introns

Summary

Summary: Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.

Top Publications

  1. pmc Parallel loss of plastid introns and their maturase in the genus Cuscuta
    Joel R McNeal
    Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
    PLoS ONE 4:e5982. 2009
  2. pmc tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence
    T M Lowe
    Department of Genetics, Washington University School of Medicine, 660 South Euclid, Box 8232, St Louis, MO 63110, USA
    Nucleic Acids Res 25:955-64. 1997
  3. pmc The transcriptional landscape of the yeast genome defined by RNA sequencing
    Ugrappa Nagalakshmi
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Science 320:1344-9. 2008
  4. pmc Genome-wide mapping of alternative splicing in Arabidopsis thaliana
    Sergei A Filichkin
    Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USA
    Genome Res 20:45-58. 2010
  5. pmc Conservation and divergence of methylation patterning in plants and animals
    Suhua Feng
    Howard Hughes Medical Institute, Department of Molecular, Cell and Developmental Biology, and Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 107:8689-94. 2010
  6. ncbi Gene prediction with a hidden Markov model and a new intron submodel
    Mario Stanke
    Institut fur Mikrobiologie und Genetik, Abteilung Bioinformatik, Universitat Gottingen, Gottingen, Germany
    Bioinformatics 19:ii215-25. 2003
  7. pmc Origin and evolution of spliceosomal introns
    Igor B Rogozin
    National Center for Biotechnology Information NLM NIH, 8600 Rockville Pike, Bldg, 38A, Bethesda, MD 20894, USA
    Biol Direct 7:11. 2012
  8. ncbi The genome sequence of Schizosaccharomyces pombe
    V Wood
    The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nature 415:871-80. 2002
  9. ncbi Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals
    Gene Yeo
    Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue Building 68 223, Cambridge, MA 02319, USA
    J Comput Biol 11:377-94. 2004
  10. ncbi Accelerating the tempo of the segmentation clock by reducing the number of introns in the Hes7 gene
    Yukiko Harima
    Institute for Virus Research, Kyoto University, Kyoto 606 8507, Japan
    Cell Rep 3:1-7. 2013

Research Grants

Detail Information

Publications343 found, 100 shown here

  1. pmc Parallel loss of plastid introns and their maturase in the genus Cuscuta
    Joel R McNeal
    Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
    PLoS ONE 4:e5982. 2009
    ..highly conserved across most land plants and their closest relatives, streptophyte algae, with nearly all plastid introns having invaded the genome in their common ancestor at least 450 million years ago...
  2. pmc tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence
    T M Lowe
    Department of Genetics, Washington University School of Medicine, 660 South Euclid, Box 8232, St Louis, MO 63110, USA
    Nucleic Acids Res 25:955-64. 1997
    ..tRNAscan-SE searches at approximately 30 000 bp/s. Additional extensions to tRNAscan-SE detect unusual tRNA homologues such as selenocysteine tRNAs, tRNA-derived repetitive elements and tRNA pseudogenes...
  3. pmc The transcriptional landscape of the yeast genome defined by RNA sequencing
    Ugrappa Nagalakshmi
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Science 320:1344-9. 2008
    The identification of untranslated regions, introns, and coding regions within an organism remains challenging...
  4. pmc Genome-wide mapping of alternative splicing in Arabidopsis thaliana
    Sergei A Filichkin
    Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USA
    Genome Res 20:45-58. 2010
    ..Deep transcriptome sequencing confirmed a majority of annotated introns and identified thousands of novel alternatively spliced mRNA isoforms...
  5. pmc Conservation and divergence of methylation patterning in plants and animals
    Suhua Feng
    Howard Hughes Medical Institute, Department of Molecular, Cell and Developmental Biology, and Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 107:8689-94. 2010
    ..In addition, the Dnmt1 cofactor Uhrf1 has a conserved function in maintaining CG methylation in both transposons and gene bodies in the mouse, Arabidopsis, and zebrafish genomes...
  6. ncbi Gene prediction with a hidden Markov model and a new intron submodel
    Mario Stanke
    Institut fur Mikrobiologie und Genetik, Abteilung Bioinformatik, Universitat Gottingen, Gottingen, Germany
    Bioinformatics 19:ii215-25. 2003
    ..Gene finding programs have achieved relatively high accuracy on short genomic sequences but do not perform well on longer sequences with an unknown number of genes in them. Here existing programs tend to predict many false exons...
  7. pmc Origin and evolution of spliceosomal introns
    Igor B Rogozin
    National Center for Biotechnology Information NLM NIH, 8600 Rockville Pike, Bldg, 38A, Bethesda, MD 20894, USA
    Biol Direct 7:11. 2012
    Evolution of exon-intron structure of eukaryotic genes has been a matter of long-standing, intensive debate. The introns-early concept, later rebranded 'introns first' held that protein-coding genes were interrupted by numerous introns ..
  8. ncbi The genome sequence of Schizosaccharomyces pombe
    V Wood
    The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nature 415:871-80. 2002
    ..Some 43% of the genes contain introns, of which there are 4,730...
  9. ncbi Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals
    Gene Yeo
    Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue Building 68 223, Cambridge, MA 02319, USA
    J Comput Biol 11:377-94. 2004
    ..Our best models out-perform previous probabilistic models in the discrimination of human 5' (donor) and 3' (acceptor) splice sites from decoys. Finally, we discuss mechanistically motivated ways of comparing models...
  10. ncbi Accelerating the tempo of the segmentation clock by reducing the number of introns in the Hes7 gene
    Yukiko Harima
    Institute for Virus Research, Kyoto University, Kyoto 606 8507, Japan
    Cell Rep 3:1-7. 2013
    ..Here, we show that reducing the number of introns within the Hes7 gene shortens the delay and results in a more rapid tempo of both Hes7 oscillation and somite ..
  11. pmc Differential chromatin marking of introns and expressed exons by H3K36me3
    Paulina Kolasinska-Zwierz
    The Gurdon Institute and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
    Nat Genet 41:376-81. 2009
    ..We also observe a novel pattern: exons are preferentially marked with H3K36me3 relative to introns. H3K36me3 exon marking is dependent on transcription and is found at lower levels in alternatively spliced exons, ..
  12. ncbi Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas
    Alexandra Z Worden
    Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039 USA
    Science 324:268-72. 2009
    ..Analyses of the Micromonas genomes offer valuable insights into ecological differentiation and the dynamic nature of early plant evolution...
  13. ncbi The sequence of the human genome
    J C Venter
    Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA
    Science 291:1304-51. 2001
    ..Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA...
  14. ncbi 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
    ..A global survey of messenger RNA splicing events identified 94,241 splice junctions (4096 of which were previously unidentified) and showed that exon skipping is the most prevalent form of alternative splicing...
  15. ncbi The amphioxus genome and the evolution of the chordate karyotype
    Nicholas H Putnam
    Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
    Nature 453:1064-71. 2008
    ..These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution...
  16. ncbi CLIP identifies Nova-regulated RNA networks in the brain
    Jernej Ule
    Howard Hughes Medical Institute, Rockefeller University, New York, NY 10021, USA
    Science 302:1212-5. 2003
    ..Thus, CLIP reveals that Nova coordinately regulates a biologically coherent set of RNAs encoding multiple components of the inhibitory synapse, an observation that may relate to the cause of abnormal motor inhibition in POMA...
  17. ncbi A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig
    Anne Sophie Van Laere
    Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala University, BMC, Box 597, SE 751 24 Uppsala, Sweden
    Nature 425:832-6. 2003
    ..The result supports the long-held view that regulatory mutations are important for controlling phenotypic variation...
  18. ncbi Friedreich's ataxia: autosomal recessive disease caused by an intronic GAA triplet repeat expansion
    V Campuzano
    Department de Genetica, University of Valencia, Spain
    Science 271:1423-7. 1996
    ..A few FRDA patients were found to have point mutations in X25, but the majority were homozygous for an unstable GAA trinucleotide expansion in the first X25 intron...
  19. pmc Group II introns: mobile ribozymes that invade DNA
    Alan M Lambowitz
    Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, USA
    Cold Spring Harb Perspect Biol 3:a003616. 2011
    Group II introns are mobile ribozymes that self-splice from precursor RNAs to yield excised intron lariat RNAs, which then invade new genomic DNA sites by reverse splicing...
  20. 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...
  21. pmc Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate
    France Denoeud
    Commissariat a l Energie Atomique, Institut de Génomique, Genoscope, Evry, France
    Science 330:1381-5. 2010
    ..This rapidly evolving animal lineage thus offers unique perspectives on the level of genome plasticity. It also illuminates issues as fundamental as the mechanisms of intron gain...
  22. pmc Identification of mammalian microRNA host genes and transcription units
    Antony Rodriguez
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
    Genome Res 14:1902-10. 2004
    ..We identified miRNAs within introns of 90 protein-coding genes with a broad spectrum of molecular functions, and in both introns and exons of 66 mRNA-..
  23. pmc Noisy splicing drives mRNA isoform diversity in human cells
    Joseph K Pickrell
    Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
    PLoS Genet 6:e1001236. 2010
    ..We estimate that the average intron has a splicing error rate of approximately 0.7% and show that introns in highly expressed genes are spliced more accurately, likely due to their shorter length...
  24. ncbi Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization
    Nicholas H Putnam
    Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
    Science 317:86-94. 2007
    ..Analysis of diverse pathways suggests that these gene "inventions" along the lineage leading to animals were likely already well integrated with preexisting eukaryotic genes in the eumetazoan progenitor...
  25. pmc Intronic microRNA precursors that bypass Drosha processing
    J Graham Ruby
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 448:83-6. 2007
    ..Here we identify an alternative pathway for miRNA biogenesis, in which certain debranched introns mimic the structural features of pre-miRNAs to enter the miRNA-processing pathway without Drosha-mediated ..
  26. ncbi Human hypertension caused by mutations in WNK kinases
    F H Wilson
    Howard Hughes Medical Institute Yale University School of Medicine, Boyer Center for Molecular Medicine, 295 Congress Avenue, New Haven, CT 06510 USA
    Science 293:1107-12. 2001
    ..WNK1 is cytoplasmic, whereas WNK4 localizes to tight junctions. The WNK kinases and their associated signaling pathway(s) may offer new targets for the development of antihypertensive drugs...
  27. pmc Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome
    Alekos Athanasiadis
    Department of Biological Sciences, Lehigh University Bethlehem, Pennsylvania, USA
    PLoS Biol 2:e391. 2004
    ..14,500 sites, and our data further suggest that the vast majority of pre-mRNAs (greater than 85%) are targeted in introns by the editing machinery...
  28. pmc Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB
    Miriam Llorian
    Department of Biochemistry, University of Cambridge, Cambridge, UK
    Nat Struct Mol Biol 17:1114-23. 2010
    ..Our results show that PTB, an archetypal splicing repressor, has variable splicing activity that predictably depends upon its binding location with respect to target exons...
  29. ncbi The ClosTron: a universal gene knock-out system for the genus Clostridium
    John T Heap
    Institute of Infection, Immunity and Inflammation, School of Molecular Medical Sciences, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
    J Microbiol Methods 70:452-64. 2007
    ..The procedure is highly efficient and reproducible, and should revolutionize functional genomic studies in clostridia...
  30. pmc A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters
    Serge Saxonov
    Biomedical Informatics Program, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 103:1412-7. 2006
    ....
  31. ncbi Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution
    Brian T Wilhelm
    Cancer Research UK Fission Yeast Functional Genomics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
    Nature 453:1239-43. 2008
    ..or exon-intron junctions give unique insight into a surprising variability in splicing efficiency across introns, genes and conditions...
  32. pmc Understanding splicing regulation through RNA splicing maps
    Joshua T Witten
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge, UK, CB2 0QH
    Trends Genet 27:89-97. 2011
    ..Here, we discuss how insights from RNA splicing maps of different RBPs inform the mechanistic models of splicing regulation...
  33. ncbi The origins of genome complexity
    Michael Lynch
    Department of Biology, Indiana University, Bloomington, IN 47405, USA
    Science 302:1401-4. 2003
    ..resulting from the retention of duplicate genes, and more abrupt increases in the abundance of spliceosomal introns and mobile genetic elements...
  34. pmc Role of RNA structure in regulating pre-mRNA splicing
    M Bryan Warf
    Institute of Molecular Biology, and Department of Chemistry, University of Oregon, Eugene, Oregon 97403, USA
    Trends Biochem Sci 35:169-78. 2010
    Pre-mRNA splicing involves removing non-coding introns from RNA transcripts. It is carried out by the spliceosome, along with other auxiliary factors...
  35. pmc Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae)
    Andrew J Alverson
    Department of Biology, Indiana University, USA
    Mol Biol Evol 27:1436-48. 2010
    ..The relatively compact Citrullus mitochondrial genome actually contains more and longer genes and introns, longer segmental duplications, and more discernibly nuclear-derived DNA...
  36. ncbi Mobile group II introns
    Alan M Lambowitz
    Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, Section of Molecular Genetics and Microbiology, University of Texas at Austin, Texas 78712, USA
    Annu Rev Genet 38:1-35. 2004
    Mobile group II introns, found in bacterial and organellar genomes, are both catalytic RNAs and retrotransposable elements...
  37. pmc Rates of in situ transcription and splicing in large human genes
    Jarnail Singh
    Department of Molecular Genetics, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
    Nat Struct Mol Biol 16:1128-33. 2009
    ..8 kb min(-1) and is similar whether transcribing long introns or exon-rich regions...
  38. pmc Muscleblind proteins regulate alternative splicing
    Thai H Ho
    Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
    EMBO J 23:3103-12. 2004
    ..The results are consistent with a mechanism for DM pathogenesis in which expanded repeats cause a loss of MBNL and/or gain of CELF activities, leading to misregulation of alternative splicing of specific pre-mRNA targets...
  39. ncbi Genome-wide analyses of alternative splicing in plants: opportunities and challenges
    W Brad Barbazuk
    Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA
    Genome Res 18:1381-92. 2008
    ..This review summarizes recent analyses of AS in plants, discusses the importance of further analysis, and suggests directions for future efforts...
  40. ncbi Variant of transcription factor 7-like 2 (TCF7L2) gene confers risk of type 2 diabetes
    Struan F A Grant
    deCODE Genetics, Sturlugata 8, 101 Reykjavik, Iceland
    Nat Genet 38:320-3. 2006
    ..It is thought to act through regulation of proglucagon gene expression in enteroendocrine cells via the Wnt signaling pathway...
  41. pmc Splicing-dependent RNA polymerase pausing in yeast
    Ross D Alexander
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, King s Buildings, Edinburgh EH9 3JR, UK
    Mol Cell 40:582-93. 2010
    ..Phosphorylated polymerase also accumulates around the 3' splice sites of constitutively expressed, endogenous yeast genes. We propose that transcriptional pausing is imposed by a checkpoint associated with cotranscriptional splicing...
  42. ncbi Use of computer-designed group II introns to disrupt Escherichia coli DExH/D-box protein and DNA helicase genes
    Jiri Perutka
    Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, and Section of Molecular, Genetics and Microbiology, School of Biological Sciences, University of Texas at Austin, Austin, TX 78712, USA
    J Mol Biol 336:421-39. 2004
    Mobile group II introns are site-specific retroelements that use a novel mobility mechanism in which the excised intron RNA inserts directly into a DNA target site and is then reverse transcribed by the associated intron-encoded protein...
  43. pmc Stochastic noise in splicing machinery
    Eugene Melamud
    Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 37:4873-86. 2009
    ..abundance can be predicted by a simple stochastic noise model that takes into account two factors: the number of introns in a gene and the expression level of a gene...
  44. ncbi Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells
    Matthew C Lorincz
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Nat Struct Mol Biol 11:1068-75. 2004
    ..As the methylated region adopts a closed chromatin structure in vivo, we propose that dense intragenic DNA methylation in mammalian cells initiates formation of a chromatin structure that reduces the efficiency of Pol II elongation...
  45. ncbi Control of stress-dependent cardiac growth and gene expression by a microRNA
    Eva van Rooij
    Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390 9148, USA
    Science 316:575-9. 2007
    ..Thus, the alphaMHC gene, in addition to encoding a major cardiac contractile protein, regulates cardiac growth and gene expression in response to stress and hormonal signaling through miR-208...
  46. pmc On the utility of short intron sequences as a reference for the detection of positive and negative selection in Drosophila
    John Parsch
    Department of Biology II, University of Munich, Planegg Martinsried, Germany
    Mol Biol Evol 27:1226-34. 2010
    ..For a set of 119 Drosophila melanogaster genes containing 195 short introns (<or=120 bp), we analyzed polymorphism and divergence at 1) 4-fold synonymous sites, 2) all sites of introns &..
  47. ncbi Long intronic noncoding RNA transcription: expression noise or expression choice?
    Rodrigo Louro
    Departamento de Bioquimica, Instituto de Quimica, Universidade de Sao Paulo, 05508 900 Sao Paulo, SP, Brazil
    Genomics 93:291-8. 2009
    ..Deciphering nature's choice of different types of messages conveyed by ncRNAs will shed light on the RNA-based layer of regulatory processes in eukaryotic cells...
  48. ncbi Distributions of exons and introns in the human genome
    Meena Kishore Sakharkar
    Nanyang Centre for Supercomputing and Visualisation, N3 2c 113b, 50 Nanyang Avenue, Nanyang Technological University, Singapore
    In Silico Biol 4:387-93. 2004
    ..The 26,564 annotated genes in the human genome (build October, 2003) contain 233,785 exons and 207,344 introns. On average, there are 8.8 exons and 7.8 introns per gene...
  49. pmc The Tpr protein regulates export of mRNAs with retained introns that traffic through the Nxf1 pathway
    John H Coyle
    Myles H Thaler Center for AIDS and Human Retrovirus Research and Department of Microbiology, University of Virginia, Charlottesville, Virginia 22908, USA
    RNA 17:1344-56. 2011
    ..To study the role of Tpr in export of mRNA with retained introns, we used reporters in which the mRNA was exported either via the Nxf1/Nxt1 pathway using a CTE or via the Crm1 ..
  50. ncbi Variation in FTO contributes to childhood obesity and severe adult obesity
    Christian Dina
    CNRS 8090 Institute of Biology, Pasteur Institute, Lille, France
    Nat Genet 39:724-6. 2007
    ..The at-risk haplotype yields a proportion of attributable risk of 22% for common obesity. We conclude that FTO contributes to human obesity and hence may be a target for subsequent functional analyses...
  51. pmc Mechanisms of intron gain and loss in Drosophila
    Paul Yenerall
    Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
    BMC Evol Biol 11:364. 2011
    It is widely accepted that orthologous genes have lost or gained introns throughout evolution. However, the specific mechanisms that generate these changes have proved elusive...
  52. pmc The in vivo kinetics of RNA polymerase II elongation during co-transcriptional splicing
    Yehuda Brody
    The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar Ilan University, Ramat Gan, Israel
    PLoS Biol 9:e1000573. 2011
    ..We generated a family of inducible gene constructs containing increasing numbers of introns and exons, which were stably integrated in human cells to serve as actively transcribing gene loci...
  53. ncbi Impaired minor tri-snRNP assembly generates differential splicing defects of U12-type introns in lymphoblasts derived from a type I SMA patient
    Nawal Boulisfane
    Institut de Génétique Moléculaire de Montpellier IGMM, CNRS UMR 5535 IFR122, Université Montpellier I and II, 1919 Route de Mende, 34293 Montpellier Cedex 5, France
    Hum Mol Genet 20:641-8. 2011
    ..We found also that splicing of some, but not all, minor introns is inhibited in these cells, demonstrating links between SMN deficiency and differential alterations of splicing ..
  54. pmc Structure and activity of putative intronic miRNA promoters
    Alex Mas Monteys
    Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52242, USA
    RNA 16:495-505. 2010
    ..These data support complex regulation of intronic miRNA expression, and have relevance to disregulation in disease settings...
  55. ncbi A muscleblind knockout model for myotonic dystrophy
    Rahul N Kanadia
    Department of Molecular Genetics and Microbiology, Powell Gene Therapy Center, Gainesville, FL 32610, USA
    Science 302:1978-80. 2003
    ..Our results support the hypothesis that manifestations of DM can result from sequestration of specific RNA binding proteins by a repetitive element expansion in a mutant RNA...
  56. ncbi How introns influence and enhance eukaryotic gene expression
    Hervé Le Hir
    Howard Hughes Medical Institute, Department of Biochemistry, MS009 Brandeis University, Waltham, MA 02454, USA
    Trends Biochem Sci 28:215-20. 2003
    ..This review summarizes recent progress in our understanding of how introns and the act of their removal by the spliceosome can influence and enhance almost every step of mRNA metabolism...
  57. pmc Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts
    Jeremy R Sanford
    Department of Molecular, Cellular, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA
    Genome Res 19:381-94. 2009
    ..This comprehensive analysis substantially expands the known roles of human SR proteins in the regulation of a diverse array of RNA transcripts...
  58. pmc A detailed history of intron-rich eukaryotic ancestors inferred from a global survey of 100 complete genomes
    Miklos Csuros
    Department of Computer Science and Operations Research, Universite de Montreal, Montreal, Quebec, Canada
    PLoS Comput Biol 7:e1002150. 2011
    Protein-coding genes in eukaryotes are interrupted by introns, but intron densities widely differ between eukaryotic lineages...
  59. pmc A sequence-based genetic map of Medicago truncatula and comparison of marker colinearity with M. sativa
    Hong Kyu Choi
    Department of Plant Pathology, University of California, Davis, California 95616, USA
    Genetics 166:1463-502. 2004
    ..sativa. The resulting comparative map, which includes 68 bridging markers, indicates that the two Medicago genomes are highly similar and establishes the basis for a Medicago composite map...
  60. pmc Extensive, recent intron gains in Daphnia populations
    Wenli Li
    Biology Department, Indiana University, Bloomington, IN 47405, USA
    Science 326:1260-2. 2009
    ..intron-gain alleles with that for derived single-base substitutions, we also provide evidence that newly arisen introns are intrinsically deleterious and tend to accumulate in population-genetic settings where random genetic drift is ..
  61. pmc The protein factors MBNL1 and U2AF65 bind alternative RNA structures to regulate splicing
    M Bryan Warf
    Institute of Molecular Biology and Department of Chemistry, University of Oregon, Eugene, OR 97403, USA
    Proc Natl Acad Sci U S A 106:9203-8. 2009
    ..Thus, U2AF65 binding can be blocked either by MBNL1 binding or by the stabilization of RNA secondary structure...
  62. ncbi The ClosTron: Mutagenesis in Clostridium refined and streamlined
    John T Heap
    BBSRC Sustainable BioEnergy Centre, School of Molecular Medical Sciences, Centre for Biomolecular Sciences, The University of Nottingham, University Park, Nottingham, NG7 2RD, UK
    J Microbiol Methods 80:49-55. 2010
    ..The improved ClosTron system supersedes the prototype plasmid pMTL007 and the original method, and exploits the potential of Group II introns more fully.
  63. ncbi Crystal structure of a self-spliced group II intron
    Navtej Toor
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, Bass Building, New Haven, CT 06511, USA
    Science 320:77-82. 2008
    Group II introns are self-splicing ribozymes that catalyze their own excision from precursor transcripts and insertion into new genetic locations...
  64. pmc Widespread selection for local RNA secondary structure in coding regions of bacterial genes
    Luba Katz
    Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Genome Res 13:2042-51. 2003
    ..These results are interpreted in terms of possible roles of RNA structures in RNA processing, regulation of mRNA stability, and translational control...
  65. ncbi Primary microRNA transcripts are processed co-transcriptionally
    Mariangela Morlando
    Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
    Nat Struct Mol Biol 15:902-9. 2008
    ....
  66. ncbi G-quadruplex structures in TP53 intron 3: role in alternative splicing and in production of p53 mRNA isoforms
    Virginie Marcel
    Group of Molecular Carcinogenesis, International Agency for Research on Cancer, 150 cours Albert Thomas, 69372, Lyon Cedex 08, France
    Carcinogenesis 32:271-8. 2011
    ..In this region, p53 pre-messenger RNA (mRNA) contains a succession of short exons (exons 2 and 3) and introns (introns 2 and 4) covering a total of 333 bp...
  67. ncbi A Pre-mRNA degradation pathway that selectively targets intron-containing genes requires the nuclear poly(A)-binding protein
    Caroline Lemieux
    RNA Group, Department of Biochemistry, Universite de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
    Mol Cell 44:108-19. 2011
    ..Our findings unveil a layer of regulation in the nucleus in which the turnover of specific pre-mRNAs, besides the turnover of mature mRNAs, is used to control gene expression...
  68. ncbi Evidence for extensive recent intron transposition in closely related fungi
    Stefano F F Torriani
    Institute of Integrative Biology, Swiss Federal Institute of Technology ETH Zurich, 8092 Zurich, Switzerland
    Curr Biol 21:2017-22. 2011
    Though spliceosomal introns are a major structural component of most eukaryotic genes and intron density varies by more than three orders of magnitude among eukaryotes [1-3], the origins of introns are poorly understood, and only a few ..
  69. ncbi Introns within ribosomal protein genes regulate the production and function of yeast ribosomes
    Julie Parenteau
    Laboratoire de génomique fonctionnelle de l Université de Sherbrooke, Departement de Microbiologie et d Infectiologie, Faculte de Medecine et des Sciences de la Sante, Universite de Sherbrooke, Quebec, Canada
    Cell 147:320-31. 2011
    ..To investigate the contribution of splicing to ribosome production and function, we systematically eliminated introns from all RP genes to evaluate their impact on RNA expression, pre-rRNA processing, cell growth, and response to ..
  70. pmc Mammalian mirtron genes
    Eugene Berezikov
    Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
    Mol Cell 28:328-36. 2007
    ..These short hairpin introns use splicing to bypass Drosha cleavage, which is otherwise essential for the generation of canonical animal ..
  71. ncbi Single-molecule analysis of Mss116-mediated group II intron folding
    Krishanthi S Karunatilaka
    Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, USA
    Nature 467:935-9. 2010
    ..Group II introns are structurally complex catalytic RNAs considered evolutionarily related to the eukaryotic spliceosome, and an ..
  72. pmc Critical association of ncRNA with introns
    David Rearick
    University of Toledo Health Science Campus, University of Toledo Health Science Campus, University of Toledo Health Science Campus, Toledo, OH 43614, USA
    Nucleic Acids Res 39:2357-66. 2011
    ..However, the significance of the presence of ncRNA within introns has not received proper attention...
  73. ncbi The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
    Olivier Jaillon
    Genoscope CEA and UMR 8030 CNRS Genoscope Université d Evry, 2 rue Gaston Cremieux, BP5706, 91057 Evry, France
    Nature 449:463-7. 2007
    ..Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants...
  74. ncbi Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms
    John S Mattick
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia QLD 4072, Australia
    Bioessays 25:930-9. 2003
    ..This paper re-examines the available evidence and suggests a new framework for considering and understanding the genomic programming of biological complexity, autopoietic development and phenotypic variation...
  75. ncbi Loss of the muscle-specific chloride channel in type 1 myotonic dystrophy due to misregulated alternative splicing
    Nicolas Charlet-B
    Department of Pathology, Baylor College of Medicine, Houston, Texas 77030, USA
    Mol Cell 10:45-53. 2002
    ..We propose that disruption of alternative splicing regulation causes a predominant pathological feature of DM1...
  76. pmc Origins of recently gained introns in Caenorhabditis
    Avril Coghlan
    Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
    Proc Natl Acad Sci U S A 101:11362-7. 2004
    The genomes of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae both contain approximately 100,000 introns, of which >6,000 are unique to one or the other species...
  77. ncbi Ultraconserved elements in the human genome
    Gill Bejerano
    Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Science 304:1321-5. 2004
    ..of the human genome are most often located either overlapping exons in genes involved in RNA processing or in introns or nearby genes involved in the regulation of transcription and development...
  78. ncbi Birth of new spliceosomal introns in fungi by multiplication of introner-like elements
    Ate van der Burgt
    Laboratory of Phytopathology, Wageningen University, 6708PB Wageningen, The Netherlands
    Curr Biol 22:1260-5. 2012
    Spliceosomal introns are noncoding sequences that separate exons in eukaryotic genes and are removed from pre-messenger RNAs by the splicing machinery...
  79. ncbi Mechanisms of alternative pre-messenger RNA splicing
    Douglas L Black
    Department of Microbiology, Immunology, and Molecular Genetics, Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, California 90095 1662, USA
    Annu Rev Biochem 72:291-336. 2003
    ..How these regulators are combined into complex systems of tissue-specific splicing is discussed. In conclusion, very recent studies are presented that point to new directions for understanding alternative splicing and its mechanisms...
  80. ncbi Association of TALS developmental disorder with defect in minor splicing component U4atac snRNA
    Patrick Edery
    Hospices Civils de Lyon, Service de Cytogénétique Constitutionnelle, Bron, F 69677, France
    Science 332:240-3. 2011
    ..Our findings demonstrate a crucial role of the minor spliceosome component U4atac snRNA in early human development and postnatal survival...
  81. ncbi Microsatellites within genes: structure, function, and evolution
    You Chun Li
    Institute of Evolution, University of Haifa, Haifa, Israel
    Mol Biol Evol 21:991-1007. 2004
    ..distributions within expressed sequence tags (ESTs) and genes including protein-coding, 3'-UTRs and 5'-UTRs, and introns; and discuss the consequences of SSR repeat-number changes in those regions of both prokaryotes and eukaryotes...
  82. pmc Ubiquitous internal gene duplication and intron creation in eukaryotes
    Xiang Gao
    Department of Biology, Indiana University, 1001 East Third Street, Bloomington, IN 47405, USA
    Proc Natl Acad Sci U S A 106:20818-23. 2009
    ..At least 7-30% of such genes have acquired novel introns, either because a prior intron in the same gene has been duplicated, or more commonly, because a spatial change ..
  83. pmc The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila
    Katsutomo Okamura
    Memorial Sloan Kettering Cancer Center, Department of Developmental Biology, 1275 York Ave, Box 252, New York, NY 10021, USA
    Cell 130:89-100. 2007
    ..These findings reveal that mirtrons are an alternate source of miRNA-type regulatory RNAs...
  84. ncbi The role of reverse transcriptase in intron gain and loss mechanisms
    Noa E Cohen
    Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel
    Mol Biol Evol 29:179-86. 2012
    ..In contrast, we suggest that RT-mediated intron loss is a mechanism that is very efficient in removing introns, and thus, its levels of activity may be a major determinant of intron number...
  85. pmc Divergence of duplicate genes in exon-intron structure
    Guixia Xu
    State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
    Proc Natl Acad Sci U S A 109:1187-92. 2012
    ..This finding suggests that structural divergences have played a more important role during the evolution of duplicate than nonduplicate genes...
  86. ncbi Human housekeeping genes are compact
    Eli Eisenberg
    Compugen Ltd, 72 Pinchas Rosen Street, Tel Aviv 69512, Israel
    Trends Genet 19:362-5. 2003
  87. pmc The peculiarities of large intron splicing in animals
    Samuel Shepard
    Department of Medicine, University of Toledo, Toledo, Ohio, USA
    PLoS ONE 4:e7853. 2009
    In mammals a considerable 92% of genes contain introns, with hundreds and hundreds of these introns reaching the incredible size of over 50,000 nucleotides...
  88. ncbi Myotonic dystrophy type 2 caused by a CCTG expansion in intron 1 of ZNF9
    C L Liquori
    Institute of Human Genetics MMC 206, 420 Delaware Street SE, University of Minnesota, Minneapolis, MN 55455, USA
    Science 293:864-7. 2001
    ..Parallels between these mutations indicate that microsatellite expansions in RNA can be pathogenic and cause the multisystemic features of DM1 and DM2...
  89. ncbi The ribozyme core of group II introns: a structure in want of partners
    François Michel
    Centre de Génétique Moléculaire du CNRS, 1 Avenue de la Terrasse, 91190 Gif sur Yvette, France
    Trends Biochem Sci 34:189-99. 2009
    Group II introns contain a large ribozyme, which catalyzes self-splicing, and the coding sequence of a reverse transcriptase, the function of which is to cooperate with the ribozyme to achieve genomic mobility...
  90. ncbi The IC-SNURF-SNRPN transcript serves as a host for multiple small nucleolar RNA species and as an antisense RNA for UBE3A
    M Runte
    Institut fur Humangenetik, Universitatsklinikum Essen, 45122 Essen, Germany
    Hum Mol Genet 10:2687-700. 2001
    ..Almost all of those snoRNAs are encoded within introns of this large transcript...
  91. pmc Usher syndrome 1D and nonsyndromic autosomal recessive deafness DFNB12 are caused by allelic mutations of the novel cadherin-like gene CDH23
    J M Bork
    Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Rockville, MD 20850, USA
    Am J Hum Genet 68:26-37. 2001
    ..A northern blot analysis of CDH23 showed a 9.5-kb transcript expressed primarily in the retina. CDH23 is also expressed in the cochlea, as is demonstrated by polymerase chain reaction amplification from cochlear cDNA...
  92. ncbi The tertiary structure of group II introns: implications for biological function and evolution
    Anna Marie Pyle
    Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute and Yale University, New Haven, CT, USA
    Crit Rev Biochem Mol Biol 45:215-32. 2010
    Group II introns are some of the largest ribozymes in nature, and they are a major source of information about RNA assembly and tertiary structural organization...
  93. ncbi Splicing segregation: the minor spliceosome acts outside the nucleus and controls cell proliferation
    Harald König
    Forschungszentrum Karlsruhe GmbH, Institut für Toxikologie und Genetik, Postfach 3640, 76021 Karlsruhe, Germany
    Cell 131:718-29. 2007
    ..We report here that partially spliced pre-mRNAs containing minor-class introns undergo nuclear export and that minor-class snRNAs are predominantly cytoplasmic in vertebrates...
  94. pmc Intron-dominated genomes of early ancestors of eukaryotes
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Hered 100:618-23. 2009
    Evolutionary reconstructions using maximum likelihood methods point to unexpectedly high densities of introns in protein-coding genes of ancestral eukaryotic forms including the last common ancestor of all extant eukaryotes...
  95. ncbi De novo origin of new genes with introns in Plasmodium vivax
    Zefeng Yang
    Department of Biology, East Carolina University, Greenville, NC 27858, USA
    FEBS Lett 585:641-4. 2011
    ..genes have often been suggested to be initially intronless, five of the genes identified in our analysis contain introns in their coding regions...
  96. pmc Nucleomorph genome of Hemiselmis andersenii reveals complete intron loss and compaction as a driver of protein structure and function
    Christopher E Lane
    Canadian Institute for Advanced Research, Integrated Microbial Biodiversity Program, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada B3H 1X5
    Proc Natl Acad Sci U S A 104:19908-13. 2007
    ..nucleomorph genome of the cryptophyte Hemiselmis andersenii and show that it is completely devoid of spliceosomal introns and genes for splicing RNAs-a case of complete intron loss in a nuclear genome. Comparison of H...
  97. pmc Characterization of intron loss events in mammals
    Jasmin Coulombe-Huntington
    Department of Human Genetics, McGill University, Montreal, Quebec H3A 1A4, Canada
    Genome Res 17:23-32. 2007
    ..The majority (68%) of the deleted introns were extremely small (<150 bp), significantly smaller than average...
  98. pmc An organellar maturase associates with multiple group II introns
    Reimo Zoschke
    Institute of Biology, Humboldt University, 10115 Berlin, Germany
    Proc Natl Acad Sci U S A 107:3245-50. 2010
    Bacterial group II introns encode maturase proteins required for splicing. In organelles of photosynthetic land plants, most of the group II introns have lost the reading frames for maturases...
  99. pmc Nuclear expression of a group II intron is consistent with spliceosomal intron ancestry
    Venkata R Chalamcharla
    Wadsworth Center, New York State Department of Health, Albany, 12208, USA
    Genes Dev 24:827-36. 2010
    Group II introns are self-splicing RNAs found in eubacteria, archaea, and eukaryotic organelles...
  100. pmc High-density yeast-tiling array reveals previously undiscovered introns and extensive regulation of meiotic splicing
    Kara Juneau
    Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 104:1522-7. 2007
    ..To this end, we have developed a genome-wide assay for mapping introns in Saccharomyces cerevisiae...
  101. pmc A novel role for minimal introns: routing mRNAs to the cytosol
    Jiang Zhu
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
    PLoS ONE 5:e10144. 2010
    b>Introns and their splicing are tightly coupled with the subsequent mRNA maturation steps, especially nucleocytoplasmic export...

Research Grants68

  1. BIOCHEMISTRY OF PRE-MRNA SPLICING
    Adrian R Krainer; Fiscal Year: 2010
    ..It involves precise excision of introns and joining of exons from primary transcripts in the nucleus to generate mature mRNA, the template for protein ..
  2. Interaction between RNA interference and RNA editing pathways
    Kazuko Nishikura; Fiscal Year: 2013
    ..are non-coding RNAs that contain inverted repeats of repetitive elements such as Alu and LINE located within introns and 3'UTRs. The biological significance of non-coding, repetitive RNA editing is largely unknown...
  3. Mechanisms of Splicing Regulation During Environmental Stress in Yeast
    Jaclyn C Greimann; Fiscal Year: 2012
    DESCRIPTION (provided by applicant): Less than 5% of Saccharomyces cerevisiae genes have introns and most yeast intron-containing genes have only one intron...
  4. PlGF-HIF1a-miRNA Axis in Sickle Pulmonary Hypertension
    Punam Malik; Fiscal Year: 2013
    ..In Aim 2, we will determine whether the genes for miRs that regulate PAI-1 expression, and are located within introns of NFYC and SKA2 genes are co-synthesized from the NFYC and SKA2 primary transcripts, or are independently ..
  5. Role of Coxiella burnetii group I introns in growth modulation
    Michael F Minnick; Fiscal Year: 2010
    ..Preliminary data show that Coxiella's single 23S rDNA encodes two self-splicing, group I introns that inhibit ribosome function. We hypothesize that group I introns play central roles in C...
  6. The Role of RNA Splicing Factors in Retinal Degeneration
    Michael Farkas; Fiscal Year: 2012
    ..that occurs in every cell of the human body where the spliceosome processes pre-mRNA transcripts by removing introns (non-coding regions) and splicing the exons (coding regions) together to form a mature mRNA transcript...
  7. Control of Cardiogenesis by microRNA Editing
    Kazuko Nishikura; Fiscal Year: 2010
    ..are non-coding RNAs that contain inverted repeats of repetitive elements such as Alu and LINE located within introns and 3'UTRs. The biological significance of non-coding, repetitive RNA editing is largely unknown...
  8. SPLICING OF MRNA PRECURSORS
    Michael R Green; Fiscal Year: 2013
    ..The primary transcripts of most eukaryotic genes (precursor mRNAs;pre-mRNAs) contain intervening sequences (introns) that are removed by RNA splicing in a two-step pathway...
  9. Functionally Significant Polymorphisms in Serotonin Pathway Genes
    Beverly H Koller; Fiscal Year: 2010
    ..this method to address not only the functionality of non-synonymous SNPs but also non- coding polymorphisms in introns and regulatory regions of the gene...
  10. SELF-SPLICING INTEINS: FUNCTION, EVOLUTION, APPLICATION
    Marlene Belfort; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Self-splicing introns and inteins attract attention for their molecular mechanisms, phylogentic diversity, role in genome evolution, and application in research, biotechnology and medicine...
  11. Mechanism Underlying Neurodegeneration Caused by Dysfunction of Pre-mRNA Splicing
    Yichang Jia; Fiscal Year: 2012
    ..transcriptome analysis revealed that only a subset of alternative splicing events, including splicing of small introns, is disrupted in the mutant cerebellum...
  12. Group II Intron Mobility and Gene Targeting
    Alan M Lambowitz; Fiscal Year: 2012
    The proposed research is a continued study of mobile group II introns and their applications in gene targeting...
  13. ESTABLISHMENT OF RESEARCH RESOURCEFOR THE IDENTIFICATION OF GENETIC AND ENVIRONM
    VAINORIOUS E; Fiscal Year: 2009
    ..Some of the same genes have been resequenced in an additional set of 20 samples, and, in a subset of these, the introns and promoter regions have been sequenced as well...
  14. The influence of genotype on the outcome of gene transfer in beta-thalassemia
    Stefano Rivella; Fiscal Year: 2013
    ..to rescue beta-thalassemia in mice by lentiviral-mediated transfer of the human beta-globin gene, its promoter, introns and large elements of the locus control region...
  15. Treatment for Dysmyelination in PMD and SPG2
    Pamela E Knapp; Fiscal Year: 2013
    ..The most severe forms of PMD are associated with missense mutations in introns or exons of the PLP1 gene. Interestingly, complete gene deletion results in a milder neurologic impairment...
  16. Male Mutation Bias and Paternal Age Effect in Mammals
    Kateryna Makova; Fiscal Year: 2010
    ..To investigate this, we will sequence introns of genes homologous between X and Y in mammals with long generation time (Cetacea and Perissodactyla) and analyze ..
  17. A Comprehensive Resource for Manipulating the Drosophila Genome
    Hugo J Bellen; Fiscal Year: 2013
    ..One-third of Mi{MIC} insertions are in coding introns of genes, and Recombination Mediated Cassette Exchange can be used to efficiently swap in DNA cassettes between ..
  18. HLA and schizophrenia: a high-throughput sequencing study
    DOUGLAS FREDERICK LEVINSON; Fiscal Year: 2013
    ..The entire targeted block of almost all exons and introns in 11 HLA genes in 8 loci (A, B, C, DRB1/3/4/5, DQA1, DQB1, DPA1, DPB1) will be amplified by long-range PCR, ..
  19. Spliceosome Mechanism Dissected at the Single Molecule Level
    Nils G Walter; Fiscal Year: 2013
    ..The spliceosome is a multi-megadalton RNA-protein complex that catalyzes in all eukaryotes the removal of introns and the ligation of exons during splicing of pre mRNAs...
  20. GENETICS OF HYPERTENSION
    Ashok Kumar; Fiscal Year: 2013
    ..re-combineered 180 Kb long BAC DNA (containing 116 Kb of the 5'-flanking region, all five exons and four introns, and 54 Kb of the 3'-UTR of the hAGT gene) and produced double transgenic mice containing either -6A or - 6G ..
  21. Molecular analysis of bipolar and schizophrenia candidate genes
    Herbert M Lachman; Fiscal Year: 2012
    ..such variants is difficult, especially when associated SNPs are found in non-coding regions - deep within introns or in intergenic regions far removed from the nearest annotated genes, which has been a common theme in GWAS...
  22. Regulation of CD45 alternative splicing by HNRPLL
    Anjana Rao; Fiscal Year: 2013
    ..the pieces of DNA that code for proteins (known as exons) are separated by intervening regions known as introns, which need to be removed through a process called gene splicing so that the exons can be joined ("spliced") ..
  23. 2011 Eukaryotic mRNA Processing Conference
    David J Stewart; Fiscal Year: 2011
    ..from yeast to man, the information encoded in the DNA sequence is interrupted by non-coding regions called introns. An RNA copy of the gene has to be read off, cut and then spliced back together to remove the introns and produce ..
  24. THE ORGANIZATION OF ANIMAL CELL NUCLEI
    Joseph G Gall; Fiscal Year: 2013
    ..We recently discovered that Xenopus oocytes store stable RNA sequences derived from the introns of most transcribed genes...
  25. Toward a comprehensive functional annotation of the human genome
    Richard M Myers; Fiscal Year: 2013
    ..This means discovering and mapping all parts of all genes, including exons, introns, promoters and cis-regulatory sequences, in previous phases of the ENCODE Project, the applicants of this ..
  26. Characterizing RNA-metal binding by Raman spectroscopy
    Paul R Carey; Fiscal Year: 2012
    ..center on four RNAs, the Hepatitis Delta Virus (HDV) ribozyme, the P4-P6 domain and Twort ribozyme from group I introns, and phenylalanine tRNA...
  27. Vertebrate Non-Coding RNPs: Integrating function, biogenesis and survival
    Joan A Steitz; Fiscal Year: 2013
    ..building blocks of the major and minor spliceosomes that remove both constitutively- and alternatively-spliced introns from pre- mRNAs. Even the 32-end formation of histone mRNAs requires the U7 snRNA...
  28. Cell Type-Specific Roles of TLR Signaling In Immune Responses
    Anthony L DeFranco; Fiscal Year: 2012
    ..In this allele, we have placed loxP sites in the introns on either side of the essential exon 3 of the myd88 gene, with the result that Cre expression in a cell will ..
  29. Global Annotation of Regulatory Elements in the Human Genome
    Richard M Myers; Fiscal Year: 2011
    ..annotation of the human genome by delineating the DNA sequence features that comprise all genes, including exons, introns, promoters and cis-regulatory sequences...
  30. Transcriptional elongation and splicing in human genes in situ
    Richard A Padgett; Fiscal Year: 2013
    ..Some genes can exceed one million base pairs in length. Many of these long genes also contain introns of hundreds of kilobases in length...
  31. Dysregulation of TGF Beta Action Pancreatic Cancer
    Murray Korc; Fiscal Year: 2012
    ..Smad7 levels lead to the functional inactivation of pRb, mice that express Rb with a floxed Stop cassette in the introns flanking exon 19 (LSL-Rb) will be bred with mice carrying LSL-KrasG12D alleles and Pdx1- Cre, in order to ..
  32. Comprehensive SNP Discovery in SLC2A9. A Candidate Gene for Uric Acid Nephropathy
    Venkata Saroja Voruganti; Fiscal Year: 2013
    ..associated with SUA and renal phenotypes in Mexican Americans 2) to resequence SLC2A9 gene (all exons, conserved introns and regulatory regions) for SNP/polymorphism discovery in 1122 founders in American Indians of the SFHS, genotype ..
  33. INTRON DYNAMICS IN BACTERIA
    Marlene Belfort; Fiscal Year: 2013
    ..Group I and group II introns are self-splicing elements with a wide phylogenetic distribution, reflecting their dispersal through different ..
  34. MECHANISMS FOR REARRANGING RNA DURING PRE-MRNA SPLICING
    Jonathan P Staley; Fiscal Year: 2013
    ..Human genes in are interrupted on average by eight introns. Moreover, nearly 95% of human genes are alternatively spliced at least 15% of the time, providing a versatile ..
  35. Cocaine Addiction and Retrotransposons
    Wade H Berrettini; Fiscal Year: 2013
    ..insertions will have little effect on neuronal function (perhaps because they occur in gene deserts or in large introns or in genes not required for that cell's function), some may interfere with normal neuronal activity because ..
  36. Gene Regulatory Networks in Development and Physiology
    ALBERTHA JOHANNA WALHOUT; Fiscal Year: 2013
    ..g. promoters, exons, introns and enhancers) to differential gene expression in the digestive tract? We, and others, have generated many C...
  37. Human DBR1 defines a new pathway of intrinsic antiviral immunity in the CNS
    Shen Ying Zhang; Fiscal Year: 2013
    ..Human DBR1 has been proposed to play a key role in the rapid turnover of lariat introns excised from pre-mRNA...
  38. Functional Genomics of Platelet Aggregation Using iPS and Derived Megakaryocytes
    Linzhao Cheng; Fiscal Year: 2013
    ..to elucidate findings in known genes (PEAR1, RGL3, and MET), most signals were in intergenic regions (38%), or in introns (55%), with only 1.6% producing missense mutations in exons...
  39. Genomic Disorders in Neurodevelopmental Disease
    IAN MORGAN CAMPBELL; Fiscal Year: 2013
    ..To explore this, we will computationally identify genes with significantly increased Alu content in introns and flanking genomic regions and compare this gene list to databases of human CNVs...
  40. MECHANISM OF PRE-MRNA SPLICING
    MAGDA KONARSKA; Fiscal Year: 2012
    ..Typically, splice site signals of alternatively spliced introns deviate from the consensus, and are often accompanied by splicing enhancer motifs...
  41. Developing Anti-viral Ribozymes to Suppress Arboviruses in Transgenic Mosquitoes
    Malcolm J Fraser; Fiscal Year: 2013
    ..Recent efforts have confirmed the effectiveness of hammerhead ribozymes and Group I introns in suppressing DENV infection in mosquito cells...
  42. ENZYMOLOGY OF A CATALYTIC RNA MOLECULE
    Daniel Herschlag; Fiscal Year: 2013
    ..Over the past two decades, group I introns have served as unparalleled systems for developing broad experimental approaches for RNA study and for deep ..
  43. Functional RNA elements in the human genome
    EUGENE WEI MING YEO; Fiscal Year: 2013
    ..is essential for proper gene expression in higher eukaryotic genomes, as the vast majority of genes contain introns that have to be accurately recognized and removed...
  44. Physical and functional probing of DEAD-box proteins as general RNA chaperones
    Rick Russell; Fiscal Year: 2013
    ..Mss116p, which function as general RNA chaperones in folding of mitochondrial group I and group II self-splicing introns. These systems are powerful for mechanistic studies because the RNAs are relatively simple and tractable, and ..
  45. Alternative pre-mRNA Splicing in Drosophila
    Donald C Rio; Fiscal Year: 2013
    ..Thus, understanding how introns are recognized and how patterns of alternative splicing are set up may allow therapeutic intervention...
  46. Effects of Anti-miR-33 on Atherosclerosis Regression and RCT in Nonhuman Primates
    RYAN EUGENE TEMEL; Fiscal Year: 2013
    ..In humans, two isoforms of this microRNA, miR-33a and miR-33b, are encoded in introns of the sterol response element binding factor (SREBF) 2 and SREBF1 genes, and co-regulate cellular lipid ..
  47. Alternative Splicing of the Drosophilia Dscam Pre-mRNA
    Brenton R Graveley; Fiscal Year: 2013
    ..Moreover, we will determine the order in which the Dscam introns are removed from the pre-mRNA as this has important implications on the splicing regulatory mechanisms...
  48. miRNAs and PPAR-gamma-induced neuroprotection
    Raghu Vemuganti; Fiscal Year: 2013
    ..are transcribed as primary miRNAs (primiRs) by RNA polymerase II from either independent miRNA genes or from the introns of protein-coding genes...
  49. The Pathogenesis of RNA Splicing Factor RP
    Eric A Pierce; Fiscal Year: 2013
    ..3, PRPF8, PRPF31, RP9 and SNRNP200 are highly conserved components of the spliceosome, the complex which excises introns from nascent RNA transcripts to generate mature mRNAs...
  50. BIOCHEMISTRY OF REGULATED PRE-MRNA SPLICING/DROSOPHILA
    Donald C Rio; Fiscal Year: 2010
    ..Thus, understanding how introns are recognized and how patterns of alternative splicing are set up may allow therapeutic intervention...
  51. Binding and Splicing mRNA
    DANIEL AALBERTS; Fiscal Year: 2009
    ..of thermodynamics in alternative splicing and intron/exon segregation, and correlations in the codon frames where introns begin...
  52. Analyzing pre-mRNA splicing by deep sequencing of splice sites
    Jonathan P Staley; Fiscal Year: 2011
    ..Human genes contain eight introns on average and greater than 93% of human genes undergo alternative splicing...
  53. MOLECULAR CHARACTERIZATION OF HERPES SIMPLEX VIRUS ICP27
    Stephen A Rice; Fiscal Year: 2013
    ..In Specific Aim 2, we will study how ICP27 promotes the retention of introns in viral mRNAs...
  54. Functional and structural characterization of spliceosomal cyclophilins
    Tara L Davis; Fiscal Year: 2011
    ..provided by applicant): The spliceosome is a complex and dynamic collection of RNA and proteins that removes introns from precursor mRNA transcripts...
  55. The Molecular Biology of DNA Tumor Viruses Conference
    Paul F Lambert; Fiscal Year: 2013
    ..have been described at the Molecular Biology of DNA Tumor Viruses Conference including the first discoveries of introns and the mRNA splicing, transcriptional enhancers and promoter regulatory elements, structure of mammalian ..
  56. Adaptive evolution of non coding DNA and gene expression divergence in Drosophila
    Peter Andolfatto; Fiscal Year: 2013
    ..2Mb) and a control reference panel of closely-linked short introns and coding sequence (~5.8Mb)...
  57. The Catalytic Mechanism of Nuclear Premessenger RNA Splicing by the Spliceosome
    Jonathan P Staley; Fiscal Year: 2013
    Eukaryotic genes, including most human genes, are interrupted by numerous introns. After transcription of such genes, the introns are excised in two phosphoryl transfer reactions catalyzed by the spliceosome, a macromolecular machine ..
  58. Study gene for alcoholism using mouse models
    Weikuan Gu; Fiscal Year: 2010
    ..Secondly, information on the introns, 5'and 3'region of the sequences will be available...
  59. Functional and structural characterization of spliceosomal cyclophilins
    Tara L Davis; Fiscal Year: 2013
    PROJECT SUMMARY The spliceosome is a complex and dynamic collection of RNA and proteins that removes introns from precursor mRNA transcripts...
  60. 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...
  61. Mechanisms of environmentally responsive splicing in S.Pombe
    Jeffrey A Pleiss; Fiscal Year: 2013
    ..In many ways, splicing in S. pombe looks similar to splicing in higher eukaryotes. Introns have been identified in nearly half of all S...
  62. Small Molecule Tools to Image Sophisticated Protein Function
    Alanna Schepartz; Fiscal Year: 2013
    ..results to develop encodable RNA tags, and apply them in collaboration to visualize the mobility of Group II introns and trafficking of the hepatitis C virus RNA genome...
  63. MITDNA MUTAGENESIS BY ENVIRONMENTAL CARCINOGENS
    Keshav Singh; Fiscal Year: 2003
    ..mitochondrial DNA (mitDNA) is extremely vulnerable to attack by environmental carcinogens because it contains no introns, has no protective histones and is continuously exposed to reactive free radicals produced within the ..
  64. NONSENSE RNA SURVEILLANCE IN HEALTH AND DISEASE
    Harry Dietz; Fiscal Year: 2000
    ..harmful effects of truncated proteins; differences between yeast and mammals might then reflect the abundance of introns in mammals and the paucity of introns in yeast. Dr...
  65. Analysis of Group I and II Introns in Mammalian Cells
    Bruce Sullenger; Fiscal Year: 2005
    The overall goal of this proposal is to explore the ability of group I and group II introns to repair genetic instructions inside mammalian cells...
  66. Genetic circuits based on allosteric ribozymes
    Andrew D Ellington; Fiscal Year: 2010
    ..developed a variety of aptazymes, based on ribozyme and deoxyribozyme ligases and Group I self-splicing introns, and have also developed novel assay formats for these aptazymes...
  67. Mechanisms Regulating Alternative pre-mRNA Splicing
    James Patton; Fiscal Year: 2005
    Most eukaryotic genes are interrupted by non-coding introns that must be removed from pre-mRNA transcripts for the production of functional proteins...
  68. INVOLVEMENT OF PROTEINS IN SPLICING GROUP I INTRONS
    Alan Lambowitz; Fiscal Year: 2002
    ..protein, the mitochondrial tyrosyl-tRNA synthetase (mt TyrRS), and other proteins in the splicing of group I introns. Group I introns use RNA catalyzed splicing reactions, but require proteins for efficient splicing in vivo, ..