5-Hydroxymethylcytosine is a predominantly stable DNA modification View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2014-12

AUTHORS

Martin Bachman, Santiago Uribe-Lewis, Xiaoping Yang, Michael Williams, Adele Murrell, Shankar Balasubramanian

ABSTRACT

5-Hydroxymethylcytosine (hmC) is an oxidation product of 5-methylcytosine which is present in the deoxyribonucleic acid (DNA) of most mammalian cells. Reduction of hmC levels in DNA is a hallmark of cancers. Elucidating the dynamics of this oxidation reaction and the lifetime of hmC in DNA is fundamental to understanding hmC function. Using stable isotope labelling of cytosine derivatives in the DNA of mammalian cells and ultrasensitive tandem liquid-chromatography mass spectrometry, we show that the majority of hmC is a stable modification, as opposed to a transient intermediate. In contrast with DNA methylation, which occurs immediately during replication, hmC forms slowly during the first 30 hours following DNA synthesis. Isotopic labelling of DNA in mouse tissues confirmed the stability of hmC in vivo and demonstrated a relationship between global levels of hmC and cell proliferation. These insights have important implications for understanding the states of chemically modified DNA bases in health and disease. More... »

PAGES

1049-1055

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nchem.2064

DOI

http://dx.doi.org/10.1038/nchem.2064

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1021457238

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/25411882


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/2008/0601", 
        "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/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "5-Methylcytosine", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Animals", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Cell Cycle", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Cell Proliferation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Cytosine", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA Methylation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "HCT116 Cells", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Humans", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "MCF-7 Cells", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Mice", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Mice, Inbred C57BL", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Cancer Research UK Cambridge Institute", 
          "id": "https://www.grid.ac/institutes/grid.470869.4", 
          "name": [
            "Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK", 
            "Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Bachman", 
        "givenName": "Martin", 
        "id": "sg:person.01134554434.01", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01134554434.01"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Cancer Research UK Cambridge Institute", 
          "id": "https://www.grid.ac/institutes/grid.470869.4", 
          "name": [
            "Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Uribe-Lewis", 
        "givenName": "Santiago", 
        "id": "sg:person.0741302373.14", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0741302373.14"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Cancer Research UK Cambridge Institute", 
          "id": "https://www.grid.ac/institutes/grid.470869.4", 
          "name": [
            "Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Yang", 
        "givenName": "Xiaoping", 
        "id": "sg:person.01165011756.47", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01165011756.47"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Cancer Research UK Cambridge Institute", 
          "id": "https://www.grid.ac/institutes/grid.470869.4", 
          "name": [
            "Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Williams", 
        "givenName": "Michael", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Bath", 
          "id": "https://www.grid.ac/institutes/grid.7340.0", 
          "name": [
            "Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK", 
            "Centre for Regenerative Medicine, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Murrell", 
        "givenName": "Adele", 
        "id": "sg:person.01307061133.30", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01307061133.30"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Cancer Research UK Cambridge Institute", 
          "id": "https://www.grid.ac/institutes/grid.470869.4", 
          "name": [
            "Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK", 
            "Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Balasubramanian", 
        "givenName": "Shankar", 
        "id": "sg:person.01141737764.78", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01141737764.78"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1016/j.cell.2011.03.022", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1001775952"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1170116", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004667708"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature06968", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004707194", 
          "https://doi.org/10.1038/nature06968"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cell.2012.11.022", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006068074"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cell.2013.02.004", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006514945"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature12362", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1008910662", 
          "https://doi.org/10.1038/nature12362"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1169786", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010093223"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1169786", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010093223"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1210944", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010479763"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/gb-2013-14-10-r119", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010713180", 
          "https://doi.org/10.1186/gb-2013-14-10-r119"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1158/0008-5472.can-11-2023", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010886279"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/jcp.1040750104", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011117718"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/0014-4827(86)90511-2", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011173204"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/ijc.27429", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1012203847"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cell.2012.07.033", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016529494"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.1014033108", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017206774"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1210597", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017751509"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.stem.2013.05.006", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1021016860"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0091-679x(08)61582-4", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022451893"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1212483", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025172508"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cell.2014.04.017", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025918901"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pone.0038156", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1027152101"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature09303", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028926361", 
          "https://doi.org/10.1038/nature09303"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.18632/oncotarget.316", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030818607"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.ceb.2013.02.017", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031856318"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.ceb.2013.02.017", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031856318"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/16.21.10397", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1032637870"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.stem.2011.07.010", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1035278748"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature12750", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037921395", 
          "https://doi.org/10.1038/nature12750"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1074/jbc.c113.464800", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1039822697"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.1310323110", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1040741628"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.tibs.2013.07.003", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042416794"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.tibs.2005.12.008", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042606459"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature10066", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045516695", 
          "https://doi.org/10.1038/nature10066"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cell.2012.04.027", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046692465"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pone.0082961", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047210616"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gad.2036011", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047865706"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.molcel.2011.04.005", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049664644"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pone.0015367", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050703076"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1220671", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1052352304"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.0912402107", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053165778"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2014-12", 
    "datePublishedReg": "2014-12-01", 
    "description": "5-Hydroxymethylcytosine (hmC) is an oxidation product of 5-methylcytosine which is present in the deoxyribonucleic acid (DNA) of most mammalian cells. Reduction of hmC levels in DNA is a hallmark of cancers. Elucidating the dynamics of this oxidation reaction and the lifetime of hmC in DNA is fundamental to understanding hmC function. Using stable isotope labelling of cytosine derivatives in the DNA of mammalian cells and ultrasensitive tandem liquid-chromatography mass spectrometry, we show that the majority of hmC is a stable modification, as opposed to a transient intermediate. In contrast with DNA methylation, which occurs immediately during replication, hmC forms slowly during the first 30 hours following DNA synthesis. Isotopic labelling of DNA in mouse tissues confirmed the stability of hmC in vivo and demonstrated a relationship between global levels of hmC and cell proliferation. These insights have important implications for understanding the states of chemically modified DNA bases in health and disease. ", 
    "genre": "research_article", 
    "id": "sg:pub.10.1038/nchem.2064", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.5136945", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.5143413", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.3643284", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1041224", 
        "issn": [
          "1755-4330", 
          "1755-4349"
        ], 
        "name": "Nature Chemistry", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "12", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "6"
      }
    ], 
    "name": "5-Hydroxymethylcytosine is a predominantly stable DNA modification", 
    "pagination": "1049-1055", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "663b925a312970712b9947c725618ad708451a39f2a3196bb52a2a9498552ad6"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "25411882"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "101499734"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1038/nchem.2064"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1021457238"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1038/nchem.2064", 
      "https://app.dimensions.ai/details/publication/pub.1021457238"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-10T17:19", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000001_0000000264/records_8672_00000424.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://www.nature.com/nchem/journal/v6/n12/full/nchem.2064.html"
  }
]
 

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/nchem.2064'

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/nchem.2064'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/nchem.2064'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/nchem.2064'


 

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

285 TRIPLES      21 PREDICATES      80 URIs      33 LITERALS      21 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1038/nchem.2064 schema:about N0908072bf25e4f9587cb70cfbfd4ef09
2 N1f5c5ac499fb405baf0f3333322fc47b
3 N2de24f79b94748ff82a4d9fd6e36be6f
4 N41a205b0715b47ceaafd806c5502f9fc
5 N467457f73bfa4eeaae232cfa48db8924
6 N5a919617d4674dfc9bf3d438eb3546be
7 N85d68daeba624dd8af63cdb84bc96749
8 N8f45240b94aa4a048d1291f909e28eb2
9 Nab5e1c21870d4790833b645993c890b6
10 Ne37630ce87c6429398d75bd84acdaac1
11 Nf7f2f00e48f248ffb9cea7c921c6b80d
12 Nfe0c7191f2a6493b84040f9dc358253a
13 anzsrc-for:06
14 anzsrc-for:0601
15 schema:author N651bdf1a8406479e844bdd484dc5891d
16 schema:citation sg:pub.10.1038/nature06968
17 sg:pub.10.1038/nature09303
18 sg:pub.10.1038/nature10066
19 sg:pub.10.1038/nature12362
20 sg:pub.10.1038/nature12750
21 sg:pub.10.1186/gb-2013-14-10-r119
22 https://doi.org/10.1002/ijc.27429
23 https://doi.org/10.1002/jcp.1040750104
24 https://doi.org/10.1016/0014-4827(86)90511-2
25 https://doi.org/10.1016/j.ceb.2013.02.017
26 https://doi.org/10.1016/j.cell.2011.03.022
27 https://doi.org/10.1016/j.cell.2012.04.027
28 https://doi.org/10.1016/j.cell.2012.07.033
29 https://doi.org/10.1016/j.cell.2012.11.022
30 https://doi.org/10.1016/j.cell.2013.02.004
31 https://doi.org/10.1016/j.cell.2014.04.017
32 https://doi.org/10.1016/j.molcel.2011.04.005
33 https://doi.org/10.1016/j.stem.2011.07.010
34 https://doi.org/10.1016/j.stem.2013.05.006
35 https://doi.org/10.1016/j.tibs.2005.12.008
36 https://doi.org/10.1016/j.tibs.2013.07.003
37 https://doi.org/10.1016/s0091-679x(08)61582-4
38 https://doi.org/10.1073/pnas.0912402107
39 https://doi.org/10.1073/pnas.1014033108
40 https://doi.org/10.1073/pnas.1310323110
41 https://doi.org/10.1074/jbc.c113.464800
42 https://doi.org/10.1093/nar/16.21.10397
43 https://doi.org/10.1101/gad.2036011
44 https://doi.org/10.1126/science.1169786
45 https://doi.org/10.1126/science.1170116
46 https://doi.org/10.1126/science.1210597
47 https://doi.org/10.1126/science.1210944
48 https://doi.org/10.1126/science.1212483
49 https://doi.org/10.1126/science.1220671
50 https://doi.org/10.1158/0008-5472.can-11-2023
51 https://doi.org/10.1371/journal.pone.0015367
52 https://doi.org/10.1371/journal.pone.0038156
53 https://doi.org/10.1371/journal.pone.0082961
54 https://doi.org/10.18632/oncotarget.316
55 schema:datePublished 2014-12
56 schema:datePublishedReg 2014-12-01
57 schema:description 5-Hydroxymethylcytosine (hmC) is an oxidation product of 5-methylcytosine which is present in the deoxyribonucleic acid (DNA) of most mammalian cells. Reduction of hmC levels in DNA is a hallmark of cancers. Elucidating the dynamics of this oxidation reaction and the lifetime of hmC in DNA is fundamental to understanding hmC function. Using stable isotope labelling of cytosine derivatives in the DNA of mammalian cells and ultrasensitive tandem liquid-chromatography mass spectrometry, we show that the majority of hmC is a stable modification, as opposed to a transient intermediate. In contrast with DNA methylation, which occurs immediately during replication, hmC forms slowly during the first 30 hours following DNA synthesis. Isotopic labelling of DNA in mouse tissues confirmed the stability of hmC in vivo and demonstrated a relationship between global levels of hmC and cell proliferation. These insights have important implications for understanding the states of chemically modified DNA bases in health and disease.
58 schema:genre research_article
59 schema:inLanguage en
60 schema:isAccessibleForFree true
61 schema:isPartOf N1704334238334211b141c44d91011a95
62 Nff6c8472426f46498347640b47c4a4c3
63 sg:journal.1041224
64 schema:name 5-Hydroxymethylcytosine is a predominantly stable DNA modification
65 schema:pagination 1049-1055
66 schema:productId N0ca22369c1984227a7a6755c9ec0484f
67 N20b1d45ba7734d469ba5cee74a8a4844
68 N261bd361565948f5b4b89307b9522a99
69 N361c9329cdc745adaa343b037fc7006f
70 Na9ee532d4056467285805094790fbe77
71 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021457238
72 https://doi.org/10.1038/nchem.2064
73 schema:sdDatePublished 2019-04-10T17:19
74 schema:sdLicense https://scigraph.springernature.com/explorer/license/
75 schema:sdPublisher Nfb10aac1bc7242df92c08b34048e6c68
76 schema:url http://www.nature.com/nchem/journal/v6/n12/full/nchem.2064.html
77 sgo:license sg:explorer/license/
78 sgo:sdDataset articles
79 rdf:type schema:ScholarlyArticle
80 N0908072bf25e4f9587cb70cfbfd4ef09 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
81 schema:name DNA
82 rdf:type schema:DefinedTerm
83 N0ca22369c1984227a7a6755c9ec0484f schema:name readcube_id
84 schema:value 663b925a312970712b9947c725618ad708451a39f2a3196bb52a2a9498552ad6
85 rdf:type schema:PropertyValue
86 N1704334238334211b141c44d91011a95 schema:issueNumber 12
87 rdf:type schema:PublicationIssue
88 N1f5c5ac499fb405baf0f3333322fc47b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
89 schema:name HCT116 Cells
90 rdf:type schema:DefinedTerm
91 N20b1d45ba7734d469ba5cee74a8a4844 schema:name nlm_unique_id
92 schema:value 101499734
93 rdf:type schema:PropertyValue
94 N261bd361565948f5b4b89307b9522a99 schema:name dimensions_id
95 schema:value pub.1021457238
96 rdf:type schema:PropertyValue
97 N2de24f79b94748ff82a4d9fd6e36be6f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
98 schema:name Cell Cycle
99 rdf:type schema:DefinedTerm
100 N361c9329cdc745adaa343b037fc7006f schema:name doi
101 schema:value 10.1038/nchem.2064
102 rdf:type schema:PropertyValue
103 N3e3d8273fb804c2399dacc3168397d43 rdf:first sg:person.0741302373.14
104 rdf:rest N922bc2fd4a6e4c6dae4bc0b7b002b91e
105 N41a205b0715b47ceaafd806c5502f9fc schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
106 schema:name Animals
107 rdf:type schema:DefinedTerm
108 N467457f73bfa4eeaae232cfa48db8924 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
109 schema:name DNA Methylation
110 rdf:type schema:DefinedTerm
111 N5a919617d4674dfc9bf3d438eb3546be schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
112 schema:name Cytosine
113 rdf:type schema:DefinedTerm
114 N5d60cdb6f50745a8a52cdccce70d8e62 rdf:first sg:person.01141737764.78
115 rdf:rest rdf:nil
116 N651bdf1a8406479e844bdd484dc5891d rdf:first sg:person.01134554434.01
117 rdf:rest N3e3d8273fb804c2399dacc3168397d43
118 N85d68daeba624dd8af63cdb84bc96749 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
119 schema:name Cell Proliferation
120 rdf:type schema:DefinedTerm
121 N8f45240b94aa4a048d1291f909e28eb2 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
122 schema:name Mice
123 rdf:type schema:DefinedTerm
124 N922bc2fd4a6e4c6dae4bc0b7b002b91e rdf:first sg:person.01165011756.47
125 rdf:rest N9aaa662969b64c4f834624407eb2c2ad
126 N9aaa662969b64c4f834624407eb2c2ad rdf:first Nb7c5548db1c84172b93a7d8f0debfc7e
127 rdf:rest Naba0d3f25983449db2467c96c77dc70f
128 Na9ee532d4056467285805094790fbe77 schema:name pubmed_id
129 schema:value 25411882
130 rdf:type schema:PropertyValue
131 Nab5e1c21870d4790833b645993c890b6 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
132 schema:name Mice, Inbred C57BL
133 rdf:type schema:DefinedTerm
134 Naba0d3f25983449db2467c96c77dc70f rdf:first sg:person.01307061133.30
135 rdf:rest N5d60cdb6f50745a8a52cdccce70d8e62
136 Nb7c5548db1c84172b93a7d8f0debfc7e schema:affiliation https://www.grid.ac/institutes/grid.470869.4
137 schema:familyName Williams
138 schema:givenName Michael
139 rdf:type schema:Person
140 Ne37630ce87c6429398d75bd84acdaac1 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
141 schema:name 5-Methylcytosine
142 rdf:type schema:DefinedTerm
143 Nf7f2f00e48f248ffb9cea7c921c6b80d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
144 schema:name MCF-7 Cells
145 rdf:type schema:DefinedTerm
146 Nfb10aac1bc7242df92c08b34048e6c68 schema:name Springer Nature - SN SciGraph project
147 rdf:type schema:Organization
148 Nfe0c7191f2a6493b84040f9dc358253a schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
149 schema:name Humans
150 rdf:type schema:DefinedTerm
151 Nff6c8472426f46498347640b47c4a4c3 schema:volumeNumber 6
152 rdf:type schema:PublicationVolume
153 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
154 schema:name Biological Sciences
155 rdf:type schema:DefinedTerm
156 anzsrc-for:0601 schema:inDefinedTermSet anzsrc-for:
157 schema:name Biochemistry and Cell Biology
158 rdf:type schema:DefinedTerm
159 sg:grant.3643284 http://pending.schema.org/fundedItem sg:pub.10.1038/nchem.2064
160 rdf:type schema:MonetaryGrant
161 sg:grant.5136945 http://pending.schema.org/fundedItem sg:pub.10.1038/nchem.2064
162 rdf:type schema:MonetaryGrant
163 sg:grant.5143413 http://pending.schema.org/fundedItem sg:pub.10.1038/nchem.2064
164 rdf:type schema:MonetaryGrant
165 sg:journal.1041224 schema:issn 1755-4330
166 1755-4349
167 schema:name Nature Chemistry
168 rdf:type schema:Periodical
169 sg:person.01134554434.01 schema:affiliation https://www.grid.ac/institutes/grid.470869.4
170 schema:familyName Bachman
171 schema:givenName Martin
172 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01134554434.01
173 rdf:type schema:Person
174 sg:person.01141737764.78 schema:affiliation https://www.grid.ac/institutes/grid.470869.4
175 schema:familyName Balasubramanian
176 schema:givenName Shankar
177 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01141737764.78
178 rdf:type schema:Person
179 sg:person.01165011756.47 schema:affiliation https://www.grid.ac/institutes/grid.470869.4
180 schema:familyName Yang
181 schema:givenName Xiaoping
182 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01165011756.47
183 rdf:type schema:Person
184 sg:person.01307061133.30 schema:affiliation https://www.grid.ac/institutes/grid.7340.0
185 schema:familyName Murrell
186 schema:givenName Adele
187 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01307061133.30
188 rdf:type schema:Person
189 sg:person.0741302373.14 schema:affiliation https://www.grid.ac/institutes/grid.470869.4
190 schema:familyName Uribe-Lewis
191 schema:givenName Santiago
192 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0741302373.14
193 rdf:type schema:Person
194 sg:pub.10.1038/nature06968 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004707194
195 https://doi.org/10.1038/nature06968
196 rdf:type schema:CreativeWork
197 sg:pub.10.1038/nature09303 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028926361
198 https://doi.org/10.1038/nature09303
199 rdf:type schema:CreativeWork
200 sg:pub.10.1038/nature10066 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045516695
201 https://doi.org/10.1038/nature10066
202 rdf:type schema:CreativeWork
203 sg:pub.10.1038/nature12362 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008910662
204 https://doi.org/10.1038/nature12362
205 rdf:type schema:CreativeWork
206 sg:pub.10.1038/nature12750 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037921395
207 https://doi.org/10.1038/nature12750
208 rdf:type schema:CreativeWork
209 sg:pub.10.1186/gb-2013-14-10-r119 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010713180
210 https://doi.org/10.1186/gb-2013-14-10-r119
211 rdf:type schema:CreativeWork
212 https://doi.org/10.1002/ijc.27429 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012203847
213 rdf:type schema:CreativeWork
214 https://doi.org/10.1002/jcp.1040750104 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011117718
215 rdf:type schema:CreativeWork
216 https://doi.org/10.1016/0014-4827(86)90511-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011173204
217 rdf:type schema:CreativeWork
218 https://doi.org/10.1016/j.ceb.2013.02.017 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031856318
219 rdf:type schema:CreativeWork
220 https://doi.org/10.1016/j.cell.2011.03.022 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001775952
221 rdf:type schema:CreativeWork
222 https://doi.org/10.1016/j.cell.2012.04.027 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046692465
223 rdf:type schema:CreativeWork
224 https://doi.org/10.1016/j.cell.2012.07.033 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016529494
225 rdf:type schema:CreativeWork
226 https://doi.org/10.1016/j.cell.2012.11.022 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006068074
227 rdf:type schema:CreativeWork
228 https://doi.org/10.1016/j.cell.2013.02.004 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006514945
229 rdf:type schema:CreativeWork
230 https://doi.org/10.1016/j.cell.2014.04.017 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025918901
231 rdf:type schema:CreativeWork
232 https://doi.org/10.1016/j.molcel.2011.04.005 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049664644
233 rdf:type schema:CreativeWork
234 https://doi.org/10.1016/j.stem.2011.07.010 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035278748
235 rdf:type schema:CreativeWork
236 https://doi.org/10.1016/j.stem.2013.05.006 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021016860
237 rdf:type schema:CreativeWork
238 https://doi.org/10.1016/j.tibs.2005.12.008 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042606459
239 rdf:type schema:CreativeWork
240 https://doi.org/10.1016/j.tibs.2013.07.003 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042416794
241 rdf:type schema:CreativeWork
242 https://doi.org/10.1016/s0091-679x(08)61582-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022451893
243 rdf:type schema:CreativeWork
244 https://doi.org/10.1073/pnas.0912402107 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053165778
245 rdf:type schema:CreativeWork
246 https://doi.org/10.1073/pnas.1014033108 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017206774
247 rdf:type schema:CreativeWork
248 https://doi.org/10.1073/pnas.1310323110 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040741628
249 rdf:type schema:CreativeWork
250 https://doi.org/10.1074/jbc.c113.464800 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039822697
251 rdf:type schema:CreativeWork
252 https://doi.org/10.1093/nar/16.21.10397 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032637870
253 rdf:type schema:CreativeWork
254 https://doi.org/10.1101/gad.2036011 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047865706
255 rdf:type schema:CreativeWork
256 https://doi.org/10.1126/science.1169786 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010093223
257 rdf:type schema:CreativeWork
258 https://doi.org/10.1126/science.1170116 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004667708
259 rdf:type schema:CreativeWork
260 https://doi.org/10.1126/science.1210597 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017751509
261 rdf:type schema:CreativeWork
262 https://doi.org/10.1126/science.1210944 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010479763
263 rdf:type schema:CreativeWork
264 https://doi.org/10.1126/science.1212483 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025172508
265 rdf:type schema:CreativeWork
266 https://doi.org/10.1126/science.1220671 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052352304
267 rdf:type schema:CreativeWork
268 https://doi.org/10.1158/0008-5472.can-11-2023 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010886279
269 rdf:type schema:CreativeWork
270 https://doi.org/10.1371/journal.pone.0015367 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050703076
271 rdf:type schema:CreativeWork
272 https://doi.org/10.1371/journal.pone.0038156 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027152101
273 rdf:type schema:CreativeWork
274 https://doi.org/10.1371/journal.pone.0082961 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047210616
275 rdf:type schema:CreativeWork
276 https://doi.org/10.18632/oncotarget.316 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030818607
277 rdf:type schema:CreativeWork
278 https://www.grid.ac/institutes/grid.470869.4 schema:alternateName Cancer Research UK Cambridge Institute
279 schema:name Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
280 Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
281 rdf:type schema:Organization
282 https://www.grid.ac/institutes/grid.7340.0 schema:alternateName University of Bath
283 schema:name Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
284 Centre for Regenerative Medicine, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
285 rdf:type schema:Organization
 




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


...