Protein-DNA interactions at a yeast replication origin View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

1992-05

AUTHORS

John F. X. Diffley, Julie H. Cocker

ABSTRACT

AN understanding of the protein-DNA interactions in vivo at origins of DNA replication in eukaryotes is essential to delineate the mechanism of initiation of DNA synthesis and its control in the cell cycle1,2. In the yeast Saccharomyces cerevisiae, a family of sequences known as autonomously replicating sequences (ARSs) function as origins of bidirectional DNA replication on plasmids and, in several instances, also in their normal chromosomal location3. Here we use nucleotide resolution genomic footprinting to investigate the association of proteins with ARS1. Nuclease protection patterns indicate that at least two different cellular factors interact with functional elements in ARS1. The first seems to be ARS-binding factor 1. The second seems to be a novel protein that generates extensive protection over the essential ARS consensus sequence and phased DNasel-sensitive sites across a functionally important flanking sequence. Hypersensitivity of this region to cleavage by copper phenanthroline indicates that it is under torsional strain, analogous to that produced at transcriptional start sites by assembly of an initiation complex. The protection in situ is similar to that generated by the origin recognition complex (ORC) protein. More... »

PAGES

169-172

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/357169a0

DOI

http://dx.doi.org/10.1038/357169a0

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1005454348

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/1579168


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": "Base Sequence", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA Replication", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA, Fungal", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA-Binding Proteins", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Electrophoresis, Agar Gel", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genome, Fungal", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Molecular Sequence Data", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Oligodeoxyribonucleotides", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Phenanthrolines", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Saccharomyces cerevisiae", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Thiourea", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Imperial Cancer Research Fund, Blanche Lane, EN6 3LD, South Mimms, Potters Bar, Hertfordshire, UK", 
          "id": "http://www.grid.ac/institutes/grid.11485.39", 
          "name": [
            "Imperial Cancer Research Fund, Blanche Lane, EN6 3LD, South Mimms, Potters Bar, Hertfordshire, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Diffley", 
        "givenName": "John F. X.", 
        "id": "sg:person.01070163466.42", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01070163466.42"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Imperial Cancer Research Fund, Blanche Lane, EN6 3LD, South Mimms, Potters Bar, Hertfordshire, UK", 
          "id": "http://www.grid.ac/institutes/grid.11485.39", 
          "name": [
            "Imperial Cancer Research Fund, Blanche Lane, EN6 3LD, South Mimms, Potters Bar, Hertfordshire, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Cocker", 
        "givenName": "Julie H.", 
        "id": "sg:person.0646410652.65", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0646410652.65"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "sg:pub.10.1038/350247a0", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007685176", 
          "https://doi.org/10.1038/350247a0"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/978-1-4612-3490-6", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050442579", 
          "https://doi.org/10.1007/978-1-4612-3490-6"
        ], 
        "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.10.1038/357128a0", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1008093514", 
          "https://doi.org/10.1038/357128a0"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/343387a0", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1012803467", 
          "https://doi.org/10.1038/343387a0"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "1992-05", 
    "datePublishedReg": "1992-05-01", 
    "description": "AN understanding of the protein-DNA interactions in vivo at origins of DNA replication in eukaryotes is essential to delineate the mechanism of initiation of DNA synthesis and its control in the cell cycle1,2. In the yeast Saccharomyces cerevisiae, a family of sequences known as autonomously replicating sequences (ARSs) function as origins of bidirectional DNA replication on plasmids and, in several instances, also in their normal chromosomal location3. Here we use nucleotide resolution genomic footprinting to investigate the association of proteins with ARS1. Nuclease protection patterns indicate that at least two different cellular factors interact with functional elements in ARS1. The first seems to be ARS-binding factor 1. The second seems to be a novel protein that generates extensive protection over the essential ARS consensus sequence and phased DNasel-sensitive sites across a functionally important flanking sequence. Hypersensitivity of this region to cleavage by copper phenanthroline indicates that it is under torsional strain, analogous to that produced at transcriptional start sites by assembly of an initiation complex. The protection in situ is similar to that generated by the origin recognition complex (ORC) protein.", 
    "genre": "article", 
    "id": "sg:pub.10.1038/357169a0", 
    "inLanguage": "en", 
    "isAccessibleForFree": false, 
    "isPartOf": [
      {
        "id": "sg:journal.1018957", 
        "issn": [
          "0028-0836", 
          "1476-4687"
        ], 
        "name": "Nature", 
        "publisher": "Springer Nature", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "6374", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "357"
      }
    ], 
    "keywords": [
      "protein-DNA interactions", 
      "DNA replication", 
      "origin recognition complex (ORC) proteins", 
      "bidirectional DNA replication", 
      "yeast Saccharomyces cerevisiae", 
      "transcriptional start site", 
      "ARS consensus sequence", 
      "yeast replication origins", 
      "essential ARS consensus sequence", 
      "different cellular factors", 
      "nuclease protection patterns", 
      "association of proteins", 
      "novel protein", 
      "replication origins", 
      "initiation complex", 
      "start site", 
      "Saccharomyces cerevisiae", 
      "flanking sequences", 
      "complex proteins", 
      "sequence functions", 
      "consensus sequence", 
      "family of sequences", 
      "cellular factors", 
      "copper phenanthroline", 
      "protection pattern", 
      "factor 1", 
      "ARS1", 
      "functional elements", 
      "protein", 
      "DNA synthesis", 
      "sequence", 
      "mechanism of initiation", 
      "replication", 
      "eukaryotes", 
      "genomics", 
      "cerevisiae", 
      "plasmid", 
      "sites", 
      "origin", 
      "torsional strain", 
      "assembly", 
      "interaction", 
      "cells", 
      "family", 
      "vivo", 
      "complexes", 
      "strains", 
      "extensive protection", 
      "mechanism", 
      "initiation", 
      "region", 
      "protection", 
      "patterns", 
      "function", 
      "understanding", 
      "phenanthroline", 
      "synthesis", 
      "hypersensitivity", 
      "factors", 
      "elements", 
      "association", 
      "situ", 
      "control", 
      "instances", 
      "normal chromosomal location3", 
      "chromosomal location3", 
      "location3", 
      "nucleotide resolution genomic", 
      "resolution genomic", 
      "ARS-binding factor 1", 
      "DNasel-sensitive sites", 
      "important flanking sequence", 
      "recognition complex (ORC) protein"
    ], 
    "name": "Protein-DNA interactions at a yeast replication origin", 
    "pagination": "169-172", 
    "productId": [
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1005454348"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1038/357169a0"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "1579168"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1038/357169a0", 
      "https://app.dimensions.ai/details/publication/pub.1005454348"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2021-11-01T18:00", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-springernature-scigraph/baseset/20211101/entities/gbq_results/article/article_250.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://doi.org/10.1038/357169a0"
  }
]
 

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.10.1038/357169a0'

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

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/357169a0'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/357169a0'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/357169a0'


 

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

210 TRIPLES      22 PREDICATES      117 URIs      103 LITERALS      18 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1038/357169a0 schema:about N0528da2ceea742c488b39ad855755ab6
2 N0ca6cadc5544442ca8937904d7d42f70
3 N0e607e6f03e24536b18aeea4d2d7beaa
4 N3905371834dc49fca4e0062effbcdeca
5 N6f049d750ea8498cadcc375b05963944
6 N95ae72e8f3994141835a3d66c4a295a2
7 N9c4f7d22d4944fceb2eeead026b11752
8 N9e18098d4e604e59a078a512d24393fc
9 Naf6cf2210be948408e634dcbb095ca64
10 Nc014106e7e874c36b2c728e47df14ab9
11 Nef0f6e739f554bb8b11dd13e708d24ef
12 anzsrc-for:06
13 anzsrc-for:0601
14 anzsrc-for:0604
15 schema:author N913df166904947e399f95b579f3174ba
16 schema:citation sg:pub.10.1007/978-1-4612-3490-6
17 sg:pub.10.1038/282039a0
18 sg:pub.10.1038/343387a0
19 sg:pub.10.1038/350247a0
20 sg:pub.10.1038/357128a0
21 schema:datePublished 1992-05
22 schema:datePublishedReg 1992-05-01
23 schema:description AN understanding of the protein-DNA interactions in vivo at origins of DNA replication in eukaryotes is essential to delineate the mechanism of initiation of DNA synthesis and its control in the cell cycle1,2. In the yeast Saccharomyces cerevisiae, a family of sequences known as autonomously replicating sequences (ARSs) function as origins of bidirectional DNA replication on plasmids and, in several instances, also in their normal chromosomal location3. Here we use nucleotide resolution genomic footprinting to investigate the association of proteins with ARS1. Nuclease protection patterns indicate that at least two different cellular factors interact with functional elements in ARS1. The first seems to be ARS-binding factor 1. The second seems to be a novel protein that generates extensive protection over the essential ARS consensus sequence and phased DNasel-sensitive sites across a functionally important flanking sequence. Hypersensitivity of this region to cleavage by copper phenanthroline indicates that it is under torsional strain, analogous to that produced at transcriptional start sites by assembly of an initiation complex. The protection in situ is similar to that generated by the origin recognition complex (ORC) protein.
24 schema:genre article
25 schema:inLanguage en
26 schema:isAccessibleForFree false
27 schema:isPartOf N84d19cd98ea84b899d1f653970c65da6
28 Na1a0a7b1e7a34c0a9db5901932d7958b
29 sg:journal.1018957
30 schema:keywords ARS consensus sequence
31 ARS-binding factor 1
32 ARS1
33 DNA replication
34 DNA synthesis
35 DNasel-sensitive sites
36 Saccharomyces cerevisiae
37 assembly
38 association
39 association of proteins
40 bidirectional DNA replication
41 cells
42 cellular factors
43 cerevisiae
44 chromosomal location3
45 complex proteins
46 complexes
47 consensus sequence
48 control
49 copper phenanthroline
50 different cellular factors
51 elements
52 essential ARS consensus sequence
53 eukaryotes
54 extensive protection
55 factor 1
56 factors
57 family
58 family of sequences
59 flanking sequences
60 function
61 functional elements
62 genomics
63 hypersensitivity
64 important flanking sequence
65 initiation
66 initiation complex
67 instances
68 interaction
69 location3
70 mechanism
71 mechanism of initiation
72 normal chromosomal location3
73 novel protein
74 nuclease protection patterns
75 nucleotide resolution genomic
76 origin
77 origin recognition complex (ORC) proteins
78 patterns
79 phenanthroline
80 plasmid
81 protection
82 protection pattern
83 protein
84 protein-DNA interactions
85 recognition complex (ORC) protein
86 region
87 replication
88 replication origins
89 resolution genomic
90 sequence
91 sequence functions
92 sites
93 situ
94 start site
95 strains
96 synthesis
97 torsional strain
98 transcriptional start site
99 understanding
100 vivo
101 yeast Saccharomyces cerevisiae
102 yeast replication origins
103 schema:name Protein-DNA interactions at a yeast replication origin
104 schema:pagination 169-172
105 schema:productId N0a20a7c7f9ad4883907b019d91cf7e20
106 N3f8803296f0e4c619ce2a798acb5cd59
107 N55997a5f1bc2450e9d90bb8c590b0bfb
108 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005454348
109 https://doi.org/10.1038/357169a0
110 schema:sdDatePublished 2021-11-01T18:00
111 schema:sdLicense https://scigraph.springernature.com/explorer/license/
112 schema:sdPublisher N7f88dccee13348d8adff4e4e2bc335c6
113 schema:url https://doi.org/10.1038/357169a0
114 sgo:license sg:explorer/license/
115 sgo:sdDataset articles
116 rdf:type schema:ScholarlyArticle
117 N0528da2ceea742c488b39ad855755ab6 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
118 schema:name Genome, Fungal
119 rdf:type schema:DefinedTerm
120 N0a20a7c7f9ad4883907b019d91cf7e20 schema:name dimensions_id
121 schema:value pub.1005454348
122 rdf:type schema:PropertyValue
123 N0ca6cadc5544442ca8937904d7d42f70 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
124 schema:name Base Sequence
125 rdf:type schema:DefinedTerm
126 N0e607e6f03e24536b18aeea4d2d7beaa schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
127 schema:name Electrophoresis, Agar Gel
128 rdf:type schema:DefinedTerm
129 N3905371834dc49fca4e0062effbcdeca schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
130 schema:name DNA Replication
131 rdf:type schema:DefinedTerm
132 N3f8803296f0e4c619ce2a798acb5cd59 schema:name pubmed_id
133 schema:value 1579168
134 rdf:type schema:PropertyValue
135 N55997a5f1bc2450e9d90bb8c590b0bfb schema:name doi
136 schema:value 10.1038/357169a0
137 rdf:type schema:PropertyValue
138 N6f049d750ea8498cadcc375b05963944 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
139 schema:name Phenanthrolines
140 rdf:type schema:DefinedTerm
141 N7f88dccee13348d8adff4e4e2bc335c6 schema:name Springer Nature - SN SciGraph project
142 rdf:type schema:Organization
143 N84d19cd98ea84b899d1f653970c65da6 schema:volumeNumber 357
144 rdf:type schema:PublicationVolume
145 N913df166904947e399f95b579f3174ba rdf:first sg:person.01070163466.42
146 rdf:rest Ne1084ddf4dbb42d0b49aff50a7062da2
147 N95ae72e8f3994141835a3d66c4a295a2 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
148 schema:name DNA-Binding Proteins
149 rdf:type schema:DefinedTerm
150 N9c4f7d22d4944fceb2eeead026b11752 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
151 schema:name Molecular Sequence Data
152 rdf:type schema:DefinedTerm
153 N9e18098d4e604e59a078a512d24393fc schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
154 schema:name Saccharomyces cerevisiae
155 rdf:type schema:DefinedTerm
156 Na1a0a7b1e7a34c0a9db5901932d7958b schema:issueNumber 6374
157 rdf:type schema:PublicationIssue
158 Naf6cf2210be948408e634dcbb095ca64 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
159 schema:name Oligodeoxyribonucleotides
160 rdf:type schema:DefinedTerm
161 Nc014106e7e874c36b2c728e47df14ab9 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
162 schema:name DNA, Fungal
163 rdf:type schema:DefinedTerm
164 Ne1084ddf4dbb42d0b49aff50a7062da2 rdf:first sg:person.0646410652.65
165 rdf:rest rdf:nil
166 Nef0f6e739f554bb8b11dd13e708d24ef schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
167 schema:name Thiourea
168 rdf:type schema:DefinedTerm
169 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
170 schema:name Biological Sciences
171 rdf:type schema:DefinedTerm
172 anzsrc-for:0601 schema:inDefinedTermSet anzsrc-for:
173 schema:name Biochemistry and Cell Biology
174 rdf:type schema:DefinedTerm
175 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
176 schema:name Genetics
177 rdf:type schema:DefinedTerm
178 sg:journal.1018957 schema:issn 0028-0836
179 1476-4687
180 schema:name Nature
181 schema:publisher Springer Nature
182 rdf:type schema:Periodical
183 sg:person.01070163466.42 schema:affiliation grid-institutes:grid.11485.39
184 schema:familyName Diffley
185 schema:givenName John F. X.
186 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01070163466.42
187 rdf:type schema:Person
188 sg:person.0646410652.65 schema:affiliation grid-institutes:grid.11485.39
189 schema:familyName Cocker
190 schema:givenName Julie H.
191 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0646410652.65
192 rdf:type schema:Person
193 sg:pub.10.1007/978-1-4612-3490-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050442579
194 https://doi.org/10.1007/978-1-4612-3490-6
195 rdf:type schema:CreativeWork
196 sg:pub.10.1038/282039a0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038416530
197 https://doi.org/10.1038/282039a0
198 rdf:type schema:CreativeWork
199 sg:pub.10.1038/343387a0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012803467
200 https://doi.org/10.1038/343387a0
201 rdf:type schema:CreativeWork
202 sg:pub.10.1038/350247a0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007685176
203 https://doi.org/10.1038/350247a0
204 rdf:type schema:CreativeWork
205 sg:pub.10.1038/357128a0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008093514
206 https://doi.org/10.1038/357128a0
207 rdf:type schema:CreativeWork
208 grid-institutes:grid.11485.39 schema:alternateName Imperial Cancer Research Fund, Blanche Lane, EN6 3LD, South Mimms, Potters Bar, Hertfordshire, UK
209 schema:name Imperial Cancer Research Fund, Blanche Lane, EN6 3LD, South Mimms, Potters Bar, Hertfordshire, UK
210 rdf:type schema:Organization
 




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


...