Genomes and Genes
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.
Publications319 found, 100 shown here
- Parallel loss of plastid introns and their maturase in the genus CuscutaJoel 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...
- Genome-wide mapping of alternative splicing in Arabidopsis thalianaSergei 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...
- Intronic microRNA precursors that bypass Drosha processingJ 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 ..
- The transcriptional landscape of the yeast genome defined by RNA sequencingUgrappa Nagalakshmi
Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
Science 320:1344-9. 2008The identification of untranslated regions, introns, and coding regions within an organism remains challenging...
- Differential chromatin marking of introns and expressed exons by H3K36me3Paulina 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, ..
- Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicateFrance 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...
- A global view of gene activity and alternative splicing by deep sequencing of the human transcriptomeMarc 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...
- Friedreich's ataxia: autosomal recessive disease caused by an intronic GAA triplet repeat expansionV 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...
- Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organizationNicholas 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...
- The amphioxus genome and the evolution of the chordate karyotypeNicholas 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...
- Human MicroRNA targetsBino 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...
- The sequence of the human genomeJ 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...
- Genome-wide analyses of alternative splicing in plants: opportunities and challengesW 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...
- Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTBMiriam 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...
- The ClosTron: a universal gene knock-out system for the genus ClostridiumJohn 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...
- Understanding splicing regulation through RNA splicing mapsJoshua 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...
- Gene prediction with a hidden Markov model and a new intron submodelMario 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...
- Extensive, recent intron gains in Daphnia populationsWenli 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 ..
- A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pigAnne 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...
- Control of stress-dependent cardiac growth and gene expression by a microRNAEva 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...
- Variation in FTO contributes to childhood obesity and severe adult obesityChristian 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...
- Identification of mammalian microRNA host genes and transcription unitsAntony 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-..
- 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...
- On the utility of short intron sequences as a reference for the detection of positive and negative selection in DrosophilaJohn 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 &..
- Variant of transcription factor 7-like 2 (TCF7L2) gene confers risk of type 2 diabetesStruan 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...
- A detailed history of intron-rich eukaryotic ancestors inferred from a global survey of 100 complete genomesMiklos Csuros
Department of Computer Science and Operations Research, Universite de Montreal, Montreal, Quebec, Canada
PLoS Comput Biol 7:e1002150. 2011Protein-coding genes in eukaryotes are interrupted by introns, but intron densities widely differ between eukaryotic lineages...
- Human hypertension caused by mutations in WNK kinasesF 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...
- The origins of genome complexityMichael 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...
- Origin and evolution of spliceosomal intronsIgor B Rogozin
National Center for Biotechnology Information NLM NIH, 8600 Rockville Pike, Bldg, 38A, Bethesda, MD 20894, USA
Biol Direct 7:11. 2012Evolution 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 ..
- Role of RNA structure in regulating pre-mRNA splicingM Bryan Warf
Institute of Molecular Biology, and Department of Chemistry, University of Oregon, Eugene, Oregon 97403, USA
Trends Biochem Sci 35:169-78. 2010Pre-mRNA splicing involves removing non-coding introns from RNA transcripts. It is carried out by the spliceosome, along with other auxiliary factors...
- Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolutionBrian T Wilhelm
Cancer Research UK Fission Yeast Functional Genomics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
Nature 453:1239-43. 2008..or exon-intron junctions give unique insight into a surprising variability in splicing efficiency across introns, genes and conditions...
- Evidence for extensive recent intron transposition in closely related fungiStefano F F Torriani
Institute of Integrative Biology, Swiss Federal Institute of Technology ETH Zurich, 8092 Zurich, Switzerland
Curr Biol 21:2017-22. 2011Though 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 ..
- Introns within ribosomal protein genes regulate the production and function of yeast ribosomesJulie 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 ..
- Mammalian mirtron genesEugene 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 ..
- Structure and activity of putative intronic miRNA promotersAlex 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...
- Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcriptsJeremy 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...
- Critical association of ncRNA with intronsDavid 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...
- Mechanisms of intron gain and loss in DrosophilaPaul Yenerall
Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
BMC Evol Biol 11:364. 2011It is widely accepted that orthologous genes have lost or gained introns throughout evolution. However, the specific mechanisms that generate these changes have proved elusive...
- Single-molecule analysis of Mss116-mediated group II intron foldingKrishanthi 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 ..
- The ClosTron: Mutagenesis in Clostridium refined and streamlinedJohn 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.
- Group II introns: mobile ribozymes that invade DNAAlan 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. 2011Group 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...
- The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phylaOlivier 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...
- Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cellsMatthew 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...
- Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organismsJohn 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...
- Loss of the muscle-specific chloride channel in type 1 myotonic dystrophy due to misregulated alternative splicingNicolas 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...
- Ultraconserved elements in the human genomeGill 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...
- Use of computer-designed group II introns to disrupt Escherichia coli DExH/D-box protein and DNA helicase genesJiri 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. 2004Mobile 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...
- Origins of recently gained introns in CaenorhabditisAvril Coghlan
Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
Proc Natl Acad Sci U S A 101:11362-7. 2004The 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...
- Birth of new spliceosomal introns in fungi by multiplication of introner-like elementsAte van der Burgt
Laboratory of Phytopathology, Wageningen University, 6708PB Wageningen, The Netherlands
Curr Biol 22:1260-5. 2012Spliceosomal introns are noncoding sequences that separate exons in eukaryotic genes and are removed from pre-messenger RNAs by the splicing machinery...
- Association of TALS developmental disorder with defect in minor splicing component U4atac snRNAPatrick 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...
- Mechanisms of alternative pre-messenger RNA splicingDouglas 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...
- The protein factors MBNL1 and U2AF65 bind alternative RNA structures to regulate splicingM 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...
- Divergence of duplicate genes in exon-intron structureGuixia 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...
- The role of reverse transcriptase in intron gain and loss mechanismsNoa 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...
- Ubiquitous internal gene duplication and intron creation in eukaryotesXiang 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 ..
- Microsatellites within genes: structure, function, and evolutionYou 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...
- Human housekeeping genes are compactEli Eisenberg
Compugen Ltd, 72 Pinchas Rosen Street, Tel Aviv 69512, Israel
Trends Genet 19:362-5. 2003
- The mirtron pathway generates microRNA-class regulatory RNAs in DrosophilaKatsutomo 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...
- Myotonic dystrophy type 2 caused by a CCTG expansion in intron 1 of ZNF9C 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...
- The peculiarities of large intron splicing in animalsSamuel Shepard
Department of Medicine, University of Toledo, Toledo, Ohio, USA
PLoS ONE 4:e7853. 2009In mammals a considerable 92% of genes contain introns, with hundreds and hundreds of these introns reaching the incredible size of over 50,000 nucleotides...
- Usher syndrome 1D and nonsyndromic autosomal recessive deafness DFNB12 are caused by allelic mutations of the novel cadherin-like gene CDH23J 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...
- The tertiary structure of group II introns: implications for biological function and evolutionAnna 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. 2010Group 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...
- The ribozyme core of group II introns: a structure in want of partnersFrançois Michel
Centre de Génétique Moléculaire du CNRS, 1 Avenue de la Terrasse, 91190 Gif sur Yvette, France
Trends Biochem Sci 34:189-99. 2009Group 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...
- De novo origin of new genes with introns in Plasmodium vivaxZefeng 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...
- Splicing segregation: the minor spliceosome acts outside the nucleus and controls cell proliferationHarald 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...
- Intron-dominated genomes of early ancestors of eukaryotesEugene V Koonin
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
J Hered 100:618-23. 2009Evolutionary 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...
- The IC-SNURF-SNRPN transcript serves as a host for multiple small nucleolar RNA species and as an antisense RNA for UBE3AM 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...
- Characterization of intron loss events in mammalsJasmin 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...
- Nucleomorph genome of Hemiselmis andersenii reveals complete intron loss and compaction as a driver of protein structure and functionChristopher 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...
- Rates of in situ transcription and splicing in large human genesJarnail 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...
- Stochastic noise in splicing machineryEugene 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...
- Nuclear expression of a group II intron is consistent with spliceosomal intron ancestryVenkata R Chalamcharla
Wadsworth Center, New York State Department of Health, Albany, 12208, USA
Genes Dev 24:827-36. 2010Group II introns are self-splicing RNAs found in eubacteria, archaea, and eukaryotic organelles...
- A novel role for minimal introns: routing mRNAs to the cytosolJiang Zhu
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
PLoS ONE 5:e10144. 2010b>Introns and their splicing are tightly coupled with the subsequent mRNA maturation steps, especially nucleocytoplasmic export...
- An organellar maturase associates with multiple group II intronsReimo Zoschke
Institute of Biology, Humboldt University, 10115 Berlin, Germany
Proc Natl Acad Sci U S A 107:3245-50. 2010Bacterial 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...
- High-density yeast-tiling array reveals previously undiscovered introns and extensive regulation of meiotic splicingKara 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...
- A single IGF1 allele is a major determinant of small size in dogsNathan B Sutter
National Human Genome Research Institute, Building 50, Room 5349, 50 South Drive MSC 8000, Bethesda, MD 20892 8000, USA
Science 316:112-5. 2007..A single IGF1 single-nucleotide polymorphism haplotype is common to all small breeds and nearly absent from giant breeds, suggesting that the same causal sequence variant is a major contributor to body size in all small dogs...
- 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...
- A phylogeny of caenorhabditis reveals frequent loss of introns during nematode evolutionSoochin Cho
Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48864, USA
Genome Res 14:1207-20. 2004Since introns were discovered 26 years ago, people have wondered how changes in intron/exon structure occur, and what role these changes play in evolution...
- Group I introns: Moving in new directionsHenrik Nielsen
Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, Copenhagen, Denmark Denmark
RNA Biol 6:375-83. 2009Group I introns are genetic elements interrupting functional genes. They are removed from precursors at the RNA level and most catalyze their own splicing...
- Exon array analyses across the NCI-60 reveal potential regulation of TOP1 by transcription pausing at guanosine quartets in the first intronWilliam C Reinhold
Laboratory of Molecular Pharmacology and Developmental Therapeutics Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20894, USA
Cancer Res 70:2191-203. 2010..The observations reported here suggest the hypothesis that there is a conserved negative transcription regulator within intron 1 of the TOP1 gene associated with a quadruplex-prone region...
- Comprehensive analysis of archaeal tRNA genes reveals rapid increase of tRNA introns in the order thermoprotealesJunichi Sugahara
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
Mol Biol Evol 25:2709-16. 2008..tRNA genes in Archaea was estimated to be approximately 15% of the whole tRNA genes, and most of the introns were known to be located at canonical positions (nucleotide position between 37 and 38) of precursor tRNA (pre-..
- Intron RNA editing is essential for splicing in plant mitochondriaBenoît Castandet
Laboratoire de Microbiologie Cellulaire et Moléculaire et Pathogénicité MCMP, UMR5234 CNRS Université Victor Segalen Bordeaux2 146 rue Léo Saignat 33076 Bordeaux Cedex, France
Nucleic Acids Res 38:7112-21. 2010..are found in non-coding regions at critical positions in the predicted secondary and tertiary structures of introns, suggesting that RNA editing could be important for splicing...
- Release of SF3 from the intron branchpoint activates the first step of pre-mRNA splicingRea M Lardelli
Graduate Program, Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, USA
RNA 16:516-28. 2010..When the spliceosome attains the proper conformation and upon the function of Prp2p, SF3 is displaced from the branchpoint allowing first step chemistry to occur...
- hnRNP H1 and intronic G runs in the splicing control of the human rpL3 geneAnnapina Russo
Dipartimento di Biochimica e Biotecnologie Mediche, Universita Federico II, Napoli 80131, Italy
Biochim Biophys Acta 1799:419-28. 2010..We propose a working model in which rpL3 recruits hnRNP H1 and, through cooperation with other splicing factors, promotes selection of the alternative splice site...
- The emergence of 'hypervirulence' in Clostridium difficileStephen T Cartman
Centre for Biomolecular Sciences, School of Molecular Medical Sciences, Nottingham Digestive Diseases Centre NIHR Biomedical Research Unit, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
Int J Med Microbiol 300:387-95. 2010..The identification of virulence factors using this approach should help lead to the rational development of therapeutic countermeasures against CDAD...
- A diversity of uncharacterized reverse transcriptases in bacteriaDawn M Simon
Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
Nucleic Acids Res 36:7219-29. 2008..reverse transcriptases (RTs) are rare in bacteria, with only three characterized classes: retrons, group II introns and diversity-generating retroelements (DGRs)...
- Global regulation of alternative splicing during myogenic differentiationChristopher S Bland
Department of Pathology and Immunology, Interdepartmental Program in Cell and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
Nucleic Acids Res 38:7651-64. 2010..These findings show that within a developmental context, AS is a highly regulated and conserved process, suggesting a major role for AS regulation in myogenic differentiation...
- Remarkable abundance and evolution of mobile group II introns in Wolbachia bacterial endosymbiontsSébastien Leclercq
Centre National de la Recherche Scientifique UMR 6556 Ecologie, Evolution, Symbiose, Universite de Poitiers, Poitiers, France
Mol Biol Evol 28:685-97. 2011..In this study, we focused on another class of transposable elements, group II introns, and conducted an in-depth analysis of their content and the microevolutionary processes responsible for their ..
- Integrative modeling defines the Nova splicing-regulatory network and its combinatorial controlsChaolin Zhang
Laboratory of Molecular Neuro Oncology, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
Science 329:439-43. 2010..Thus, we have developed a general approach to understanding mammalian RNA regulation at the systems level...
- The in vivo kinetics of RNA polymerase II elongation during co-transcriptional splicingYehuda 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...
- Investigation of loss and gain of introns in the compact genomes of pufferfishes (Fugu and Tetraodon)Yong Hwee Loh
Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research, Biopolis, Singapore
Mol Biol Evol 25:526-35. 2008..The introns lost in pufferfishes and mammals are significantly shorter than the mean size of introns in the genome...
- Structural organization of the human gene encoding nuclear lamin A and nuclear lamin CF Lin
Department of Medicine, Mount Sinai School of Medicine, New York, New York 10029
J Biol Chem 268:16321-6. 1993..Analysis of the intron positions in these genes supports the hypothesis that the nuclear lamins and other intermediate filament proteins arose from a common ancestor...
- Genome-wide functional analysis of human 5' untranslated region intronsCan Cenik
Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology, 250 Longwood Avenue, SGMB 322, Boston, MA 02115, USA
Genome Biol 11:R29. 2010Approximately 35% of human genes contain introns within the 5' untranslated region (UTR). Introns in 5'UTRs differ from those in coding regions and 3'UTRs with respect to nucleotide composition, length distribution and density...
- Imprinted expression of the Igf2r gene depends on an intronic CpG islandA Wutz
Institute of Molecular Pathology, Vienna, Austria
Nature 389:745-9. 1997..The production of an antisense RNA by the repressed parental allele is reminiscent of the imprinting of the Igf2/H19 gene pair and may indicate that expression competition could play a general role in imprinting...
- Gene expression enhancement mediated by the 5' UTR intron of the rice rubi3 gene varied remarkably among tissues in transgenic rice plantsJianli Lu
Department of Crop Science, North Carolina State University, Raleigh, NC 27695, USA
Mol Genet Genomics 279:563-72. 2008b>Introns are important sequence elements that modulate the expression of genes. Using the GUS reporter gene driven by the promoter of the rice (Oryza sativa L...
- Mystery of intron gain: new data and new modelsScott William Roy
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
Trends Genet 25:67-73. 2009Despite their ubiquity, the mechanisms and evolutionary forces responsible for the origins of spliceosomal introns remain mysterious...
- Intronic microRNAs support their host genes by mediating synergistic and antagonistic regulatory effectsDominik Lutter
Institute of Bioinformatics and Systems Biology, CMB, Helmholtz Zentrum Munchen, Germany
BMC Genomics 11:224. 2010..About 37% of mammalian microRNAs appear to be located within introns of protein coding genes, linking their expression to the promoter-driven regulation of the host gene...
- Scipio: using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related speciesOliver Keller
Universitat Gottingen, Institut fur Informatik, Lotzestr 16 18, 37083 Göttingen, Germany
BMC Bioinformatics 9:278. 2008..Finding the corresponding gene of a given protein sequence by means of conventional tools is error prone, and cannot be completed without manual inspection, which is time consuming and requires considerable experience...
- MicroRNA-33 and the SREBP host genes cooperate to control cholesterol homeostasisS Hani Najafi-Shoushtari
Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
Science 328:1566-9. 2010..We show here that microRNAs (miR-33a/b) embedded within introns of the SREBP genes target the adenosine triphosphate-binding cassette transporter A1 (ABCA1), an important ..
- Tissue-dependent enhancement of transgene expression by introns of replacement histone H3 genes of ArabidopsisN Chaubet-Gigot
, CNRS, Universit Louis Pasteur, Strasbourg, France
Plant Mol Biol 45:17-30. 2001..We demonstrate that the introns located within the 5'-untranslated regions (5'-UTR) of the two Arabidopsis replacement H3 genes will abolish the ..
- Complete plastid genome sequence of the chickpea (Cicer arietinum) and the phylogenetic distribution of rps12 and clpP intron losses among legumes (Leguminosae)Robert K Jansen
Section of Integrative Biology and Institute of Cellular and Molecular Biology, Biological Laboratories 404, University of Texas, Austin, TX 78712, USA
Mol Phylogenet Evol 48:1204-17. 2008..Two genes have lost their introns, one in the 3'exon of the transpliced gene rps12, and the one between exons 1 and 2 of clpP; this represents the ..
Research Grants101 found, 100 shown here
- MECHANISM OF PRE-MRNA SPLICINGMAGDA KONARSKA; Fiscal Year: 2009..Typically, splice site signals of alternatively spliced introns deviate from the consensus, and are often accompanied by splicing enhancer motifs...
- MITDNA MUTAGENESIS BY ENVIRONMENTAL CARCINOGENSKeshav 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 ..
- Involvement of Proteins in Splicing Group I and Group II IntronsAlan Lambowitz; Fiscal Year: 2009The proposed research is a continued study of the involvement of proteins in splicing group I and II introns. These introns use RNA-catalyzed splicing mechanisms, but require proteins to help fold the intron RNA into the catalyti- ..
- Involvement of Proteins in Splicing Group I and Group II IntronsAlan Lambowitz; Fiscal Year: 2009The proposed research is a continued study of the involvement of proteins in splicing group I and II introns. These introns use RNA-catalyzed splicing mechanisms, but require proteins to help fold the intrpn RNA into the catalyti- cally ..
- Involvement of Proteins in Splicing Group I and Group II IntronsAlan Lambowitz; Fiscal Year: 2007The proposed research is a continued study of the involvement of proteins in splicing group I and II introns. These introns use RNA-catalyzed splicing mechanisms, but require proteins to help fold the intron RNA into the catalyti- cally ..
- Involvement of Proteins in Splicing Group I and Group II IntronsAlan M Lambowitz; Fiscal Year: 2010The proposed research is a continued study of the involvement of proteins in splicing group I and II introns. These introns use RNA-catalyzed splicing mechanisms, but require proteins to help fold the intron RNA into the catalyti- ..
- BIOCHEMISTRY OF PRE-MRNA SPLICINGADRIAN KRAINER; Fiscal Year: 2007Pre-mRNA splicing is an essential step in gene expression. It involves precise excision of introns and joining of exons from primary transcripts in the nucleus to generate mature mRNA, the template for protein synthesis in the cytoplasm...
- BIOCHEMISTRY OF PRE-MRNA SPLICINGADRIAN KRAINER; Fiscal Year: 2009Pre-mRNA splicing is an essential step in gene expression. It involves precise excision of introns and joining of exons from primary transcripts in the nucleus to generate mature mRNA, the template for protein synthesis in the ..
- BIOCHEMISTRY OF PRE-MRNA SPLICINGAdrian R Krainer; Fiscal Year: 2010Pre-mRNA splicing is an essential step in gene expression. It involves precise excision of introns and joining of exons from primary transcripts in the nucleus to generate mature mRNA, the template for protein synthesis in the ..
- Group II Intron Mobility and Gene TargetingAlan M Lambowitz; Fiscal Year: 2010The proposed research is a continued study of mobile group II introns and their applications in gene targeting...
- Transcriptional elongation and splicing in human genes in situRichard A Padgett; Fiscal Year: 2010..Some genes can exceed one million base pairs in length. Many of these long genes also contain introns of hundreds of kilobases in length...
- MECHANISM OF PRE-MRNA SPLICINGMAGDA KONARSKA; Fiscal Year: 2010..Typically, splice site signals of alternatively spliced introns deviate from the consensus, and are often accompanied by splicing enhancer motifs...
- SPLICING OF MRNA PRECURSORSMichael R Green; Fiscal Year: 2010The 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...
- GROUP II INTRON RNA SPLICING AND MOBILITYAlan Lambowitz; Fiscal Year: 2002..continued biochemical-genetics studies of the protein-dependent splicing and mobility reactions of group II introns. Group II intron mobility is mediated by intron-encoded reverse transcriptases that also function as maturases to ..
- Group II Intron Mobility and Gene TargetingAlan Lambowitz; Fiscal Year: 2006The proposed research is a continued study of group II intron mobility mechanisms and the development of group II introns as vectors for targeted gene disruption and site-specific DNA insertion...
- The Mammalian Cellular Splicing Machine - Structure and FunctionRuth Sperling; Fiscal Year: 2010Most eukaryotic pre-mRNAs contain non-coding sequences (introns) that must be removed in order to accurately place the coding sequences (exons) in the correct reading frame...
- Involvement of Proteins in Group I + II Intron SplicingAlan Lambowitz; Fiscal Year: 2006The proposed research is a continued study of the involvement of proteins in splicing group I and group II introns. These introns use RNA-catalyzed splicing mechanisms, but require proteins for efficient splicing in vivo to help fold ..
- The influence of genotype on the outcome of gene transfer in beta-thalassemiaStefano Rivella; Fiscal Year: 2010..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...
- The Catalytic Mechanism of Nuclear Premessenger RNA Splicing by the SpliceosomeJonathan P Staley; Fiscal Year: 2010Eukaryotic 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 ..
- REGULATION AND GENE EXPRESSION OF CYTOCHROME CFred Sherman; Fiscal Year: 2001..is responsible for degrading RNA in nuclei, including abnormal cyc1-512 mRNAs, normal mRNAs retained in nuclei, introns of mRNA, introns of tRNA, and spacer sequences processed from rRNA...
- Physical and functional probing of DEAD-box proteins as general RNA chaperonesRick Russell; Fiscal Year: 2009..was shown in 2002 that the Neurospora crassa CYT-19 protein functions in folding of several mitochondrial group I introns. Further work indicated that CYT-19 can also interact productively with group II introns, indicating that it ..
- Physical and functional probing of DEAD-box proteins as general RNA chaperonesRick Russell; Fiscal Year: 2010..was shown in 2002 that the Neurospora crassa CYT-19 protein functions in folding of several mitochondrial group I introns. Further work indicated that CYT-19 can also interact productively with group II introns, indicating that it ..
- Analysis of Group I and II Introns in Mammalian CellsBruce Sullenger; Fiscal Year: 2005The overall goal of this proposal is to explore the ability of group I and group II introns to repair genetic instructions inside mammalian cells...
- Kinetic Dissection of the RNA Chaperone Protein CYT-19Rick Russell; Fiscal Year: 2007..colleagues showed that the Neurospora crassa CYT-19 protein functions by accelerating folding of several group I introns. These introns also require the splicing factor CYT-18, additionally suggesting that CYT-19 may be targeted to ..
- Genetic circuits based on allosteric ribozymesAndrew 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...
- Genetic circuits based on allosteric ribozymesAndrew Ellington; Fiscal Year: 2007..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...
- Mechanisms Regulating Alternative pre-mRNA SplicingJames Patton; Fiscal Year: 2005Most eukaryotic genes are interrupted by non-coding introns that must be removed from pre-mRNA transcripts for the production of functional proteins...
- MECHANISMS OF JUXTAGLOMERULAR CELL RENIN GENE EXPRESSIONDaniel Catanzaro; Fiscal Year: 1999....
- MOLECULAR ANALYSIS OF THE WAXY MUTANTS OF MAIZESusan Wessler; Fiscal Year: 1993..Whereas Group I and II introns are thought to be evolving into mobile DNA, the Ds elements may be mobile DNA evolving into introns...
- EXON LIGATION--THE SPLICEOSOME AND GROUP 11 INTRONSMelissa Moore; Fiscal Year: 1999The removal of introns by RNA splicing is an essential step in the expression of almost all human genes...
- MECHANISM OF SEQUENCE SPECIFIC RETROTRANSPOSITION OF R2Thomas Eickbush; Fiscal Year: 1999..target primed reverse transcription mechanism is believed to used by most other non-LTR elements, the group II introns, an is likely the origin of SINEs, processed pseudogenes and maybe even of introns...
- Analysis of mRNA Polyadenylation across Species and TissuesBin Tian; Fiscal Year: 2009..In addition, a large fraction of human genes have polyadenylation events in introns, leading to mRNA variants with different protein coding sequence and indicating dynamic interplay between ..
- Analysis of mRNA Polyadenylation across Species and TissuesBin Tian; Fiscal Year: 2009..In addition, a large fraction of human genes have polyadenylation events in introns, leading to mRNA variants with different protein coding sequence and indicating dynamic interplay between ..
- GENE EXPRESSION IN CELL ORGANELLESRICHARD HALLICK; Fiscal Year: 1993How have introns evolved? Did they occur early in the prebiotic world and contribute to the formation of ancient genes by "exon shuffling," or have they been inserted into genes as mobile genetic elements throughout evolution? Important ..
- Biochemical Characterization of p68 RNA HelicaseZhi Ren Liu; Fiscal Year: 2007Summary Remove of introns from messenger RNA precursors (pre-mRNA) is an essential process in eukaryotic gene expression...
- SPLICING OF MRNA PRECURSORSMichael Green; Fiscal Year: 2007..The primary transcripts of eukaryotic structural genes (precursor mRNAs; pre-mRNAs) contain intervening sequences (introns) that are removed by RNA splicing...