Anatomy and evolution of a DNA replication origin View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2021-07-12

AUTHORS

Yutaka Yamamoto, Eric A. Gustafson, Michael S. Foulk, Heidi S. Smith, Susan A. Gerbi

ABSTRACT

DNA amplification occurs at the DNA puff II/9A locus in the fungus fly Sciara coprophila. As a foundation to study the molecular mechanism for the initiating events of II/9A DNA re-replication, we have sequenced 14 kb spanning a DNase hypersensitive site (DHS) upstream of the 1 kb amplification origin and through transcription units II/9–1 and II/9–2 downstream of the origin. These elements are annotated as well as the ORC binding site at the origin and the transition point (TP) between continuous and discontinuous DNA syntheses that marks the origin of bidirectional replication at the nucleotide level. A 9 bp motif found at the TP is repeated near the other end of the 1 kb ORI and may identify a putative second TP. The steroid hormone ecdysone induces DNA amplification as well as transcription and puffing at locus II/9A. Within the 14 kb, several matches to the ecdysone response element (EcRE) consensus sequence were identified, including some in the amplification origin region. EcRE O-P is at a central axis of a remarkable symmetry, equidistant to the TPs that are themselves equidistant to EcRE O-1 and EcRE O-2. DNA sequence alterations have occurred throughout the II/9A region in a newly discovered polymorphism (#2). Polymorphism #2 is not specific to developmental stage, sex, or tissue, and it does not impair DNA amplification. The DHS, both 9 bp TP sequences, and EcREs O-1, O-P, and O-2 are conserved between the polymorphism #1 and #2 sequences, suggesting their functional importance and retention during evolutionary selection. Moreover, a 72 bp sequence in the Sciara DHS at DNA puff II/9A is conserved in DNA puff C-3 of Rhynchosciara americana. Comparisons are discussed between the Sciara II/9A amplicon and the chorion locus amplicon on the third chromosome of Drosophila. More... »

PAGES

199-214

References to SciGraph publications

  • 2001-07. Maintenance of the DNA puff expanded state is independent of active replication and transcription in CHROMOSOMA
  • 1999-09. DNA replication during amplification of the C3 puff of Rhynchosciara americana initiates at multiple sites in a 6 kb region in CHROMOSOMA
  • 1968-09. Extra Replications in the “DNA-puffs” ofSciara coprophila in CHROMOSOMA
  • 2017-04-05. EcR recruits dMi-2 and increases efficiency of dMi-2-mediated remodelling to constrain transcription of hormone-regulated genes in NATURE COMMUNICATIONS
  • 1957-11. Autoradiography of Polytene Chromosomes of Rhynchosciara angelae at Different Stages of Larval Development in NATURE
  • 2003-11-06. Methylation at lysine 4 of histone H3 in ecdysone-dependent development of Drosophila in NATURE
  • 2002-06-08. A DNase I hypersensitive site flanks an origin of DNA replication and amplification in Sciara in CHROMOSOMA
  • 2007-01-12. Developmentally regulated histone modifications in Drosophila follicle cells: initiation of gene amplification is associated with histone H3 and H4 hyperacetylation and H1 phosphorylation in CHROMOSOMA
  • 2013-06-05. The ecdysone receptor (ScEcR-A) binds DNA puffs at the start of DNA amplification in Sciara coprophila in CHROMOSOME RESEARCH
  • 2001-06. Cyclin-dependent kinases prevent DNA re-replication through multiple mechanisms in NATURE
  • 2012-03-07. ORC1 BAH domain links H4K20me2 to DNA replication licensing and Meier-Gorlin syndrome in NATURE
  • 2002-12. Role for a Drosophila Myb-containing protein complex in site-specific DNA replication in NATURE
  • 2013-01-16. Isolation and characterization of the ecdysone receptor and its heterodimeric partner ultraspiracle through development in Sciara coprophila in CHROMOSOMA
  • 2004-07. Chromatin regulates origin activity in Drosophila follicle cells in NATURE
  • 2020-03-16. Proximity-dependent biotin labelling reveals CP190 as an EcR/Usp molecular partner in SCIENTIFIC REPORTS
  • 2010-10-17. The histone H4 Lys 20 methyltransferase PR-Set7 regulates replication origins in mammalian cells in NATURE CELL BIOLOGY
  • 1985-10. Regulatory elements controlling chorion gene expression are conserved between flies and moths in NATURE
  • 1979-11. Isolation and characterisation of a yeast chromosomal replicator in NATURE
  • 1955-01. Behavior of polytene chromosomes of rhynchosciara angelae at different stages of larval development in CHROMOSOMA
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/s00412-021-00756-x

    DOI

    http://dx.doi.org/10.1007/s00412-021-00756-x

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1139631978

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/34254172


    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/2008/0604", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Genetics", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Box G \u2013 Sidney Frank Life Sciences Building room 260, 02912, Providence, RI, USA", 
              "id": "http://www.grid.ac/institutes/grid.40263.33", 
              "name": [
                "Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Box G \u2013 Sidney Frank Life Sciences Building room 260, 02912, Providence, RI, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Yamamoto", 
            "givenName": "Yutaka", 
            "id": "sg:person.01201571210.67", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01201571210.67"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Zipher Medical Affairs Co., 380 Wareham Street, 02738, Marion, MA, USA", 
              "id": "http://www.grid.ac/institutes/None", 
              "name": [
                "Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Box G \u2013 Sidney Frank Life Sciences Building room 260, 02912, Providence, RI, USA", 
                "Zipher Medical Affairs Co., 380 Wareham Street, 02738, Marion, MA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Gustafson", 
            "givenName": "Eric A.", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Biology, Mercyhurst University, 501 East 38th Street, 16546, Erie, PA, USA", 
              "id": "http://www.grid.ac/institutes/grid.419747.8", 
              "name": [
                "Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Box G \u2013 Sidney Frank Life Sciences Building room 260, 02912, Providence, RI, USA", 
                "Department of Biology, Mercyhurst University, 501 East 38th Street, 16546, Erie, PA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Foulk", 
            "givenName": "Michael S.", 
            "id": "sg:person.0634665610.87", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0634665610.87"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Box G \u2013 Sidney Frank Life Sciences Building room 260, 02912, Providence, RI, USA", 
              "id": "http://www.grid.ac/institutes/grid.40263.33", 
              "name": [
                "Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Box G \u2013 Sidney Frank Life Sciences Building room 260, 02912, Providence, RI, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Smith", 
            "givenName": "Heidi S.", 
            "id": "sg:person.01251226604.28", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01251226604.28"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Box G \u2013 Sidney Frank Life Sciences Building room 260, 02912, Providence, RI, USA", 
              "id": "http://www.grid.ac/institutes/grid.40263.33", 
              "name": [
                "Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Box G \u2013 Sidney Frank Life Sciences Building room 260, 02912, Providence, RI, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Gerbi", 
            "givenName": "Susan A.", 
            "id": "sg:person.01350107022.39", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01350107022.39"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1007/bf01183126", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1014922925", 
              "https://doi.org/10.1007/bf01183126"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ncomms14806", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1084514071", 
              "https://doi.org/10.1038/ncomms14806"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/bf00329733", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1031548057", 
              "https://doi.org/10.1007/bf00329733"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00412-006-0092-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1026681314", 
              "https://doi.org/10.1007/s00412-006-0092-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00412-012-0395-4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1012829401", 
              "https://doi.org/10.1007/s00412-012-0395-4"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00412-002-0194-4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1030208534", 
              "https://doi.org/10.1007/s00412-002-0194-4"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature02080", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1002552267", 
              "https://doi.org/10.1038/nature02080"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/317453a0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1001581647", 
              "https://doi.org/10.1038/317453a0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/282039a0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1038416530", 
              "https://doi.org/10.1038/282039a0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s004120000119", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1016272787", 
              "https://doi.org/10.1007/s004120000119"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature10956", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1000435052", 
              "https://doi.org/10.1038/nature10956"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10577-013-9360-1", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1035180194", 
              "https://doi.org/10.1007/s10577-013-9360-1"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/180983a0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1000869223", 
              "https://doi.org/10.1038/180983a0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s004120050380", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1004476626", 
              "https://doi.org/10.1007/s004120050380"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature02694", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1040566175", 
              "https://doi.org/10.1038/nature02694"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/35082600", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1036007845", 
              "https://doi.org/10.1038/35082600"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature01228", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1012414621", 
              "https://doi.org/10.1038/nature01228"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ncb2113", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1003880134", 
              "https://doi.org/10.1038/ncb2113"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41598-020-61514-0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1125677767", 
              "https://doi.org/10.1038/s41598-020-61514-0"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2021-07-12", 
        "datePublishedReg": "2021-07-12", 
        "description": "DNA amplification occurs at the DNA puff II/9A locus in the fungus fly Sciara coprophila. As a foundation to study the molecular mechanism for the initiating events of II/9A DNA re-replication, we have sequenced 14\u00a0kb spanning a DNase hypersensitive site (DHS) upstream of the 1\u00a0kb amplification origin and through transcription units II/9\u20131 and II/9\u20132 downstream of the origin. These elements are annotated as well as the ORC binding site at the origin and the transition point (TP) between continuous and discontinuous DNA syntheses that marks the origin of bidirectional replication at the nucleotide level. A 9\u00a0bp motif found at the TP is repeated near the other end of the 1 kb ORI and may identify a putative second TP. The steroid hormone ecdysone induces DNA amplification as well as transcription and puffing at locus II/9A. Within the 14 kb, several matches to the ecdysone response element (EcRE) consensus sequence were identified, including some in the amplification origin region. EcRE O-P is at a central axis of a remarkable symmetry, equidistant to the TPs that are themselves equidistant to EcRE O-1 and EcRE O-2. DNA sequence alterations have occurred throughout the II/9A region in a newly discovered polymorphism (#2). Polymorphism #2 is not specific to developmental stage, sex, or tissue, and it does not impair DNA amplification. The DHS, both 9\u00a0bp TP sequences, and EcREs O-1, O-P, and O-2 are conserved between the polymorphism #1 and #2 sequences, suggesting their functional importance and retention during evolutionary selection. Moreover, a 72 bp sequence in the Sciara DHS at DNA puff II/9A is conserved in DNA puff C-3 of Rhynchosciara americana. Comparisons are discussed between the Sciara II/9A amplicon and the chorion locus amplicon on the third chromosome of Drosophila.", 
        "genre": "article", 
        "id": "sg:pub.10.1007/s00412-021-00756-x", 
        "inLanguage": "en", 
        "isAccessibleForFree": false, 
        "isFundedItemOf": [
          {
            "id": "sg:grant.2511488", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.7029623", 
            "type": "MonetaryGrant"
          }
        ], 
        "isPartOf": [
          {
            "id": "sg:journal.1312277", 
            "issn": [
              "0009-5915", 
              "1432-0886"
            ], 
            "name": "Chromosoma", 
            "publisher": "Springer Nature", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "2-3", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "130"
          }
        ], 
        "keywords": [
          "steroid hormone ecdysone", 
          "DNA replication origins", 
          "DNA amplification", 
          "DNA sequence alterations", 
          "discontinuous DNA synthesis", 
          "amplification origins", 
          "Sciara coprophila", 
          "hormone ecdysone", 
          "third chromosome", 
          "TP sequence", 
          "bp motif", 
          "replication origins", 
          "DNA puffs", 
          "evolutionary selection", 
          "Rhynchosciara americana", 
          "site upstream", 
          "bidirectional replication", 
          "consensus sequence", 
          "bp sequence", 
          "molecular mechanisms", 
          "origin region", 
          "functional importance", 
          "developmental stages", 
          "nucleotide level", 
          "sequence alterations", 
          "DNA synthesis", 
          "kb", 
          "sequence", 
          "polymorphism", 
          "amplicons", 
          "Drosophila", 
          "amplification", 
          "coprophila", 
          "transcription", 
          "chromosomes", 
          "ecdysone", 
          "loci", 
          "fungi", 
          "DNA", 
          "motif", 
          "origin", 
          "upstream", 
          "americana", 
          "remarkable symmetry", 
          "replication", 
          "downstream", 
          "region", 
          "evolution", 
          "sites", 
          "tissue", 
          "alterations", 
          "mechanism", 
          "Ori", 
          "selection", 
          "stage", 
          "synthesis", 
          "DHS", 
          "events", 
          "ORC", 
          "importance", 
          "levels", 
          "puffs", 
          "elements", 
          "axis", 
          "retention", 
          "end", 
          "central axis", 
          "sex", 
          "comparison", 
          "transition point", 
          "foundation", 
          "match", 
          "point", 
          "symmetry", 
          "second transition point", 
          "DNA puff II/9A locus", 
          "puff II/9A locus", 
          "II/9A locus", 
          "II/9A DNA", 
          "DNase hypersensitive site (DHS) upstream", 
          "hypersensitive site (DHS) upstream", 
          "kb amplification origin", 
          "transcription units II/9\u20131", 
          "units II/9\u20131", 
          "II/9\u20131", 
          "II/9\u20132 downstream", 
          "kb ORI", 
          "putative second TP", 
          "locus II/9A.", 
          "II/9A.", 
          "ecdysone response element (EcRE) consensus sequence", 
          "response element (EcRE) consensus sequence", 
          "element (EcRE) consensus sequence", 
          "amplification origin region", 
          "EcRE O", 
          "II/9A region", 
          "bp TP sequences", 
          "Sciara DHS", 
          "DNA puff C", 
          "puff C", 
          "Sciara II/9A amplicon", 
          "II/9A amplicon", 
          "chorion locus amplicon", 
          "locus amplicon"
        ], 
        "name": "Anatomy and evolution of a DNA replication origin", 
        "pagination": "199-214", 
        "productId": [
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1139631978"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1007/s00412-021-00756-x"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "34254172"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1007/s00412-021-00756-x", 
          "https://app.dimensions.ai/details/publication/pub.1139631978"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2022-01-01T19:02", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-springernature-scigraph/baseset/20220101/entities/gbq_results/article/article_899.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://doi.org/10.1007/s00412-021-00756-x"
      }
    ]
     

    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.10.1007/s00412-021-00756-x'

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

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/s00412-021-00756-x'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/s00412-021-00756-x'

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

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/s00412-021-00756-x'


     

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

    281 TRIPLES      22 PREDICATES      149 URIs      122 LITERALS      7 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1007/s00412-021-00756-x schema:about anzsrc-for:06
    2 anzsrc-for:0604
    3 schema:author N60ccd29eb7c140ba92e906ca567e0a7b
    4 schema:citation sg:pub.10.1007/bf00329733
    5 sg:pub.10.1007/bf01183126
    6 sg:pub.10.1007/s00412-002-0194-4
    7 sg:pub.10.1007/s00412-006-0092-2
    8 sg:pub.10.1007/s00412-012-0395-4
    9 sg:pub.10.1007/s004120000119
    10 sg:pub.10.1007/s004120050380
    11 sg:pub.10.1007/s10577-013-9360-1
    12 sg:pub.10.1038/180983a0
    13 sg:pub.10.1038/282039a0
    14 sg:pub.10.1038/317453a0
    15 sg:pub.10.1038/35082600
    16 sg:pub.10.1038/nature01228
    17 sg:pub.10.1038/nature02080
    18 sg:pub.10.1038/nature02694
    19 sg:pub.10.1038/nature10956
    20 sg:pub.10.1038/ncb2113
    21 sg:pub.10.1038/ncomms14806
    22 sg:pub.10.1038/s41598-020-61514-0
    23 schema:datePublished 2021-07-12
    24 schema:datePublishedReg 2021-07-12
    25 schema:description DNA amplification occurs at the DNA puff II/9A locus in the fungus fly Sciara coprophila. As a foundation to study the molecular mechanism for the initiating events of II/9A DNA re-replication, we have sequenced 14 kb spanning a DNase hypersensitive site (DHS) upstream of the 1 kb amplification origin and through transcription units II/9–1 and II/9–2 downstream of the origin. These elements are annotated as well as the ORC binding site at the origin and the transition point (TP) between continuous and discontinuous DNA syntheses that marks the origin of bidirectional replication at the nucleotide level. A 9 bp motif found at the TP is repeated near the other end of the 1 kb ORI and may identify a putative second TP. The steroid hormone ecdysone induces DNA amplification as well as transcription and puffing at locus II/9A. Within the 14 kb, several matches to the ecdysone response element (EcRE) consensus sequence were identified, including some in the amplification origin region. EcRE O-P is at a central axis of a remarkable symmetry, equidistant to the TPs that are themselves equidistant to EcRE O-1 and EcRE O-2. DNA sequence alterations have occurred throughout the II/9A region in a newly discovered polymorphism (#2). Polymorphism #2 is not specific to developmental stage, sex, or tissue, and it does not impair DNA amplification. The DHS, both 9 bp TP sequences, and EcREs O-1, O-P, and O-2 are conserved between the polymorphism #1 and #2 sequences, suggesting their functional importance and retention during evolutionary selection. Moreover, a 72 bp sequence in the Sciara DHS at DNA puff II/9A is conserved in DNA puff C-3 of Rhynchosciara americana. Comparisons are discussed between the Sciara II/9A amplicon and the chorion locus amplicon on the third chromosome of Drosophila.
    26 schema:genre article
    27 schema:inLanguage en
    28 schema:isAccessibleForFree false
    29 schema:isPartOf N2d7c194db212432faea418147177ae19
    30 N68e739d49dde49e9abe796cb031e683e
    31 sg:journal.1312277
    32 schema:keywords DHS
    33 DNA
    34 DNA amplification
    35 DNA puff C
    36 DNA puff II/9A locus
    37 DNA puffs
    38 DNA replication origins
    39 DNA sequence alterations
    40 DNA synthesis
    41 DNase hypersensitive site (DHS) upstream
    42 Drosophila
    43 EcRE O
    44 II/9A DNA
    45 II/9A amplicon
    46 II/9A locus
    47 II/9A region
    48 II/9A.
    49 II/9–1
    50 II/9–2 downstream
    51 ORC
    52 Ori
    53 Rhynchosciara americana
    54 Sciara DHS
    55 Sciara II/9A amplicon
    56 Sciara coprophila
    57 TP sequence
    58 alterations
    59 americana
    60 amplicons
    61 amplification
    62 amplification origin region
    63 amplification origins
    64 axis
    65 bidirectional replication
    66 bp TP sequences
    67 bp motif
    68 bp sequence
    69 central axis
    70 chorion locus amplicon
    71 chromosomes
    72 comparison
    73 consensus sequence
    74 coprophila
    75 developmental stages
    76 discontinuous DNA synthesis
    77 downstream
    78 ecdysone
    79 ecdysone response element (EcRE) consensus sequence
    80 element (EcRE) consensus sequence
    81 elements
    82 end
    83 events
    84 evolution
    85 evolutionary selection
    86 foundation
    87 functional importance
    88 fungi
    89 hormone ecdysone
    90 hypersensitive site (DHS) upstream
    91 importance
    92 kb
    93 kb ORI
    94 kb amplification origin
    95 levels
    96 loci
    97 locus II/9A.
    98 locus amplicon
    99 match
    100 mechanism
    101 molecular mechanisms
    102 motif
    103 nucleotide level
    104 origin
    105 origin region
    106 point
    107 polymorphism
    108 puff C
    109 puff II/9A locus
    110 puffs
    111 putative second TP
    112 region
    113 remarkable symmetry
    114 replication
    115 replication origins
    116 response element (EcRE) consensus sequence
    117 retention
    118 second transition point
    119 selection
    120 sequence
    121 sequence alterations
    122 sex
    123 site upstream
    124 sites
    125 stage
    126 steroid hormone ecdysone
    127 symmetry
    128 synthesis
    129 third chromosome
    130 tissue
    131 transcription
    132 transcription units II/9–1
    133 transition point
    134 units II/9–1
    135 upstream
    136 schema:name Anatomy and evolution of a DNA replication origin
    137 schema:pagination 199-214
    138 schema:productId N0070de0c1ddb47769d5529ab646e4ce3
    139 N99a0aa07c8e440f9b54f682559738a0c
    140 Nfa2dfd1a005c4fd1834a74c5f92afad8
    141 schema:sameAs https://app.dimensions.ai/details/publication/pub.1139631978
    142 https://doi.org/10.1007/s00412-021-00756-x
    143 schema:sdDatePublished 2022-01-01T19:02
    144 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    145 schema:sdPublisher N32dc3664fc16466ab05a6002f84c7c93
    146 schema:url https://doi.org/10.1007/s00412-021-00756-x
    147 sgo:license sg:explorer/license/
    148 sgo:sdDataset articles
    149 rdf:type schema:ScholarlyArticle
    150 N0070de0c1ddb47769d5529ab646e4ce3 schema:name pubmed_id
    151 schema:value 34254172
    152 rdf:type schema:PropertyValue
    153 N2d7c194db212432faea418147177ae19 schema:volumeNumber 130
    154 rdf:type schema:PublicationVolume
    155 N32dc3664fc16466ab05a6002f84c7c93 schema:name Springer Nature - SN SciGraph project
    156 rdf:type schema:Organization
    157 N4013d6681e434762805ed74183b769db schema:affiliation grid-institutes:None
    158 schema:familyName Gustafson
    159 schema:givenName Eric A.
    160 rdf:type schema:Person
    161 N4d05d6bd511143149c945d9ef75bbbd8 rdf:first N4013d6681e434762805ed74183b769db
    162 rdf:rest Nc1bf62f8bb0c4917bba284cce1eeb7cf
    163 N4e8b1419b2ad467ca43833193e1e1232 rdf:first sg:person.01350107022.39
    164 rdf:rest rdf:nil
    165 N60ccd29eb7c140ba92e906ca567e0a7b rdf:first sg:person.01201571210.67
    166 rdf:rest N4d05d6bd511143149c945d9ef75bbbd8
    167 N68e739d49dde49e9abe796cb031e683e schema:issueNumber 2-3
    168 rdf:type schema:PublicationIssue
    169 N73145de88a934be4a9671da15b7365b4 rdf:first sg:person.01251226604.28
    170 rdf:rest N4e8b1419b2ad467ca43833193e1e1232
    171 N99a0aa07c8e440f9b54f682559738a0c schema:name doi
    172 schema:value 10.1007/s00412-021-00756-x
    173 rdf:type schema:PropertyValue
    174 Nc1bf62f8bb0c4917bba284cce1eeb7cf rdf:first sg:person.0634665610.87
    175 rdf:rest N73145de88a934be4a9671da15b7365b4
    176 Nfa2dfd1a005c4fd1834a74c5f92afad8 schema:name dimensions_id
    177 schema:value pub.1139631978
    178 rdf:type schema:PropertyValue
    179 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    180 schema:name Biological Sciences
    181 rdf:type schema:DefinedTerm
    182 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
    183 schema:name Genetics
    184 rdf:type schema:DefinedTerm
    185 sg:grant.2511488 http://pending.schema.org/fundedItem sg:pub.10.1007/s00412-021-00756-x
    186 rdf:type schema:MonetaryGrant
    187 sg:grant.7029623 http://pending.schema.org/fundedItem sg:pub.10.1007/s00412-021-00756-x
    188 rdf:type schema:MonetaryGrant
    189 sg:journal.1312277 schema:issn 0009-5915
    190 1432-0886
    191 schema:name Chromosoma
    192 schema:publisher Springer Nature
    193 rdf:type schema:Periodical
    194 sg:person.01201571210.67 schema:affiliation grid-institutes:grid.40263.33
    195 schema:familyName Yamamoto
    196 schema:givenName Yutaka
    197 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01201571210.67
    198 rdf:type schema:Person
    199 sg:person.01251226604.28 schema:affiliation grid-institutes:grid.40263.33
    200 schema:familyName Smith
    201 schema:givenName Heidi S.
    202 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01251226604.28
    203 rdf:type schema:Person
    204 sg:person.01350107022.39 schema:affiliation grid-institutes:grid.40263.33
    205 schema:familyName Gerbi
    206 schema:givenName Susan A.
    207 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01350107022.39
    208 rdf:type schema:Person
    209 sg:person.0634665610.87 schema:affiliation grid-institutes:grid.419747.8
    210 schema:familyName Foulk
    211 schema:givenName Michael S.
    212 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0634665610.87
    213 rdf:type schema:Person
    214 sg:pub.10.1007/bf00329733 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031548057
    215 https://doi.org/10.1007/bf00329733
    216 rdf:type schema:CreativeWork
    217 sg:pub.10.1007/bf01183126 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014922925
    218 https://doi.org/10.1007/bf01183126
    219 rdf:type schema:CreativeWork
    220 sg:pub.10.1007/s00412-002-0194-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030208534
    221 https://doi.org/10.1007/s00412-002-0194-4
    222 rdf:type schema:CreativeWork
    223 sg:pub.10.1007/s00412-006-0092-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026681314
    224 https://doi.org/10.1007/s00412-006-0092-2
    225 rdf:type schema:CreativeWork
    226 sg:pub.10.1007/s00412-012-0395-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012829401
    227 https://doi.org/10.1007/s00412-012-0395-4
    228 rdf:type schema:CreativeWork
    229 sg:pub.10.1007/s004120000119 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016272787
    230 https://doi.org/10.1007/s004120000119
    231 rdf:type schema:CreativeWork
    232 sg:pub.10.1007/s004120050380 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004476626
    233 https://doi.org/10.1007/s004120050380
    234 rdf:type schema:CreativeWork
    235 sg:pub.10.1007/s10577-013-9360-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035180194
    236 https://doi.org/10.1007/s10577-013-9360-1
    237 rdf:type schema:CreativeWork
    238 sg:pub.10.1038/180983a0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000869223
    239 https://doi.org/10.1038/180983a0
    240 rdf:type schema:CreativeWork
    241 sg:pub.10.1038/282039a0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038416530
    242 https://doi.org/10.1038/282039a0
    243 rdf:type schema:CreativeWork
    244 sg:pub.10.1038/317453a0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001581647
    245 https://doi.org/10.1038/317453a0
    246 rdf:type schema:CreativeWork
    247 sg:pub.10.1038/35082600 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036007845
    248 https://doi.org/10.1038/35082600
    249 rdf:type schema:CreativeWork
    250 sg:pub.10.1038/nature01228 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012414621
    251 https://doi.org/10.1038/nature01228
    252 rdf:type schema:CreativeWork
    253 sg:pub.10.1038/nature02080 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002552267
    254 https://doi.org/10.1038/nature02080
    255 rdf:type schema:CreativeWork
    256 sg:pub.10.1038/nature02694 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040566175
    257 https://doi.org/10.1038/nature02694
    258 rdf:type schema:CreativeWork
    259 sg:pub.10.1038/nature10956 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000435052
    260 https://doi.org/10.1038/nature10956
    261 rdf:type schema:CreativeWork
    262 sg:pub.10.1038/ncb2113 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003880134
    263 https://doi.org/10.1038/ncb2113
    264 rdf:type schema:CreativeWork
    265 sg:pub.10.1038/ncomms14806 schema:sameAs https://app.dimensions.ai/details/publication/pub.1084514071
    266 https://doi.org/10.1038/ncomms14806
    267 rdf:type schema:CreativeWork
    268 sg:pub.10.1038/s41598-020-61514-0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1125677767
    269 https://doi.org/10.1038/s41598-020-61514-0
    270 rdf:type schema:CreativeWork
    271 grid-institutes:None schema:alternateName Zipher Medical Affairs Co., 380 Wareham Street, 02738, Marion, MA, USA
    272 schema:name Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Box G – Sidney Frank Life Sciences Building room 260, 02912, Providence, RI, USA
    273 Zipher Medical Affairs Co., 380 Wareham Street, 02738, Marion, MA, USA
    274 rdf:type schema:Organization
    275 grid-institutes:grid.40263.33 schema:alternateName Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Box G – Sidney Frank Life Sciences Building room 260, 02912, Providence, RI, USA
    276 schema:name Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Box G – Sidney Frank Life Sciences Building room 260, 02912, Providence, RI, USA
    277 rdf:type schema:Organization
    278 grid-institutes:grid.419747.8 schema:alternateName Department of Biology, Mercyhurst University, 501 East 38th Street, 16546, Erie, PA, USA
    279 schema:name Department of Biology, Mercyhurst University, 501 East 38th Street, 16546, Erie, PA, USA
    280 Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Box G – Sidney Frank Life Sciences Building room 260, 02912, Providence, RI, USA
    281 rdf:type schema:Organization
     




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


    ...