suppression of the Interferon Response by the Hepatitis C Virus
    FRANCIS VINCENT CHISARI; Fiscal Year: 2010
  10. 2012 Fragile X and Autism-Related Disorders: From Basic Neuroscience to Improved
    ELIZABETH MARA BERRY-KRAVIS; Fiscal Year: 2012

Detail Information

Publications328 found, 100 shown here

  1. pmc A new mathematical model for relative quantification in real-time RT-PCR
    M W Pfaffl
    Institute of Physiology, FML Weihenstephan, Center of Life and Food Sciences, Technical University of Munich, Germany
    Nucleic Acids Res 29:e45. 2001
    ..High accuracy and reproducibility (<2.5% variation) were reached in LightCycler PCR using the established mathematical model...
  2. ncbi Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
    Benjamin P Lewis
    Cell 120:15-20. 2005
    ..Targeting was also detected in open reading frames. In sum, well over one third of human genes appear to be conserved miRNA targets...
  3. ncbi The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
    R C Lee
    Harvard University, Department of Cellular and Developmental Biology, Cambridge, Massachusetts 02138
    Cell 75:843-54. 1993
    ..elegans and found to contain sequences complementary to a repeated sequence element in the 3' untranslated region (UTR) of lin-14 mRNA, suggesting that lin-4 regulates lin-14 translation via an antisense RNA-RNA interaction...
  4. pmc BLAT--the BLAST-like alignment tool
    W James Kent
    Department of Biology and Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Genome Res 12:656-64. 2002
    ..BLAT is compared with other alignment programs on various test sets and then used in several genome-wide applications. http://genome.ucsc.edu hosts a web-based BLAT server for the human genome...
  5. pmc The human genome browser at UCSC
    W James Kent
    Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
    Genome Res 12:996-1006. 2002
    ..The conceptual and technical framework of the browser, its underlying MYSQL database, and overall use are described. The web site currently serves over 50,000 pages per day to over 3000 different users...
  6. pmc Relative expression software tool (REST) for group-wise comparison and statistical analysis of relative expression results in real-time PCR
    Michael W Pfaffl
    Institute of Physiology, FML Weihenstephan, Center of Life and Food Sciences, Technical University of Munich, Germany
    Nucleic Acids Res 30:e36. 2002
    ..The latest software version of REST and examples for the correct use can be downloaded at http://www.wzw.tum.de/gene-quantification/...
  7. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
    ..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...
  8. ncbi Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets
    Claus Lindbjerg Andersen
    Molecular Diagnostic Laboratory, Department of Clinical Biochemistry, Aarhus University Hospital, Skejby, DK 8200 Aarhus N, Denmark
    Cancer Res 64:5245-50. 2004
    ..The presented strategy can be applied to evaluate the suitability of any normalization gene candidate in any kind of experimental design and should allow more reliable normalization of RT-PCR data...
  9. doi Mapping and quantifying mammalian transcriptomes by RNA-Seq
    Ali Mortazavi
    Division of Biology, MC 156 29, California Institute of Technology, Pasadena, California 91125, USA
    Nat Methods 5:621-8. 2008
    ..We observed 1.45 x 10(5) distinct splices, and alternative splices were prominent, with 3,500 different genes expressing one or more alternate internal splices...
  10. ncbi RNA maps reveal new RNA classes and a possible function for pervasive transcription
    Philipp Kapranov
    Affymetrix Laboratory, Affymetrix, Inc, 3420 Central Expressway, Santa Clara, CA, 95051, USA
    Science 316:1484-8. 2007
    ..These data support a highly interleaved organization of the human transcriptome...
  11. ncbi Prediction of mammalian microRNA targets
    Benjamin P Lewis
    Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Cell 115:787-98. 2003
    ..The predicted regulatory targets of mammalian miRNAs were enriched for genes involved in transcriptional regulation but also encompassed an unexpectedly broad range of other functions...
  12. ncbi Defective LPS signaling in C3H/HeJ and C57BL/10ScCr mice: mutations in Tlr4 gene
    A Poltorak
    Howard Hughes Medical Institute and the Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75235 9050, USA
    Science 282:2085-8. 1998
    ..Destructive mutations of Tlr4 predispose to the development of Gram-negative sepsis, leaving most aspects of immune function intact...
  13. ncbi The role of site accessibility in microRNA target recognition
    Michael Kertesz
    Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
    Nat Genet 39:1278-84. 2007
    ..Our study thus demonstrates that target accessibility is a critical factor in microRNA function...
  14. pmc Obesity is associated with macrophage accumulation in adipose tissue
    Stuart P Weisberg
    Division of Moleuclar Genetics, Department of Pediatrics, Columbia University, New York, New York 10032, USA
    J Clin Invest 112:1796-808. 2003
    ..Adipose tissue macrophage numbers increase in obesity and participate in inflammatory pathways that are activated in adipose tissues of obese individuals...
  15. pmc RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays
    John C Marioni
    Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
    Genome Res 18:1509-17. 2008
    ..Based on our observations, we propose an empirical protocol and a statistical framework for the analysis of gene expression using ultra-high-throughput sequencing technology...
  16. ncbi Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data
    Christian Ramakers
    Department of Anatomy and Embryology K2 283, Experimental and Molecular Cardiology Group, Academic Medical Centre, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
    Neurosci Lett 339:62-6. 2003
    ..A computer program to perform this calculation is available on request (e-mail: bioinfo@amc.uva.nl; subject: LinRegPCR)...
  17. ncbi Control of translation and mRNA degradation by miRNAs and siRNAs
    Marco Antonio Valencia-Sanchez
    Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, University of Arizona, Tucson, Arizona 85721, USA
    Genes Dev 20:515-24. 2006
    ..An emerging theme is that miRNAs, and siRNAs to some extent, target mRNAs to the general eukaryotic machinery for mRNA degradation and translation control...
  18. pmc MicroRNA targeting specificity in mammals: determinants beyond seed pairing
    Andrew Grimson
    Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Mol Cell 27:91-105. 2007
    ..Because it predicts site efficacy without recourse to evolutionary conservation, the model also identifies effective nonconserved sites and siRNA off-targets...
  19. ncbi MicroRNAs: small RNAs with a big role in gene regulation
    Lin He
    Cold Spring Harbor Laboratory, Watson School of Biological Sciences, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
    Nat Rev Genet 5:522-31. 2004
  20. ncbi Regulated translation initiation controls stress-induced gene expression in mammalian cells
    H P Harding
    Skirball Institute of Biomolecular Medicine The Department of Medicine, Kaplan Cancer Center New York University School of Medicine, New York, NY 10016, USA
    Mol Cell 6:1099-108. 2000
    ..Mammalian cells thus utilize an ancient pathway to regulate gene expression in response to diverse stress signals...
  21. pmc Fast and effective prediction of microRNA/target duplexes
    Marc Rehmsmeier
    Universitat Bielefeld, International NRW Graduate School in Bioinformatics and Genome Research, Postfach 10 01 31, 33501 Bielefeld, Germany
    RNA 10:1507-17. 2004
    ..RNAhybrid, with its accompanying programs RNAcalibrate and RNAeffective, is available for download and as a Web tool on the Bielefeld Bioinformatics Server (http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/)...
  22. ncbi A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA
    G Hutvagner
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
    Science 293:834-8. 2001
    ..Targeted destruction in cultured human cells of the messenger RNA encoding the enzyme Dicer, which acts in the RNA interference pathway, leads to accumulation of the let-7 ..
  23. ncbi Modulation of hepatitis C virus RNA abundance by a liver-specific MicroRNA
    Catherine L Jopling
    Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
    Science 309:1577-81. 2005
    MicroRNAs are small RNA molecules that regulate messenger RNA (mRNA) expression. MicroRNA 122 (miR-122) is specifically expressed and highly abundant in the human liver...
  24. pmc NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
    Kim D Pruitt
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Rm 6An 12J, 45 Center Drive, Bethesda, MD 20892 6510, USA
    Nucleic Acids Res 35:D61-5. 2007
    ..The format of all RefSeq records is validated, and an increasing number of tests are being applied to evaluate the quality of sequence and annotation, especially in the context of complete genomic sequence...
  25. ncbi IRE1 couples endoplasmic reticulum load to secretory capacity by processing the XBP-1 mRNA
    Marcella Calfon
    Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
    Nature 415:92-6. 2002
    ..XBP-1 is essential for immunoglobulin secretion and development of plasma cells, and high levels of XBP-1 messenger RNA are found in specialized secretory cells...
  26. pmc Stochastic mRNA synthesis in mammalian cells
    Arjun Raj
    Courant Institute of Mathematical Sciences, New York University, New York, New York, USA
    PLoS Biol 4:e309. 2006
    ..These results demonstrate that gene expression in mammalian cells is subject to large, intrinsically random fluctuations and raise questions about how cells are able to function in the face of such noise...
  27. doi Stem cell transcriptome profiling via massive-scale mRNA sequencing
    Nicole Cloonan
    Expression Genomics Laboratory, Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, Queensland, 4072, Australia
    Nat Methods 5:613-9. 2008
    ....
  28. ncbi Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells
    S M Elbashir
    Department of Cellular Biochemistry, Max-Planck-Institute for Biophysical Chemistry, , Germany
    Nature 411:494-8. 2001
    ..The mediators of sequence-specific messenger RNA degradation are 21- and 22-nucleotide small interfering RNAs (siRNAs) generated by ribonuclease III cleavage ..
  29. ncbi Listening to silence and understanding nonsense: exonic mutations that affect splicing
    Luca Cartegni
    Cold Spring Harbor Laboratory, PO Box 100, Cold Spring Harbor, New York 11724, USA
    Nat Rev Genet 3:285-98. 2002
    ..As the splicing mechanisms that depend on exonic signals are elucidated, new therapeutic approaches to treating certain genetic diseases can begin to be explored...
  30. ncbi IRF-7 is the master regulator of type-I interferon-dependent immune responses
    Kenya Honda
    Department of Immunology, Graduate School of Medicine and Faculty of Medicine, University of Tokyo, Hongo 7 3 1, Bunkyo ku, Tokyo 113 0033, Japan
    Nature 434:772-7. 2005
    ..Thus, all elements of IFN responses, whether the systemic production of IFN in innate immunity or the local action of IFN from plasmacytoid dendritic cells in adaptive immunity, are under the control of IRF-7...
  31. ncbi Antisense transcription in the mammalian transcriptome
    S Katayama
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Centre GSC, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, 230 0045, Japan
    Science 309:1564-6. 2005
    ..We present experimental evidence that perturbation of an antisense RNA can alter the expression of sense messenger RNAs, suggesting that antisense transcription contributes to control of transcriptional outputs in mammals...
  32. ncbi GMAP: a genomic mapping and alignment program for mRNA and EST sequences
    Thomas D Wu
    Department of Bioinformatics Genentech, Inc, South San Francisco, CA 94080, USA
    Bioinformatics 21:1859-75. 2005
    ....
  33. pmc Summaries of Affymetrix GeneChip probe level data
    Rafael A Irizarry
    Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
    Nucleic Acids Res 31:e15. 2003
    ..In particular, improvements in the ability to detect differentially expressed genes are demonstrated...
  34. ncbi Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs
    Antonio J Giraldez
    Developmental Genetics Program, Skirball Institute of Biomolecular Medicine, and Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA
    Science 312:75-9. 2006
    ..approach and in vivo target validation, we find that miR-430 directly regulates several hundred target messenger RNA molecules (mRNAs). Most targets are maternally expressed mRNAs that accumulate in the absence of miR-430...
  35. ncbi Mechanisms of gene silencing by double-stranded RNA
    Gunter Meister
    Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, New York 10021, USA
    Nature 431:343-9. 2004
    ..These short dsRNAs guide RNA silencing by specific and distinct mechanisms. Many components of the RNA silencing machinery still need to be identified and characterized, but a more complete understanding of the process is imminent...
  36. ncbi Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA
    Cesar Llave
    Center for Gene Research and Biotechnology, and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
    Science 297:2053-6. 2002
    Micro-RNAs (miRNAs) are regulatory molecules that mediate effects by interacting with messenger RNA (mRNA) targets...
  37. ncbi The transcription factor snail is a repressor of E-cadherin gene expression in epithelial tumour cells
    E Batlle
    Unitat de Biologia Cel lular i Molecular, Institut Municipal d Investigacio Medica, Universitat Pompeu Fabra, Dr Aiguader 80, 08003 Barcelona, Spain
    Nat Cell Biol 2:84-9. 2000
    ..Inhibition of Snail function in epithelial cancer cell lines lacking E-cadherin protein restores the expression of the E-cadherin gene...
  38. ncbi The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae
    Derrick H Lenz
    Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
    Cell 118:69-82. 2004
    ..Hfq mediates interactions between small, regulatory RNAs (sRNAs) and specific messenger RNA (mRNA) targets. These interactions typically alter the stability of the target transcripts...
  39. ncbi Osteoprotegerin ligand is a cytokine that regulates osteoclast differentiation and activation
    D L Lacey
    Department of Pathology, Amgen, Inc, Thousand Oaks, California 91320 1789, USA
    Cell 93:165-76. 1998
    ..These data suggest that OPGL is an osteoclast differentiation and activation factor. The effects of OPGL are blocked in vitro and in vivo by OPG, suggesting that OPGL and OPG are key extracellular regulators of osteoclast development...
  40. ncbi Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs
    Gunter Meister
    Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10021, USA
    Mol Cell 15:185-97. 2004
    ..The specific role of Ago2 in guiding target RNA cleavage was confirmed independently by siRNA-based depletion of individual Ago members in combination with a sensitive positive-readout reporter assay...
  41. ncbi A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development
    Xuemei Chen
    Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
    Science 303:2022-5. 2004
    ..Here, I show that miRNA172, which can base-pair with the messenger RNA of a floral homeotic gene, APETALA2, regulates APETALA2 expression primarily through translational inhibition...
  42. ncbi The polycomb group protein EZH2 is involved in progression of prostate cancer
    Sooryanarayana Varambally
    Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
    Nature 419:624-9. 2002
    ..Amounts of both EZH2 messenger RNA and EZH2 protein are increased in metastatic prostate cancer; in addition, clinically localized prostate ..
  43. ncbi The orphan nuclear receptor REV-ERBalpha controls circadian transcription within the positive limb of the mammalian circadian oscillator
    Nicolas Preitner
    Department of Molecular Biology, Sciences II, University of Geneva, 30, Quai Ernest Ansermet, CH 1211 4, Geneva, Switzerland
    Cell 110:251-60. 2002
    ..While REV-ERBalpha influences the period length and affects the phase-shifting properties of the clock, it is not required for circadian rhythm generation...
  44. pmc Stress granules and processing bodies are dynamically linked sites of mRNP remodeling
    Nancy Kedersha
    Division of Rheumatology and Immunology, Harvard Medical School, Brigham and Women s Hospital, Boston, MA 02115, USA
    J Cell Biol 169:871-84. 2005
    ..We propose that mRNA released from disassembled polysomes is sorted and remodeled at SGs, from which selected transcripts are delivered to PBs for degradation...
  45. pmc miRBase: tools for microRNA genomics
    Sam Griffiths-Jones
    Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, UK
    Nucleic Acids Res 36:D154-8. 2008
    ..miRBase is available at http://microrna.sanger.ac.uk/...
  46. ncbi Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs
    Lee P Lim
    Rosetta Inpharmatics, Merck and Co, 401 Terry Avenue N, Seattle, Washington 98109, USA
    Nature 433:769-73. 2005
    ..on transcript levels, we transfected miRNAs into human cells and used microarrays to examine changes in the messenger RNA profile...
  47. ncbi Genome-wide atlas of gene expression in the adult mouse brain
    Ed S Lein
    Allen Institute for Brain Science, Seattle, Washington 98103, USA
    Nature 445:168-76. 2007
    ..This highly standardized atlas provides an open, primary data resource for a wide variety of further studies concerning brain organization and function...
  48. ncbi Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma
    Miriam F Moffatt
    National Heart and Lung Institute, Imperial College, London SW3 6LY, UK
    Nature 448:470-3. 2007
    ..The results indicate that genetic variants regulating ORMDL3 expression are determinants of susceptibility to childhood asthma...
  49. ncbi ER stress induces cleavage of membrane-bound ATF6 by the same proteases that process SREBPs
    J Ye
    Department of Molecular Genetics, University of Texas, Southwestern Medical Center, Dallas, TX 75390, USA
    Mol Cell 6:1355-64. 2000
    ..ATF6 processing did not require SCAP, which is essential for SREBP processing. We conclude that S1P and S2P are required for the ER stress response as well as for lipid synthesis...
  50. pmc A large-scale analysis of mRNA polyadenylation of human and mouse genes
    Bin Tian
    Department of Biochemistry and Molecular Biology, New Jersey Medical School UMDNJ, Newark, NJ 07101, USA
    Nucleic Acids Res 33:201-12. 2005
    ..This large-scale study provides important insights into the mechanism of polyadenylation in mammalian species and represents a genomic view of the regulation of gene expression by alternative polyadenylation...
  51. pmc Human MicroRNA targets
    Bino John
    Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, New York, USA
    PLoS Biol 2:e363. 2004
    ..microrna.org. Our analysis suggests that miRNA genes, which are about 1% of all human genes, regulate protein production for 10% or more of all human genes...
  52. pmc Significance analysis of microarrays applied to the ionizing radiation response
    V G Tusher
    Departments of Medicine and Biochemistry, Stanford University, 269 Campus Drive, Center for Clinical Sciences Research 1115, Stanford, CA 94305-5151, USA
    Proc Natl Acad Sci U S A 98:5116-21. 2001
    ..Surprisingly, four nucleotide excision repair genes were induced, suggesting that this repair pathway for UV-damaged DNA might play a previously unrecognized role in repairing DNA damaged by ionizing radiation...
  53. ncbi The nuclear RNase III Drosha initiates microRNA processing
    Yoontae Lee
    Institute of Molecular Biology and Genetics and School of Biological Sciences, Seoul National University, Seoul 151 742, Korea
    Nature 425:415-9. 2003
    ..Thus, the two RNase III proteins, Drosha and Dicer, may collaborate in the stepwise processing of miRNAs, and have key roles in miRNA-mediated gene regulation in processes such as development and differentiation...
  54. pmc Chronic inflammation in fat plays a crucial role in the development of obesity-related insulin resistance
    Haiyan Xu
    Millennium Pharmaceuticals, Cambridge, Massachusetts, USA
    J Clin Invest 112:1821-30. 2003
    ..We propose that obesity-related insulin resistance is, at least in part, a chronic inflammatory disease initiated in adipose tissue...
  55. pmc Alternative isoform regulation in human tissue transcriptomes
    Eric T Wang
    Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Nature 456:470-6. 2008
    ....
  56. pmc The MicroRNA miR-124 promotes neuronal differentiation by triggering brain-specific alternative pre-mRNA splicing
    Eugene V Makeyev
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
    Mol Cell 27:435-48. 2007
    ..Thus, miR-124 promotes NS development, at least in part by regulating an intricate network of NS-specific alternative splicing...
  57. ncbi The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans
    B J Reinhart
    Department of Molecular Biology, Massachusetts General Hospital, and Harvard Medical School, Boston 02114, USA
    Nature 403:901-6. 2000
    ..We propose that the sequential stage-specific expression of the lin-4 and let-7 regulatory RNAs triggers transitions in the complement of heterochronic regulatory proteins to coordinate developmental timing...
  58. doi Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
    Qun Pan
    Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada
    Nat Genet 40:1413-5. 2008
    ..From a comparison with quantitative alternative splicing microarray profiling data, we also show that mRNA-Seq data provide reliable measurements for exon inclusion levels...
  59. pmc A mammalian microRNA expression atlas based on small RNA library sequencing
    Pablo Landgraf
    Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Box 186, The Rockefeller University, New York, NY 10021, USA
    Cell 129:1401-14. 2007
    ..We also propose a subclassification scheme for miRNAs for assisting future experimental and computational functional analyses...
  60. pmc Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis
    Tomasz Czechowski
    Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
    Plant Physiol 139:5-17. 2005
    ..The developed PCR primers or hybridization probes for the novel reference genes will enable better normalization and quantification of transcript levels in Arabidopsis in the future...
  61. ncbi Twist, a master regulator of morphogenesis, plays an essential role in tumor metastasis
    Jing Yang
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Cell 117:927-39. 2004
    ..These results establish a mechanistic link between Twist, EMT, and tumor metastasis...
  62. ncbi Polycomb complexes repress developmental regulators in murine embryonic stem cells
    Laurie A Boyer
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 441:349-53. 2006
    ..Our results indicate that dynamic repression of developmental pathways by Polycomb complexes may be required for maintaining ES cell pluripotency and plasticity during embryonic development...
  63. ncbi Splicing in disease: disruption of the splicing code and the decoding machinery
    Guey Shin Wang
    Department of Pathology, Baylor College of Medicine, Houston, Texas 77030, USA
    Nat Rev Genet 8:749-61. 2007
    ..An unexpectedly large fraction of exonic mutations exhibit a primary pathogenic effect on splicing. Furthermore, normal genetic variation significantly contributes to disease severity and susceptibility by affecting splicing efficiency...
  64. ncbi PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes
    Vamsi K Mootha
    Whitehead Institute MIT Center for Genome Research, Cambridge, Massachusetts, USA
    Nat Genet 34:267-73. 2003
    ..Our results associate this gene set with clinically important variation in human metabolism and illustrate the value of pathway relationships in the analysis of genomic profiling experiments...
  65. ncbi Guideline to reference gene selection for quantitative real-time PCR
    Aleksandar Radonic
    Charité Campus Charité Mitte, II Medizinische Klinik mit Schwerpunkt Onkologie und Hämatologie, Humboldt Universitat, Berlin, Germany
    Biochem Biophys Res Commun 313:856-62. 2004
    ..Our results show that "Classical" reference genes are indeed unsuitable, whereas the RNA polymerase II gene was the gene with the most constant expression in different tissues and following stimulation in CCRF-HSB-2 cells...
  66. pmc The miR-200 family determines the epithelial phenotype of cancer cells by targeting the E-cadherin repressors ZEB1 and ZEB2
    Sun Mi Park
    The Ben May Department for Cancer Research, The University of Chicago, Chicago, Illinois 60637, USA
    Genes Dev 22:894-907. 2008
    ..Conversely, inhibition of miR-200 reduced E-cadherin expression, increased expression of Vimentin, and induced EMT. Our data identify miR-200 as a powerful marker and determining factor of the epithelial phenotype of cancer cells...
  67. ncbi Argonaute2 is the catalytic engine of mammalian RNAi
    Jidong Liu
    Cold Spring Harbor Laboratory, Watson School of Biological Sciences, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Science 305:1437-41. 2004
    ..and biochemically distinct, with a single mammalian family member, Argonaute2, being responsible for messenger RNA cleavage activity...
  68. pmc Accumulation of miR-155 and BIC RNA in human B cell lymphomas
    Peggy S Eis
    Department of Biomolecular Chemistry, University of Wisconsin Medical School, 1300 University Avenue, Madison, WI 53706, USA
    Proc Natl Acad Sci U S A 102:3627-32. 2005
    ..Because patients with activated B cell-type DLBCL have a poorer clinical prognosis, quantification of this microRNA may be diagnostically useful...
  69. ncbi Asymmetry in the assembly of the RNAi enzyme complex
    Dianne S Schwarz
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Lazare Research Building, 364 Plantation Street, Worcester, MA 01605, USA
    Cell 115:199-208. 2003
    ..Thus, the common step of RISC assembly is an unexpected source of asymmetry for both siRNA function and miRNA biogenesis...
  70. pmc miRecords: an integrated resource for microRNA-target interactions
    Feifei Xiao
    Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA
    Nucleic Acids Res 37:D105-10. 2009
    ..The miRecords is available at http://miRecords.umn.edu/miRecords...
  71. ncbi Stress signaling from the lumen of the endoplasmic reticulum: coordination of gene transcriptional and translational controls
    R J Kaufman
    Department of Biological Chemistry and Howard Hughes Medical Institute, The University of Michigan Medical Center, Ann Arbor, Michigan 48109 0650 USA
    Genes Dev 13:1211-33. 1999
  72. ncbi Prokaryotic toxin-antitoxin stress response loci
    Kenn Gerdes
    Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK 5230 Odense M, Denmark
    Nat Rev Microbiol 3:371-82. 2005
    ..It has been proposed that toxin-antitoxin loci function in bacterial programmed cell death, but evidence now indicates that these loci provide a control mechanism that helps free-living prokaryotes cope with nutritional stress...
  73. pmc Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling
    Nicholas T Ingolia
    Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, and California Institute for Quantitative Biosciences, San Francisco, CA 94158, USA
    Science 324:218-23. 2009
    Techniques for systematically monitoring protein translation have lagged far behind methods for measuring messenger RNA (mRNA) levels...
  74. pmc A gene atlas of the mouse and human protein-encoding transcriptomes
    Andrew I Su
    The Genomics Institute of the Novartis Research Foundation, 10675 John J Hopkins Drive, San Diego, CA 92121, USA
    Proc Natl Acad Sci U S A 101:6062-7. 2004
    ..We describe hundreds of regions of correlated transcription and show that some are subject to both tissue and parental allele-specific expression, suggesting a link between spatial expression and imprinting...
  75. ncbi Functional interaction of beta-catenin with the transcription factor LEF-1
    J Behrens
    Max Delbruck Centre for Molecular Medicine, Berlin, Germany
    Nature 382:638-42. 1996
    ..Thus beta-catenin regulates gene expression by direct interaction with transcription factors such as LEF-1, providing a molecular mechanism for the transmission of signals, from cell-adhesion components or wnt protein to the nucleus...
  76. pmc Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by downregulation of miR398 and important for oxidative stress tolerance
    Ramanjulu Sunkar
    Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521, USA
    Plant Cell 18:2051-65. 2006
    ..Thus, relieving miR398-guided suppression of CSD2 in transgenic plants is an effective new approach to improving plant productivity under oxidative stress conditions...
  77. ncbi Quantitative expression of toll-like receptor 1-10 mRNA in cellular subsets of human peripheral blood mononuclear cells and sensitivity to CpG oligodeoxynucleotides
    Veit Hornung
    Department of Internal Medicine, Division of Clinical Pharmacology, University of Munich, Munich, Germany
    J Immunol 168:4531-7. 2002
    ..In addition, selective regulation of TLR7 expression in PDC and B cells by CpG ODN revealed TLR7 as a candidate TLR potentially involved in modulating the recognition of CpG motifs...
  78. pmc Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome
    Charles Addo-Quaye
    Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA 16802, USA
    Curr Biol 18:758-62. 2008
    ..This empirical method is broadly applicable to the discovery and quantification of cleaved targets of small RNAs without a priori predictions...
  79. pmc AU-rich elements and associated factors: are there unifying principles?
    Carine Barreau
    UMR 6061 CNRS Génétique et développement, IFR 140 Génétique Fonctionnelle Agronomie et Santé, Universite de Rennes 1, Faculte de Medecine, CS 34317, 35043 Rennes Cedex, France
    Nucleic Acids Res 33:7138-50. 2005
    ..The potential relationship between mRNA stability and translation is also discussed. Finally, we present several hypotheses that could unify the published data and suggest avenues for future research...
  80. ncbi HIV-1 entry cofactor: functional cDNA cloning of a seven-transmembrane, G protein-coupled receptor
    Y Feng
    Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases NIAID, NIH, Bethesda, MD 20892, USA
    Science 272:872-7. 1996
    ..Antibodies to fusin blocked cell fusion and infection with normal CD4-positive human target cells. Fusin messenger RNA levels correlated with HIV-1 permissiveness in diverse human cell types...
  81. doi A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome
    Marc Sultan
    Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
    Science 321:956-60. 2008
    ..On the basis of known transcripts, RNA-Seq can detect 25% more genes than can microarrays. A global survey of messenger RNA splicing events identified 94,241 splice junctions (4096 of which were previously unidentified) and showed ..
  82. pmc GENCODE: producing a reference annotation for ENCODE
    Jennifer Harrow
    Wellcome Trust Sanger Institute, Wellcome Trust Campus, Hinxton, Cambridge CB10 1SA, UK
    Genome Biol 7:S4.1-9. 2006
    ..This was achieved by a combination of initial manual annotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results...
  83. ncbi A system for stable expression of short interfering RNAs in mammalian cells
    Thijn R Brummelkamp
    Division of Molecular Carcinogenesis, Division of Tumor Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands
    Science 296:550-3. 2002
    ..Therefore, the pSUPER vector constitutes a new and powerful system to analyze gene function in a variety of mammalian cell types...
  84. pmc Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes
    Oliver H Tam
    Cold Spring Harbor Laboratory, Watson School of Biological Sciences and Howard Hughes Medical Institute, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
    Nature 453:534-8. 2008
    ..Our findings indicate a function for pseudogenes in regulating gene expression by means of the RNA interference pathway and may, in part, explain the evolutionary pressure to conserve argonaute-mediated catalysis in mammals...
  85. ncbi A microRNA in a multiple-turnover RNAi enzyme complex
    Gyorgy Hutvagner
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Lazare Research Building, Room 825, 364 Plantation Street, Worcester, MA 01605, USA
    Science 297:2056-60. 2002
    ..Each let-7-containing complex directs multiple rounds of RNA cleavage, which explains the remarkable efficiency of the RNAi pathway in human cells...
  86. ncbi PUMA, a novel proapoptotic gene, is induced by p53
    K Nakano
    Regulation of Cell Growth Laboratory, National Cancer Institute at Frederick, Maryland 21702, USA
    Mol Cell 7:683-94. 2001
    ..Antisense inhibition of PUMA expression reduced the apoptotic response to p53, and PUMA is likely to play a role in mediating p53-induced cell death through the cytochrome c/Apaf-1-dependent pathway...
  87. ncbi Global analysis of protein localization in budding yeast
    Won Ki Huh
    Howard Hughes Medical Institute, University of California San Francisco, Department of Biochemistry and Biophysics, 600 16th Street, San Francisco, California 94143 2240, USA
    Nature 425:686-91. 2003
    ....
  88. pmc The role of microRNA-1 and microRNA-133 in skeletal muscle proliferation and differentiation
    Jian Fu Chen
    Carolina Cardiovascular Biology Center, Department of Cell and Developmental Biology, University of North Carolina Chapel Hill, North Carolina 27599, USA
    Nat Genet 38:228-33. 2006
    ..Together, our studies suggest a molecular mechanism in which miRNAs participate in transcriptional circuits that control skeletal muscle gene expression and embryonic development...
  89. ncbi Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells
    H Niwa
    Centre for Genome Research, The University of Edinburgh, King s Buildings, Edinburgh, UK
    Nat Genet 24:372-6. 2000
    ....
  90. pmc Targeted disruption of the mouse transforming growth factor-beta 1 gene results in multifocal inflammatory disease
    M M Shull
    Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati College of Medicine, Ohio 45267 0524
    Nature 359:693-9. 1992
    ..TGF-beta 1-deficient mice may be valuable models for human immune and inflammatory disorders, including autoimmune diseases, transplant rejection and graft versus host reactions...
  91. ncbi MicroRNA pathways in flies and worms: growth, death, fat, stress, and timing
    Victor Ambros
    Dartmouth Medical School, Department of Genetics, Hanover, NH 03755, USA
    Cell 113:673-6. 2003
    ..In C. elegans, a homolog of the well-known fly developmental regulator hunchback acts downstream of the microRNAs lin-4 and let-7 in a pathway controlling developmental timing...
  92. pmc Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution
    D Allan Drummond
    FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
    Cell 134:341-52. 2008
    ....
  93. ncbi Identification of ubiquitin ligases required for skeletal muscle atrophy
    S C Bodine
    Regeneron Pharmaceuticals, 777 Old Saw Mill River Road, Tarrytown, NY, 10591 6707, USA
    Science 294:1704-8. 2001
    ..Overexpression of MAFbx in myotubes produced atrophy, whereas mice deficient in either MAFbx or MuRF1 were found to be resistant to atrophy. These proteins are potential drug targets for the treatment of muscle atrophy...
  94. ncbi Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells
    Ian Chambers
    Institute for Stem Cell Research, University of Edinburgh, King s Buildings, West Mains Road, Edinburgh EH9 3JQ, Scotland
    Cell 113:643-55. 2003
    ..These findings establish a central role for Nanog in the transcription factor hierarchy that defines ES cell identity...
  95. pmc Comparing protein abundance and mRNA expression levels on a genomic scale
    Dov Greenbaum
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 8114, USA
    Genome Biol 4:117. 2003
    ..We also merge many of the available yeast protein-abundance datasets, using the resulting larger 'meta-dataset' to find correlations between protein and mRNA expression, both globally and within smaller categories...
  96. ncbi Post-transcriptional regulation of gene expression in trypanosomes and leishmanias
    Christine Clayton
    Zentrum für Molekualre Biologie der Universität Heidelberg, Im Neuenheimer Feld 282, D69120 Heidelberg, Germany
    Mol Biochem Parasitol 156:93-101. 2007
    ..Thus the regulation of gene expression is post-transcriptional. We here discuss recent results concerning the enzymes required for mRNA degradation, and components of the translation initiation machinery, and how both are regulated...
  97. ncbi Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays
    S A Bustin
    Academic Department of Surgery, St Bartholomew s and the Royal London School of Medicine and Dentistry, Queen Mary and Westfield College, London E1 1BB, UK
    J Mol Endocrinol 25:169-93. 2000
    ..It illustrates the usefulness of these assays by demonstrating the significantly different levels of transcription between individuals of the housekeeping gene family, glyceraldehyde-3-phosphate-dehydrogenase (GAPDH)...
  98. ncbi Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans
    B Wightman
    Department of Molecular Biology, Massachusetts General Hospital, Boston 02114
    Cell 75:855-62. 1993
    ..These data suggest a molecular mechanism for Lin-14p temporal gradient formation: the lin-4 RNAs base pair to sites in the lin-14 3'UTR to form multiple RNA duplexes that down-regulate lin-14 translation...
  99. ncbi WAF1, a potential mediator of p53 tumor suppression
    W S El-Deiry
    Oncology Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231
    Cell 75:817-25. 1993
    ..These studies define a gene whose expression is directly induced by p53 and that could be an important mediator of p53-dependent tumor growth suppression...
  100. pmc A microRNA polycistron as a potential human oncogene
    Lin He
    Cold Spring Harbor Laboratory, Watson School of Biological Sciences, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
    Nature 435:828-33. 2005
    ..Together, these studies indicate that non-coding RNAs, specifically microRNAs, can modulate tumour formation, and implicate the mir-17-92 cluster as a potential human oncogene...
  101. ncbi Mdm2 promotes the rapid degradation of p53
    Y Haupt
    Lautenberg Center for General and Tumor Immunology, The Hebrew University Haddassah Medical School, Jerusalem, Israel
    Nature 387:296-9. 1997
    ..During recovery from DNA damage, maximal Mdm2 induction coincides with rapid p53 loss. We propose that the Mdm2-promoted degradation of p53 provides a new mechanism to ensure effective termination of the p53 signal...

Research Grants72

  1. Role of Polyamines in MYCN-Amplified Neuroblastoma
    ANDRE BACHMANN; Fiscal Year: 2009
    ..The proposed methods and techniques to pursue this work are: Northern blot, RT-PCR, nuclear run-ons, messenger RNA half-life studies, Western blot, yeast two-hybrid, co-immunoprecipitation, GST-pull down, site-directed ..
  2. Epigenomic Events in Development of the Locus Coeruleus Noradrenergic Neurons
    Jan Krzysztof Blusztajn; Fiscal Year: 2012
    ..comprehensive characterization of the genome-wide developmental pattern of the LCNN transcriptome [for both messenger RNA (mRNA) and microRNA (miRNA)], the DNA CpG methylome, and genome-wide maps of methylated histone H3 (e.g...
  3. Regulation of Cardiac Kv Channel Expression
    Edwin S Levitan; Fiscal Year: 2013
    ..Experiments in the current funding period showed that Kv4.3 messenger RNA (mRNA), which limits Ito channel expression in humans, is destabilized in cultured cardiac myocytes by stretch ..
  4. HORMONAL REGULATION OF MESSENGER RNA STABILITY
    Daniel R Schoenberg; Fiscal Year: 2013
    ....
  5. Coronavirus RNA Replication
    DAVID ALVIN BRIAN; Fiscal Year: 2012
    ..Shared signals among coronaviruses for genome replication and for subgenomic messenger RNA synthesis are likely to contribute to virus recombination and the cross-species selection of new coronavirus ..
  6. microRNA and Down Syndrome
    Karl H Obrietan; Fiscal Year: 2010
    ..are generally regarded as negative regulators of gene expression that inhibit translation and/or promote messenger RNA (mRNA) degradation by base-pairing to complementary sequences within protein-coding mRNA transcripts...
  7. Microbial regulation of intestinal gene expression through microRNA
    Sushila Dalal; Fiscal Year: 2012
    ..Heat shock protein expression is known to be regulated by the 3'untranslated region (3'UTR) of its messenger RNA, the same region that microRNAs are known to target...
  8. Nonsense Mediated RNA Decay Regulation in Erythropoiesis &Thalassemia
    LAWRENCE BENJAMIN GARDNER; Fiscal Year: 2012
    ..We have identified a novel mechanism that controls the stability of messenger RNA, the carrier of genetic information from DNA to proteins in a cell...
  9. Suppression of the Interferon Response by the Hepatitis C Virus
    FRANCIS VINCENT CHISARI; Fiscal Year: 2010
    ..shown to be much less sensitive to inhibition by PKR activation than other IRES elements and capped cellular messenger RNA. In Specific Aim 1 in this application, we will identify the molecular nature of the HCV-induced/related ..
  10. 2012 Fragile X and Autism-Related Disorders: From Basic Neuroscience to Improved
    ELIZABETH MARA BERRY-KRAVIS; Fiscal Year: 2012
    ..FMRP has been found to be involved in the regulation of specific messenger RNA transport, localization and expression in neurons...
  11. The Role of a New Cleavage and Polyadenylation Specificity Factor (CPSF73-II)
    Qingshun Q Li; Fiscal Year: 2010
    ..be applicable to other higher eukaryotes, including humans, in understanding the gene's contributions in messenger RNA processing which is a critical step in gene expression and regulation...
  12. A Novel Epigenetic Gene Silencing Technology
    MING MING contact ZHOU; Fiscal Year: 2010
    ..RNA interference (RNAi) that blocks gene translation to protein by small interfering RNA (siRNA)-triggered messenger RNA destruction has had transformative impact in research and also generated enormous excitement and hope for new ..
  13. Defining the messenger RNP code in the brain
    EUGENE WEI MING YEO; Fiscal Year: 2013
    ..applicant): RNA binding proteins (RBPs) interact with functional RNA elements embedded within pre- and mature messenger RNA to form messenger ribonucleoprotein (mRNP) complexes...
  14. Polyvalent siRNA-Gold Nanoparticle Constructs to Eradicate Glioma
    Emily S Day; Fiscal Year: 2012
    ..In RNAi, short double-stranded ribonucleic acid (RNA) sequences delivered to a cell induce the encoded messenger RNA to be degraded, thereby silencing gene expression...
  15. Small heat shock proteins in smooth muscle plasticity
    William T Gerthoffer; Fiscal Year: 2013
    ..b>Messenger RNA decay, RNA cleavage activity and miRISC protein composition will be assayed after knockdown of HSP27...
  16. Coupling of Transcription with Pre-mRNA Metabolism
    DAVID LEONARD BENTLEY; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Making messenger RNA (mRNA), the primary event in expression of protein coding genes is central to the life of all cells and its corruption is a hallmark of cancer cells...
  17. Ribozymes for studies and treatment of cytomegalovirus infections
    Fenyong Liu; Fiscal Year: 2012
    ..g. HCMV messenger RNA and the genetic material of HIV which is made of RNA...
  18. Chemoprotective effects of natural products on colonic adult stem cells
    Bhimanagouda S Patil; Fiscal Year: 2013
    ..to the development of colon cancer, it is vital that the effect of chemopreventive diets on microRNAs, their messenger RNA (mRNA) targets, and epigenetic modifications on both the histone and DNA levels in intestinal stem cells be ..
  19. Micro RNA-146a (miRNA-146a) signaling in Alzheimers disease (AD)
    Walter J Lukiw; Fiscal Year: 2013
    ..Micro RNA (miRNA)-mediated messenger RNA (mRNA) interference is a newly discovered genetic mechanism involved in the regulation of gene expression at ..
  20. mRNA Capping Enzymes
    STEWART H SHUMAN; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): The m7GpppN cap is a defining feature of eukaryal messenger RNA that is required for mRNA stability and efficient translation...
  21. Global analysis of mRNA decay in Bacillus subtilis
    David H Bechhofer; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Our laboratory seeks to understand the process of messenger RNA decay in the model Gram-positive bacterium, Bacillus subtilis...
  22. Deciphering the Composition of oskar mRNP via in vivo Fluorescence Imaging
    DIANA BRATU; Fiscal Year: 2010
    Coupled with temporally regulated translation, subcellular localization of messenger RNA is an important mechanism of post-transcriptional regulation of gene expression...
  23. Mechanism of HigB-mediated ribosome-dependent mRNA degradation
    MARC ANTHONY SCHURECK; Fiscal Year: 2013
    ..vulgaris. HigB cleaves ribosome-bound messenger RNA (mRNA) at adenosine-rich sequences...
  24. POSTTRANSCRIPTIONAL REGULATION OF ONCOGENE MESSENGER RNA
    GARY ALAN BREWER; Fiscal Year: 2012
    ..We are studying the mechanisms by which AUF1 controls these genes, which will help us to understand processes by which normal cells can become cancer cells. ..
  25. High-Throughput Assay for the Discovery of Small Molecule Inhibitors of microRNA
    Alexander Deiters; Fiscal Year: 2011
    ..They bind to untranslated regions in messenger RNA and induce a down-regulation of their transcription...
  26. Recognition of Regulatory and Pathogenic RNA by Muscleblind Zinc Fingers
    PETER EDWIN WRIGHT; Fiscal Year: 2010
    ..type 2 myotonic dystrophy, diseases that are associated with CUG and CCUG repeat expansions in untranslated messenger RNA. The expanded RNA repeats accumulate in nuclear foci that aberrantly sequester muscleblind and thereby disrupt ..
  27. 2011 Eukaryotic mRNA Processing Conference
    David J Stewart; Fiscal Year: 2011
    ..in August 2009 and attracted 335 scientists internationally, who are actively investigating various aspects of messenger RNA maturation in eukaryotic cells, using genetic, biochemical, molecular, and cell biological approaches...
  28. THE ORGANIZATION OF ANIMAL CELL NUCLEI
    Joseph G Gall; Fiscal Year: 2013
    ..the synthesis of RNA by the chromosomes (transcription) and the processing of this RNA into the mature messenger RNA (splicing)...
  29. Toward a comprehensive functional annotation of the human genome
    Richard M Myers; Fiscal Year: 2013
    ..factors and major cofactors with high resolution in two or more cell types;2) map and quantify all messenger RNA transcripts, microRNAs and other non-ribosomal RNAs in more than 300 well-defined, uncultured cell types;3) ..
  30. Fragile X Mental Retardation Protein translation regulator function: interactions
    MIHAELA R MIHAILESCU; Fiscal Year: 2013
    ..FMRP is an RNA binding protein involved in the transport and translation regulation of specific messenger RNA (mRNA) targets...
  31. Site-directed RNA editing: a new method to correct disease causing mutations
    Joshua J C Rosenthal; Fiscal Year: 2013
    ..As a target for gene therapy, mRNA offers advantages over DNA. Messenger RNA is cytoplasmic, a readily available substrate, and unlike DNA in which 'mistakes'will be maintained, ..
  32. Structural basis of mRNA decapping by Dcp2: conformational changes &co-activator
    JEFFREY SCOTT MUGRIDGE; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Cellular regulation of messenger RNA (mRNA) is crucial for proper gene expression. One of the major pathways used to regulate eukaryotic mRNA is 5'-to-3'decay...
  33. Gene silencing therapeutics for chronic infections in cystic fibrosis
    DAVID ELIHU GREENBERG; Fiscal Year: 2013
    ..These molecules block messenger RNA and block the formation of protein...
  34. The Role of DEAD-box Proteins in Gene Expression
    Elizabeth J Tran; Fiscal Year: 2013
    ..Numerous studies have shown that steps such as transcription, messenger RNA (mRNA) processing and mRNA decay, are highly coupled, forming an intricate molecular circuit for regulation of ..
  35. Viral and Microbial RNA Modifying Enzymes
    STEWART H SHUMAN; Fiscal Year: 2013
    ..This project aims to illuminate the mechanisms and structures of viral enzymes that cap the 5'end of messenger RNA. The m7GpppN cap is a distinctive feature of eukaryal cellular and viral mRNA that is required for mRNA ..
  36. Cocaine Regulation of miRNAs in Rats with Differing Vulnerability to Drug Abuse
    Stanley J Watson; Fiscal Year: 2012
    ..expression occur following either acute or repeated drug use or whether any miRNA might underlie any known messenger RNA (or protein) changes known to occur following drugs use (or abuse)...
  37. Biogenesis of Small Ribonucleoproteins
    A Gregory Matera; Fiscal Year: 2013
    ..As key elements of the spliceosome, the Sm-class small nuclear (sn)RNPs are essential for pre-messenger RNA splicing...
  38. Post-transcriptional control of inflammatory gene expression
    Thomas A Hamilton; Fiscal Year: 2013
    ..to cancer development and spread and uses a mechanism that involves altering the rate at which the chemokine messenger RNA is degraded...
  39. Kinetoplastid SL RNA biogenesis
    David A Campbell; Fiscal Year: 2013
    ..of the spliced leader (SL) RNA, a small RNA that contributes the 5'-end sequence to every nuclear messenger RNA by a trans-splicing reaction and is conserved extraordinarily at the primary sequence level throughout the ..
  40. Regulation of AU-rich element-mediated mRNA decay
    Ching Yi Chen; Fiscal Year: 2013
    ..PUBLIC HEALTH RELEVANCE: Aberrant regulation of messenger RNA (mRNA) stability has been implicated in various pathological processes...
  41. Mechanism of Actin mRNA Localization and Localized Translation in Neurons
    Robert H Singer; Fiscal Year: 2013
    ..Over the years of this grant we discovered that an important mode of regulation is the ability of messenger RNA to become localized at specific regions in cells where synthesis of specific proteins can be spatially ..
  42. REGULATION OF GENE EXPRESSION IN CARTILAGE
    Linda Sandell; Fiscal Year: 2009
    ..period are focused on deciphering the regulation chondrogenesis at the level of gene transcription, precursor messenger RNA (pre-mRNA) alternative splicing and protein synthesis...
  43. STRUCTURE AND FUNCTION OF TRANSFER RIBONUCLEIC ACIDS
    Uttam L RajBhandary; Fiscal Year: 2013
    ..which involves the translation of genetic information present in the form of nucleotide sequences in a messenger RNA into amino acid sequences of a protein, is one of the important steps in gene expression...
  44. Micro-RNAs in the Sclera: Role in Ocular Growth, and Implications for Myopia
    Ravikanth Metlapally; Fiscal Year: 2013
    ..We expect that the proposed studies will set up a strong platform for deeper mechanistic investigations involving miRNAs, and will establish some potential scleral targets for manipulating ocular growth. ..
  45. New tools for targeting sympathetic neurons that control blood pressure
    John P Horn; Fiscal Year: 2013
    ..b>Messenger RNA will be purified from manually sorted identified neurons, then amplified and analyzed with microarrays to ..
  46. Comprehensive Characterization and Classification of the Human Transcriptome
    THOMAS RAYMOND GINGERAS; Fiscal Year: 2011
    ..However, the utility of these and other genomic resources are dependent upon having a complete and high quality catalogue of transcribed regions. ..
  47. Mechanism and targets of non-stop decay in eukaryotic translation
    KRISTIN SMITH-KOUTMOU; Fiscal Year: 2013
    ..b>Messenger RNA (mRNA) is surveilled during translation by at least three quality control mechanisms committed to the ..
  48. RNA recognition by maternal gene silencers in nematodes
    SEAN PATRICK RYDER; Fiscal Year: 2012
    ..provided by applicant): The primary goal of my lab is to define the basis by which non-coding elements in messenger RNA sequences define differential regulation of gene expression...
  49. Dissecting Translational Regulation by Genome-Wide Mapping of Initiation Factors
    OLIVIA SELFRIDGE RISSLAND; Fiscal Year: 2013
    ..expression is post-transcriptional regulation, which is normally mediated through specific sequences in the messenger RNA (mRNA) itself and often results in changes in mRNA stability and/or modulation of translational initiation...
  50. spFRET for Expression Profiling mRNA: Discovering Markers for Stroke Diagnosis
    Steven Allan Soper; Fiscal Year: 2013
    ..The molecular assay and novel hardware will be used to evaluate the potential of a messenger RNA marker panel as an unprecedented blood-based test (using peripheral blood mononucleated cells, PBMC) for the ..
  51. Attomole-Level High-Throughput Genomics
    PATRICE MARIE MILOS; Fiscal Year: 2012
    ....
  52. Control of protective immunity by innate pathways sensing bacterial viability
    JULIE MAGARIAN BLANDER; Fiscal Year: 2013
    ..We identified the signature molecule, prokaryotic messenger RNA, which alerts professional phagocytic cells of the innate immune system to the presence of viable microbes in ..
  53. Roles of MiR-17-92 Cluster MicroRNAs in K-Ras-Induced Pancreatic Tumorigenesis
    BRIAN JOSEPH QUATTROCHI; Fiscal Year: 2013
    ..Through the use of multiple target prediction algorithms and data from a messenger RNA microarray profile of PDECs expressing KrasG12D, probable targets of the miR-17~92 cluster that are expressed ..
  54. BIOCHEMISTRY OF REGULATED PRE-MRNA SPLICING/DROSOPHILA
    Donald C Rio; Fiscal Year: 2010
    ..of the research proposed in this grant is to elucidate biochemical mechanisms used to regulate splicing of messenger RNA precursors (pre-mRNA) during development in the fruit fly,Drosophila melanogaster...
  55. Mechanism and functions of small RNA pathways in Neurospora
    Yi Liu; Fiscal Year: 2013
    ..miRNAs) and various small interfering RNAs (siRNAs), associate with and guide Argonaute family proteins to messenger RNA targets, resulting in the silencing of gene expression in diverse biological processes...
  56. Binding and Splicing mRNA
    DANIEL AALBERTS; Fiscal Year: 2009
    ..provided by applicant): Gene expression is often regulated by the binding of small RNAs or proteins to messenger RNA;examples include mRNA splicing, microRNA, and degradation signals...
  57. Regulation of translation initiation in eukaryotes
    Vincent P Mauro; Fiscal Year: 2010
    This proposal describes experiments to investigate the scope and importance of base-pairing between messenger RNA (mRNA) and ribosomal RNA (rRNA) as a mechanism for regulating translation in eukaryotes...
  58. Erythropoietin-encoding mRNA for treatment of anemia
    Katalin Kariko; Fiscal Year: 2010
    ..The product we are developing, a structurally-modified messenger RNA (the intermediary between DNA and protein), is an alternative to protein delivery and gene therapy that will ..
  59. Elucidation of Integrator's Function
    Ramin Shiekhattar; Fiscal Year: 2013
    ..Aberrant regulation of small nuclear RNA processing could result in defective messenger RNA processing through deregulation of splicesome and may lead to cellular transformation and oncogenesis...
  60. INITIATION OF MRNA DECAY IN BACILLUS SUBTILIS
    David H Bechhofer; Fiscal Year: 2010
    Project Summary: Our laboratory seeks to understand the control of messenger RNA decay in the gram-positive bacterium, Bacillus subtilis...
  61. Trans-Splicing in Drosophila
    Brenton R Graveley; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Abstract: Pre-messenger RNA (pre-mRNA) splicing is a process in which introns are removed to join exons together...
  62. Cancer Genomics Center
    Raju Kucherlapati; Fiscal Year: 2009
    ..Our proposed approach also has the ability to generate additional useful data for tumor and patient stratification. ..
  63. CONTROL OF CELL FUNCTION VIA SELECTIVE MRNA TRANSLATION
    Lee Gehrke; Fiscal Year: 2002
    ..The immediate goals of the work are to define the biochemical basis of selective and competitive messenger RNA (mRNA) translation and to analyze the structure and function of specific ribonucleoprotein complexes...
  64. VIRAL PROTEINS IN ROTAVIRUS REPLICATION
    John Patton; Fiscal Year: 1991
    ..The replication of each segment of the genome proceeds in an asymmetrical manner with viral messenger RNA (mRNA; plus- strand RNA) serving as the template for minus-strand RNA to produce dsRNA...
  65. DNA-crosslinked gels: New advanced biomaterials
    NOSHIR LANGRANA; Fiscal Year: 2006
    ..allows for the design of gels that are degraded by particular restriction endonucleases or by particular messenger RNA strands...
  66. Functional studies of the Fragile X Mental Retardation Protein: switching from re
    Mihaela Mihailescu; Fiscal Year: 2009
    ..FMRP is an RNA binding protein believed to be involved in the transport and translation regulation of specific messenger RNA (mRNA) targets...
  67. HUMAN PAPILLOMAVIRUS GENE EXPRESSION IN CERVICAL CANCER
    DAVID SMOTKIN; Fiscal Year: 1992
    ..It is proposed that: 1. HPV messenger RNA will be mapped and quantitated in benign warts and invasive tumors...
  68. MOLECULAR GENETICS OF C. ELEGANS RNA POLYMERASE II
    DONALD RIDDLE; Fiscal Year: 1990
    ..The enzyme RNA polymerase II, which is responsible for the synthesis of messenger RNA, plays such a central role in cellular activity that its expression, control and activity must be examined if ..
  69. POLYADENYLATION OF MESSENGER RNA PRECURSORS REGULATION
    PHILLIP SHARP; Fiscal Year: 1990
    Polyadenylation of messenger RNA precursors is a critical step in the synthesis of mRNAs in eucaryotic organisms and an event that is regulated for some transcription units...
  70. FUNCTIONAL SPLICEOSOME AND EXTRINSIC SPLICING FACTORS
    Ren Jang Lin; Fiscal Year: 2006
    DESCRIPTION (provided by applicant): The majority of messenger RNA sequences in eukaryotes are in fragments that need to be correctly spliced in order to be translated into functional proteins...
  71. IMMOBILIZED CELL FREE TRANSLATION SYSTEMS
    William Scouten; Fiscal Year: 1992
    ..of this research is to prepare an immobilized protein synthesis system based on in vitro translation of messenger RNA. This research is, in a way, an extension of the investigators laboratory's interest in solid phase ..
  72. NUCLEOCYTOPLASMIC TRAFFICKING
    David Goldfarb; Fiscal Year: 1992
    ..Precursor RNAs are retained in the nucleus, while processed messenger RNA, transfer RNA and ribosomal subunits are transported to the cytoplasm...