RNAi-mediated pathways in the nucleus View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2005-01

AUTHORS

Marjori A. Matzke, James A. Birchler

ABSTRACT

Key PointsThere is increasing evidence that RNA interference (RNAi)-mediated pathways have important roles in gene regulation at the nuclear-genome level. Key proteins of the RNAi machinery (Dicer, Argonaute, RNA-dependent RNA polymerase) function together with small RNAs to target epigenetic modifications and silencing of homologous regions of the genome.RNA-directed DNA methylation has been well documented in plants and recent reports indicate that it might occur in mammalian cells. RNA-directed DNA methylation can target DNA sequences that are as short as 30 bp for dense cytosine methylation, in contrast to histone modifications, which take place in the context of nucleosomes and comprise 147 bp of DNA.RNAi-mediated heterochromatin formation is important for centromere stucture and function in fission yeast, Drosophila melanogaster, mammals and perhaps other organisms. RNAi-mediated heterochromatin can also be induced at non-centromeric, interstitial regions to silence retrotransposons and regulate endogenous genes.In Neurospora crassa, unpaired DNA can be silenced during meiosis by an RNAi-related pathway. This process might silence new transposon inserts. A similar pathway operates during meiosis in Caenorhabditis elegans.Pairing-sensitive silencing in D. melanogaster, which involves greater silencing of somatically paired transgenes than unpaired copies, is intensified by mutations in the RNAi pathway.RNAi-mediated heterochromatin marks internal eliminated sequences for deletion in developing macronuclei of Tetrahymena thermophila, perhaps to remove transposons that have invaded the germline genome of micronuclei.Transposable elements and related repeats are primary targets for RNAi-mediated pathways in the nucleus, consistent with a role for RNAi in host defence against invasive sequences.Despite the importance of RNAi-mediated pathways in establishing epigenetic modifications, not all DNA methylation and heterochromatin formation is induced by RNA. For example, N. crassa, which has the machinery for RNAi, does not seem to use the RNAi pathway for heterochromatin formation or DNA methylation.Important questions for future research concern the universality of various RNAi-mediated nuclear pathways and the molecular composition of nuclear silencing-effector complexes. More... »

PAGES

24-35

References to SciGraph publications

  • 2003-06-12. Unpaired genes do not silence their paired neighbors in CURRENT GENETICS
  • 2003-10-30. Maintenance of heterochromatin by RNA interference of tandem repeats in NATURE GENETICS
  • 2003-11-16. Structure and conserved RNA binding of the PAZ domain in NATURE
  • 2000-04. Mutations in ATRX, encoding a SWI/SNF-like protein, cause diverse changes in the pattern of DNA methylation in NATURE GENETICS
  • 2004-04. The role of MET1 in RNA-directed de novoand maintenance methylation of CG dinucleotides in PLANT MOLECULAR BIOLOGY
  • 2004-10-10. RITS acts in cis to promote RNA interference–mediated transcriptional and post-transcriptional silencing in NATURE GENETICS
  • 2004-07. Role of transposable elements in heterochromatin and epigenetic control in NATURE
  • 2004-02-24. RNase III enzymes and the initiation of gene silencing in NATURE STRUCTURAL & MOLECULAR BIOLOGY
  • 2003-02. RNA interference is required for normal centromere function infission yeast in CHROMOSOME RESEARCH
  • 2001-11. A histone H3 methyltransferase controls DNA methylation in Neurospora crassa in NATURE
  • 2004-09. The roles of histone modifications and small RNA in centromere function in CHROMOSOME RESEARCH
  • 2001-03. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins in NATURE
  • 2004-09-15. The role of RNA interference in heterochromatic silencing in NATURE
  • 2004-09-15. RNA silencing in plants in NATURE
  • 2001-03. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain in NATURE
  • 2001-07. A role of the Drosophila homeless gene in repression of Stellate in male meiosis in CHROMOSOMA
  • 2004-07-11. Dicer is essential for formation of the heterochromatin structure in vertebrate cells in NATURE CELL BIOLOGY
  • 2000-06. Transgene silencing by the host genome defense: implications for the evolution of epigenetic control mechanisms in plants and vertebrates in PLANT MOLECULAR BIOLOGY
  • 2004-08-15. Induction of DNA methylation and gene silencing by short interfering RNAs in human cells in NATURE
  • 2004-07. MicroRNAs: small RNAs with a big role in gene regulation in NATURE REVIEWS GENETICS
  • 2002-03-17. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase in NATURE
  • 2003-12-21. Meiotic pairing and imprinted X chromatin assembly in Caenorhabditis elegans in NATURE GENETICS
  • Journal

    TITLE

    Nature Reviews Genetics

    ISSUE

    1

    VOLUME

    6

    Related Patents

  • Transgenic Plants Having Increased Tolerance To Aluminum
  • Methods For Collecting And Detecting Oligonucleotides
  • Methods And Compostions For Modulating The Mirna Pathway
  • Transgenic Plants Having Increased Tolerance To Aluminum
  • Transgenic Plants Having Altered Biomass Composition
  • Recombinant Dna Constructs And Methods For Controlling Gene Expression
  • Rna Sequence-Specific Mediators Of Rna Interference
  • Rna Interference Mediating Small Rna Molecules
  • Transgenic Plants Having Increased Tolerance To Aluminum
  • Rna Interference Mediating Small Rna Molecules
  • Transgenic Plants Having Altered Biomass Composition
  • Rna Interference Mediating Small Rna Molecules
  • Plant Micrornas And Methods Of Use Thereof
  • Methods And Compositions For Modulating The Mirna Pathway
  • Rna Sequence-Specific Mediators Of Rna Interference
  • Rna Interference Mediating Small Rna Molecules
  • Rna Sequence-Specific Mediators Of Rna Interference
  • Methods And Materials For High Throughput Testing Of Transgene Combinations
  • Rna Sequence-Specific Mediators Of Rna Interference
  • Transgenic Plants Having Increased Biomass
  • Transgenic Plants Having Increased Tolerance To Aluminum
  • Transgenic Plants Having Altered Biomass Composition
  • Rna Interference Mediating Small Rna Molecules
  • Transgenic Plants Having Altered Biomass Composition
  • Methods And Dna Constructs For Autoregulating Transgene Silencing
  • Rna Interference Mediating Small Rna Molecules
  • Rna Sequence-Specific Mediators Of Rna Interference
  • In Vivo Production Of Small Interfering Rnas That Mediate Gene Silencing
  • Transgenic Plants Having Increased Biomass
  • Methods, Compositions, And Kits For Collecting And Detecting Oligonucleotides
  • Modulating Light Response Pathways In Plants, Increasing Light-Related Tolerances In Plants, And Increasing Biomass In Plants
  • Rna Interference Mediating Small Rna Molecules
  • Transgenic Plants Having Altered Biomass Composition
  • Rna Sequence-Specific Mediators Of Rna Interference
  • Rna Interference Mediating Small Rna Molecules
  • Rna Interference Mediating Small Rna Molecules
  • Rna Interference Mediating Small Rna Molecules
  • Rna Sequence-Specific Mediators Of Rna Interference
  • Rna Interference Mediating Small Rna Molecules
  • Transgenic Plants Having Increased Tolerance To Aluminum
  • Rna Sequence-Specific Mediators Of Rna Interference
  • Rna Interference Mediating Small Rna Molecules
  • Rna Interference Mediating Small Rna Molecules
  • Recombinant Dna Constructs And Methods For Controlling Gene Expression
  • Sirna Inhibition Of Pi3k P85, P110, And Akt2 And Methods Of Use
  • Rna Sequence-Specific Mediators Of Rna Interference
  • Methods For Collecting And Detecting Oligonucleotides
  • Rna Sequence-Specific Mediators Of Rna Interference
  • Recombinant Dna Constructs And Methods For Controlling Gene Expression
  • Recombinant Dna Constructs And Methods For Controlling Gene Expression
  • Methods, Compositions, And Kits For Collecting And Detecting Oligonucleotides
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/nrg1500

    DOI

    http://dx.doi.org/10.1038/nrg1500

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1006972186

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/15630419


    Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
    Incoming Citations Browse incoming citations for this publication using opencitations.net

    JSON-LD is the canonical representation for SciGraph data.

    TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

    [
      {
        "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
        "about": [
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Biological Sciences", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0601", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Biochemistry and Cell Biology", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Genetics", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Animals", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Cell Nucleus", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "DNA Methylation", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Gene Silencing", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Heterochromatin", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Mammals", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Meiosis", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Models, Genetic", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Multigene Family", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "RNA Interference", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "RNA Processing, Post-Transcriptional", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "RNA, Small Interfering", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, UZA2, Pharmazie Zentrum, Althanstrasse 14/2D-541, A-1090, Vienna, Austria", 
              "id": "http://www.grid.ac/institutes/grid.24194.3a", 
              "name": [
                "Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, UZA2, Pharmazie Zentrum, Althanstrasse 14/2D-541, A-1090, Vienna, Austria"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Matzke", 
            "givenName": "Marjori A.", 
            "id": "sg:person.01366677656.47", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01366677656.47"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Division of Biological Sciences, University of Missouri, 117 Tucker Hall, 65211, Columbia, Missouri, USA", 
              "id": "http://www.grid.ac/institutes/grid.134936.a", 
              "name": [
                "Division of Biological Sciences, University of Missouri, 117 Tucker Hall, 65211, Columbia, Missouri, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Birchler", 
            "givenName": "James A.", 
            "id": "sg:person.0577755340.61", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0577755340.61"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1023/a:1022815931524", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1036577790", 
              "https://doi.org/10.1023/a:1022815931524"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1023/b:chro.0000036584.40567.e5", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1052128690", 
              "https://doi.org/10.1023/b:chro.0000036584.40567.e5"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng1283", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1043285362", 
              "https://doi.org/10.1038/ng1283"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s11103-004-0179-1", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1011870278", 
              "https://doi.org/10.1007/s11103-004-0179-1"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/35104508", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1018899294", 
              "https://doi.org/10.1038/35104508"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/74191", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1026545365", 
              "https://doi.org/10.1038/74191"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrg1379", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1001799892", 
              "https://doi.org/10.1038/nrg1379"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00294-003-0412-5", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1045251519", 
              "https://doi.org/10.1007/s00294-003-0412-5"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature02651", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1050259576", 
              "https://doi.org/10.1038/nature02651"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng1452", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1006451203", 
              "https://doi.org/10.1038/ng1452"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s004120100136", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1024795199", 
              "https://doi.org/10.1007/s004120100136"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng1252", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1029916094", 
              "https://doi.org/10.1038/ng1252"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ncb1155", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1009605920", 
              "https://doi.org/10.1038/ncb1155"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1023/a:1006484806925", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1033006586", 
              "https://doi.org/10.1023/a:1006484806925"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature02129", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015025248", 
              "https://doi.org/10.1038/nature02129"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature02875", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1039222604", 
              "https://doi.org/10.1038/nature02875"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature731", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1030808591", 
              "https://doi.org/10.1038/nature731"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/35065132", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1020526163", 
              "https://doi.org/10.1038/35065132"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nsmb729", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015922363", 
              "https://doi.org/10.1038/nsmb729"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature02889", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1040340027", 
              "https://doi.org/10.1038/nature02889"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/35065138", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1018164085", 
              "https://doi.org/10.1038/35065138"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature02874", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1025532636", 
              "https://doi.org/10.1038/nature02874"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2005-01", 
        "datePublishedReg": "2005-01-01", 
        "description": "Key PointsThere is increasing evidence that RNA interference (RNAi)-mediated pathways have important roles in gene regulation at the nuclear-genome level. Key proteins of the RNAi machinery (Dicer, Argonaute, RNA-dependent RNA polymerase) function together with small RNAs to target epigenetic modifications and silencing of homologous regions of the genome.RNA-directed DNA methylation has been well documented in plants and recent reports indicate that it might occur in mammalian cells. RNA-directed DNA methylation can target DNA sequences that are as short as 30 bp for dense cytosine methylation, in contrast to histone modifications, which take place in the context of nucleosomes and comprise 147 bp of DNA.RNAi-mediated heterochromatin formation is important for centromere stucture and function in fission yeast, Drosophila melanogaster, mammals and perhaps other organisms. RNAi-mediated heterochromatin can also be induced at non-centromeric, interstitial regions to silence retrotransposons and regulate endogenous genes.In Neurospora crassa, unpaired DNA can be silenced during meiosis by an RNAi-related pathway. This process might silence new transposon inserts. A similar pathway operates during meiosis in Caenorhabditis elegans.Pairing-sensitive silencing in D. melanogaster, which involves greater silencing of somatically paired transgenes than unpaired copies, is intensified by mutations in the RNAi pathway.RNAi-mediated heterochromatin marks internal eliminated sequences for deletion in developing macronuclei of Tetrahymena thermophila, perhaps to remove transposons that have invaded the germline genome of micronuclei.Transposable elements and related repeats are primary targets for RNAi-mediated pathways in the nucleus, consistent with a role for RNAi in host defence against invasive sequences.Despite the importance of RNAi-mediated pathways in establishing epigenetic modifications, not all DNA methylation and heterochromatin formation is induced by RNA. For example, N. crassa, which has the machinery for RNAi, does not seem to use the RNAi pathway for heterochromatin formation or DNA methylation.Important questions for future research concern the universality of various RNAi-mediated nuclear pathways and the molecular composition of nuclear silencing-effector complexes.", 
        "genre": "article", 
        "id": "sg:pub.10.1038/nrg1500", 
        "isAccessibleForFree": false, 
        "isPartOf": [
          {
            "id": "sg:journal.1023607", 
            "issn": [
              "1471-0056", 
              "1471-0064"
            ], 
            "name": "Nature Reviews Genetics", 
            "publisher": "Springer Nature", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "1", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "6"
          }
        ], 
        "keywords": [
          "heterochromatin formation", 
          "DNA methylation", 
          "RNAi pathway", 
          "epigenetic modifications", 
          "pairing-sensitive silencing", 
          "RNAi-related pathways", 
          "context of nucleosomes", 
          "bp of DNA", 
          "unpaired copies", 
          "invasive sequences", 
          "unpaired DNA", 
          "heterochromatin marks", 
          "RNAi machinery", 
          "fission yeast", 
          "D. melanogaster", 
          "histone modifications", 
          "Caenorhabditis elegans", 
          "cytosine methylation", 
          "Drosophila melanogaster", 
          "germline genome", 
          "gene regulation", 
          "small RNAs", 
          "endogenous genes", 
          "transposable elements", 
          "N. crassa", 
          "nuclear pathways", 
          "mammalian cells", 
          "Neurospora crassa", 
          "related repeats", 
          "DNA sequences", 
          "RNA interference", 
          "Tetrahymena thermophila", 
          "key proteins", 
          "RNAi", 
          "homologous regions", 
          "methylation", 
          "transposon inserts", 
          "RNA", 
          "similar pathways", 
          "melanogaster", 
          "genome", 
          "crassa", 
          "meiosis", 
          "pathway", 
          "silencing", 
          "host defense", 
          "molecular composition", 
          "machinery", 
          "DNA", 
          "sequence", 
          "primary target", 
          "interstitial regions", 
          "Key PointsThere", 
          "BP", 
          "elegans", 
          "retrotransposons", 
          "heterochromatin", 
          "nucleosomes", 
          "important role", 
          "transposon", 
          "mammals", 
          "thermophila", 
          "macronucleus", 
          "yeast", 
          "genes", 
          "repeats", 
          "organisms", 
          "recent reports", 
          "transgene", 
          "plants", 
          "protein", 
          "nucleus", 
          "deletion", 
          "mutations", 
          "regulation", 
          "modification", 
          "role", 
          "copies", 
          "future research concerns", 
          "defense", 
          "cells", 
          "formation", 
          "micronuclei", 
          "region", 
          "complexes", 
          "target", 
          "important questions", 
          "inserts", 
          "marks", 
          "function", 
          "composition", 
          "contrast", 
          "evidence", 
          "importance", 
          "levels", 
          "elements", 
          "stucture", 
          "interference", 
          "process", 
          "report", 
          "questions", 
          "example", 
          "context", 
          "place", 
          "research concerns", 
          "concern", 
          "universality"
        ], 
        "name": "RNAi-mediated pathways in the nucleus", 
        "pagination": "24-35", 
        "productId": [
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1006972186"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1038/nrg1500"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "15630419"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1038/nrg1500", 
          "https://app.dimensions.ai/details/publication/pub.1006972186"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2022-12-01T06:24", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-springernature-scigraph/baseset/20221201/entities/gbq_results/article/article_391.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://doi.org/10.1038/nrg1500"
      }
    ]
     

    Download the RDF metadata as:  json-ld nt turtle xml License info

    HOW TO GET THIS DATA PROGRAMMATICALLY:

    JSON-LD is a popular format for linked data which is fully compatible with JSON.

    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1038/nrg1500'

    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/nrg1500'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/nrg1500'

    RDF/XML is a standard XML format for linked data.

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/nrg1500'


     

    This table displays all metadata directly associated to this object as RDF triples.

    318 TRIPLES      21 PREDICATES      168 URIs      137 LITERALS      19 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1038/nrg1500 schema:about N15111e197a72431fa96e4e99b5dfe591
    2 N23c502b7f9ab49069631ccc941287596
    3 N2eb72bce60df45d8a367528f26d7ea74
    4 N321e457712924ff3b0659d1c6ab601c1
    5 N5810808a41c7436f9d9e689400435fa8
    6 N623728b86e034495b546aca283519659
    7 N7440441301ac425db26404cc840e160b
    8 N769d91edb43b4896ab7a64a28117e9f6
    9 Na09bdc0f211c4ec180a840294397c21a
    10 Na7d8d18bd8bf4e28ab3030cb953dad38
    11 Nc637326c722345dd96849b3d351c2ca2
    12 Necca86ec796b4bc394e25dfb62e2fe44
    13 anzsrc-for:06
    14 anzsrc-for:0601
    15 anzsrc-for:0604
    16 schema:author Nebc26f97265843f5828209682f959957
    17 schema:citation sg:pub.10.1007/s00294-003-0412-5
    18 sg:pub.10.1007/s004120100136
    19 sg:pub.10.1007/s11103-004-0179-1
    20 sg:pub.10.1023/a:1006484806925
    21 sg:pub.10.1023/a:1022815931524
    22 sg:pub.10.1023/b:chro.0000036584.40567.e5
    23 sg:pub.10.1038/35065132
    24 sg:pub.10.1038/35065138
    25 sg:pub.10.1038/35104508
    26 sg:pub.10.1038/74191
    27 sg:pub.10.1038/nature02129
    28 sg:pub.10.1038/nature02651
    29 sg:pub.10.1038/nature02874
    30 sg:pub.10.1038/nature02875
    31 sg:pub.10.1038/nature02889
    32 sg:pub.10.1038/nature731
    33 sg:pub.10.1038/ncb1155
    34 sg:pub.10.1038/ng1252
    35 sg:pub.10.1038/ng1283
    36 sg:pub.10.1038/ng1452
    37 sg:pub.10.1038/nrg1379
    38 sg:pub.10.1038/nsmb729
    39 schema:datePublished 2005-01
    40 schema:datePublishedReg 2005-01-01
    41 schema:description Key PointsThere is increasing evidence that RNA interference (RNAi)-mediated pathways have important roles in gene regulation at the nuclear-genome level. Key proteins of the RNAi machinery (Dicer, Argonaute, RNA-dependent RNA polymerase) function together with small RNAs to target epigenetic modifications and silencing of homologous regions of the genome.RNA-directed DNA methylation has been well documented in plants and recent reports indicate that it might occur in mammalian cells. RNA-directed DNA methylation can target DNA sequences that are as short as 30 bp for dense cytosine methylation, in contrast to histone modifications, which take place in the context of nucleosomes and comprise 147 bp of DNA.RNAi-mediated heterochromatin formation is important for centromere stucture and function in fission yeast, Drosophila melanogaster, mammals and perhaps other organisms. RNAi-mediated heterochromatin can also be induced at non-centromeric, interstitial regions to silence retrotransposons and regulate endogenous genes.In Neurospora crassa, unpaired DNA can be silenced during meiosis by an RNAi-related pathway. This process might silence new transposon inserts. A similar pathway operates during meiosis in Caenorhabditis elegans.Pairing-sensitive silencing in D. melanogaster, which involves greater silencing of somatically paired transgenes than unpaired copies, is intensified by mutations in the RNAi pathway.RNAi-mediated heterochromatin marks internal eliminated sequences for deletion in developing macronuclei of Tetrahymena thermophila, perhaps to remove transposons that have invaded the germline genome of micronuclei.Transposable elements and related repeats are primary targets for RNAi-mediated pathways in the nucleus, consistent with a role for RNAi in host defence against invasive sequences.Despite the importance of RNAi-mediated pathways in establishing epigenetic modifications, not all DNA methylation and heterochromatin formation is induced by RNA. For example, N. crassa, which has the machinery for RNAi, does not seem to use the RNAi pathway for heterochromatin formation or DNA methylation.Important questions for future research concern the universality of various RNAi-mediated nuclear pathways and the molecular composition of nuclear silencing-effector complexes.
    42 schema:genre article
    43 schema:isAccessibleForFree false
    44 schema:isPartOf N2036eefafee64539ae7b4861cc871a87
    45 N7bf34b177132431a965083e13a68569c
    46 sg:journal.1023607
    47 schema:keywords BP
    48 Caenorhabditis elegans
    49 D. melanogaster
    50 DNA
    51 DNA methylation
    52 DNA sequences
    53 Drosophila melanogaster
    54 Key PointsThere
    55 N. crassa
    56 Neurospora crassa
    57 RNA
    58 RNA interference
    59 RNAi
    60 RNAi machinery
    61 RNAi pathway
    62 RNAi-related pathways
    63 Tetrahymena thermophila
    64 bp of DNA
    65 cells
    66 complexes
    67 composition
    68 concern
    69 context
    70 context of nucleosomes
    71 contrast
    72 copies
    73 crassa
    74 cytosine methylation
    75 defense
    76 deletion
    77 elegans
    78 elements
    79 endogenous genes
    80 epigenetic modifications
    81 evidence
    82 example
    83 fission yeast
    84 formation
    85 function
    86 future research concerns
    87 gene regulation
    88 genes
    89 genome
    90 germline genome
    91 heterochromatin
    92 heterochromatin formation
    93 heterochromatin marks
    94 histone modifications
    95 homologous regions
    96 host defense
    97 importance
    98 important questions
    99 important role
    100 inserts
    101 interference
    102 interstitial regions
    103 invasive sequences
    104 key proteins
    105 levels
    106 machinery
    107 macronucleus
    108 mammalian cells
    109 mammals
    110 marks
    111 meiosis
    112 melanogaster
    113 methylation
    114 micronuclei
    115 modification
    116 molecular composition
    117 mutations
    118 nuclear pathways
    119 nucleosomes
    120 nucleus
    121 organisms
    122 pairing-sensitive silencing
    123 pathway
    124 place
    125 plants
    126 primary target
    127 process
    128 protein
    129 questions
    130 recent reports
    131 region
    132 regulation
    133 related repeats
    134 repeats
    135 report
    136 research concerns
    137 retrotransposons
    138 role
    139 sequence
    140 silencing
    141 similar pathways
    142 small RNAs
    143 stucture
    144 target
    145 thermophila
    146 transgene
    147 transposable elements
    148 transposon
    149 transposon inserts
    150 universality
    151 unpaired DNA
    152 unpaired copies
    153 yeast
    154 schema:name RNAi-mediated pathways in the nucleus
    155 schema:pagination 24-35
    156 schema:productId N31ececff84a94e88b7704cd27b8c09d6
    157 N5513f35778f14a1891aef73636d31b95
    158 N749dd24a66a3460cab79637613f59b83
    159 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006972186
    160 https://doi.org/10.1038/nrg1500
    161 schema:sdDatePublished 2022-12-01T06:24
    162 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    163 schema:sdPublisher Ncbef294db20d434397d1985c2a14ce8e
    164 schema:url https://doi.org/10.1038/nrg1500
    165 sgo:license sg:explorer/license/
    166 sgo:sdDataset articles
    167 rdf:type schema:ScholarlyArticle
    168 N15111e197a72431fa96e4e99b5dfe591 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    169 schema:name RNA, Small Interfering
    170 rdf:type schema:DefinedTerm
    171 N2036eefafee64539ae7b4861cc871a87 schema:volumeNumber 6
    172 rdf:type schema:PublicationVolume
    173 N23c502b7f9ab49069631ccc941287596 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    174 schema:name Mammals
    175 rdf:type schema:DefinedTerm
    176 N2eb72bce60df45d8a367528f26d7ea74 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    177 schema:name DNA Methylation
    178 rdf:type schema:DefinedTerm
    179 N31ececff84a94e88b7704cd27b8c09d6 schema:name doi
    180 schema:value 10.1038/nrg1500
    181 rdf:type schema:PropertyValue
    182 N321e457712924ff3b0659d1c6ab601c1 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    183 schema:name Heterochromatin
    184 rdf:type schema:DefinedTerm
    185 N5513f35778f14a1891aef73636d31b95 schema:name dimensions_id
    186 schema:value pub.1006972186
    187 rdf:type schema:PropertyValue
    188 N5810808a41c7436f9d9e689400435fa8 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    189 schema:name Multigene Family
    190 rdf:type schema:DefinedTerm
    191 N623728b86e034495b546aca283519659 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    192 schema:name RNA Processing, Post-Transcriptional
    193 rdf:type schema:DefinedTerm
    194 N7440441301ac425db26404cc840e160b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    195 schema:name Models, Genetic
    196 rdf:type schema:DefinedTerm
    197 N749dd24a66a3460cab79637613f59b83 schema:name pubmed_id
    198 schema:value 15630419
    199 rdf:type schema:PropertyValue
    200 N769d91edb43b4896ab7a64a28117e9f6 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    201 schema:name Cell Nucleus
    202 rdf:type schema:DefinedTerm
    203 N7bf34b177132431a965083e13a68569c schema:issueNumber 1
    204 rdf:type schema:PublicationIssue
    205 N912ceb72f12c492db4dd87836d0bafff rdf:first sg:person.0577755340.61
    206 rdf:rest rdf:nil
    207 Na09bdc0f211c4ec180a840294397c21a schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    208 schema:name Animals
    209 rdf:type schema:DefinedTerm
    210 Na7d8d18bd8bf4e28ab3030cb953dad38 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    211 schema:name RNA Interference
    212 rdf:type schema:DefinedTerm
    213 Nc637326c722345dd96849b3d351c2ca2 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    214 schema:name Meiosis
    215 rdf:type schema:DefinedTerm
    216 Ncbef294db20d434397d1985c2a14ce8e schema:name Springer Nature - SN SciGraph project
    217 rdf:type schema:Organization
    218 Nebc26f97265843f5828209682f959957 rdf:first sg:person.01366677656.47
    219 rdf:rest N912ceb72f12c492db4dd87836d0bafff
    220 Necca86ec796b4bc394e25dfb62e2fe44 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    221 schema:name Gene Silencing
    222 rdf:type schema:DefinedTerm
    223 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    224 schema:name Biological Sciences
    225 rdf:type schema:DefinedTerm
    226 anzsrc-for:0601 schema:inDefinedTermSet anzsrc-for:
    227 schema:name Biochemistry and Cell Biology
    228 rdf:type schema:DefinedTerm
    229 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
    230 schema:name Genetics
    231 rdf:type schema:DefinedTerm
    232 sg:journal.1023607 schema:issn 1471-0056
    233 1471-0064
    234 schema:name Nature Reviews Genetics
    235 schema:publisher Springer Nature
    236 rdf:type schema:Periodical
    237 sg:person.01366677656.47 schema:affiliation grid-institutes:grid.24194.3a
    238 schema:familyName Matzke
    239 schema:givenName Marjori A.
    240 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01366677656.47
    241 rdf:type schema:Person
    242 sg:person.0577755340.61 schema:affiliation grid-institutes:grid.134936.a
    243 schema:familyName Birchler
    244 schema:givenName James A.
    245 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0577755340.61
    246 rdf:type schema:Person
    247 sg:pub.10.1007/s00294-003-0412-5 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045251519
    248 https://doi.org/10.1007/s00294-003-0412-5
    249 rdf:type schema:CreativeWork
    250 sg:pub.10.1007/s004120100136 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024795199
    251 https://doi.org/10.1007/s004120100136
    252 rdf:type schema:CreativeWork
    253 sg:pub.10.1007/s11103-004-0179-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011870278
    254 https://doi.org/10.1007/s11103-004-0179-1
    255 rdf:type schema:CreativeWork
    256 sg:pub.10.1023/a:1006484806925 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033006586
    257 https://doi.org/10.1023/a:1006484806925
    258 rdf:type schema:CreativeWork
    259 sg:pub.10.1023/a:1022815931524 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036577790
    260 https://doi.org/10.1023/a:1022815931524
    261 rdf:type schema:CreativeWork
    262 sg:pub.10.1023/b:chro.0000036584.40567.e5 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052128690
    263 https://doi.org/10.1023/b:chro.0000036584.40567.e5
    264 rdf:type schema:CreativeWork
    265 sg:pub.10.1038/35065132 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020526163
    266 https://doi.org/10.1038/35065132
    267 rdf:type schema:CreativeWork
    268 sg:pub.10.1038/35065138 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018164085
    269 https://doi.org/10.1038/35065138
    270 rdf:type schema:CreativeWork
    271 sg:pub.10.1038/35104508 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018899294
    272 https://doi.org/10.1038/35104508
    273 rdf:type schema:CreativeWork
    274 sg:pub.10.1038/74191 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026545365
    275 https://doi.org/10.1038/74191
    276 rdf:type schema:CreativeWork
    277 sg:pub.10.1038/nature02129 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015025248
    278 https://doi.org/10.1038/nature02129
    279 rdf:type schema:CreativeWork
    280 sg:pub.10.1038/nature02651 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050259576
    281 https://doi.org/10.1038/nature02651
    282 rdf:type schema:CreativeWork
    283 sg:pub.10.1038/nature02874 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025532636
    284 https://doi.org/10.1038/nature02874
    285 rdf:type schema:CreativeWork
    286 sg:pub.10.1038/nature02875 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039222604
    287 https://doi.org/10.1038/nature02875
    288 rdf:type schema:CreativeWork
    289 sg:pub.10.1038/nature02889 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040340027
    290 https://doi.org/10.1038/nature02889
    291 rdf:type schema:CreativeWork
    292 sg:pub.10.1038/nature731 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030808591
    293 https://doi.org/10.1038/nature731
    294 rdf:type schema:CreativeWork
    295 sg:pub.10.1038/ncb1155 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009605920
    296 https://doi.org/10.1038/ncb1155
    297 rdf:type schema:CreativeWork
    298 sg:pub.10.1038/ng1252 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029916094
    299 https://doi.org/10.1038/ng1252
    300 rdf:type schema:CreativeWork
    301 sg:pub.10.1038/ng1283 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043285362
    302 https://doi.org/10.1038/ng1283
    303 rdf:type schema:CreativeWork
    304 sg:pub.10.1038/ng1452 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006451203
    305 https://doi.org/10.1038/ng1452
    306 rdf:type schema:CreativeWork
    307 sg:pub.10.1038/nrg1379 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001799892
    308 https://doi.org/10.1038/nrg1379
    309 rdf:type schema:CreativeWork
    310 sg:pub.10.1038/nsmb729 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015922363
    311 https://doi.org/10.1038/nsmb729
    312 rdf:type schema:CreativeWork
    313 grid-institutes:grid.134936.a schema:alternateName Division of Biological Sciences, University of Missouri, 117 Tucker Hall, 65211, Columbia, Missouri, USA
    314 schema:name Division of Biological Sciences, University of Missouri, 117 Tucker Hall, 65211, Columbia, Missouri, USA
    315 rdf:type schema:Organization
    316 grid-institutes:grid.24194.3a schema:alternateName Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, UZA2, Pharmazie Zentrum, Althanstrasse 14/2D-541, A-1090, Vienna, Austria
    317 schema:name Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, UZA2, Pharmazie Zentrum, Althanstrasse 14/2D-541, A-1090, Vienna, Austria
    318 rdf:type schema:Organization
     




    Preview window. Press ESC to close (or click here)


    ...