Epigenetic traits inscribed in chromatin accessibility in aged hematopoietic stem cells View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2022-05-16

AUTHORS

Naoki Itokawa, Motohiko Oshima, Shuhei Koide, Naoya Takayama, Wakako Kuribayashi, Yaeko Nakajima-Takagi, Kazumasa Aoyama, Satoshi Yamazaki, Kiyoshi Yamaguchi, Yoichi Furukawa, Koji Eto, Atsushi Iwama

ABSTRACT

Hematopoietic stem cells (HSCs) exhibit considerable cell-intrinsic changes with age. Here, we present an integrated analysis of transcriptome and chromatin accessibility of aged HSCs and downstream progenitors. Alterations in chromatin accessibility preferentially take place in HSCs with aging, which gradually resolve with differentiation. Differentially open accessible regions (open DARs) in aged HSCs are enriched for enhancers and show enrichment of binding motifs of the STAT, ATF, and CNC family transcription factors that are activated in response to external stresses. Genes linked to open DARs show significantly higher levels of basal expression and their expression reaches significantly higher peaks after cytokine stimulation in aged HSCs than in young HSCs, suggesting that open DARs contribute to augmented transcriptional responses under stress conditions. However, a short-term stress challenge that mimics infection is not sufficient to induce persistent chromatin accessibility changes in young HSCs. These results indicate that the ongoing and/or history of exposure to external stresses may be epigenetically inscribed in HSCs to augment their responses to external stimuli. More... »

PAGES

2691

References to SciGraph publications

  • 2020-11-05. Aging and leukemic evolution of hematopoietic stem cells under various stress conditions in INFLAMMATION AND REGENERATION
  • 2019-10-31. The functional mechanisms of mutations in myelodysplastic syndrome in LEUKEMIA
  • 2019-11-18. Do haematopoietic stem cells age? in NATURE REVIEWS IMMUNOLOGY
  • 2019-01-31. Deregulated Polycomb functions in myeloproliferative neoplasms in INTERNATIONAL JOURNAL OF HEMATOLOGY
  • 2019-02-11. Haematopoietic stem cell activity and interactions with the niche in NATURE REVIEWS MOLECULAR CELL BIOLOGY
  • 2014-12-05. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 in GENOME BIOLOGY
  • 2012-08-17. The role of mutations in epigenetic regulators in myeloid malignancies in NATURE REVIEWS CANCER
  • 2020-03-04. Defining trained immunity and its role in health and disease in NATURE REVIEWS IMMUNOLOGY
  • 2016-04-13. Age-dependent modulation of vascular niches for haematopoietic stem cells in NATURE
  • 2020-03-19. JAK–STAT pathway targeting for the treatment of inflammatory bowel disease in NATURE REVIEWS GASTROENTEROLOGY & HEPATOLOGY
  • 1996-09. The aging of hematopoietic stem cells in NATURE MEDICINE
  • 2018-05-07. Adrenergic nerve degeneration in bone marrow drives aging of the hematopoietic stem cell niche in NATURE MEDICINE
  • 2016-08-15. Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution in NATURE GENETICS
  • 2019-03-06. Accumulation of genetic and epigenetic alterations in normal cells and cancer risk in NPJ PRECISION ONCOLOGY
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/s41467-022-30440-2

    DOI

    http://dx.doi.org/10.1038/s41467-022-30440-2

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1147893610

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/35577813


    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"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Cell Differentiation", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Chromatin", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Epigenesis, Genetic", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Epigenomics", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Hematopoietic Stem Cells", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan", 
              "id": "http://www.grid.ac/institutes/grid.26999.3d", 
              "name": [
                "Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan", 
                "Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Itokawa", 
            "givenName": "Naoki", 
            "id": "sg:person.011044425553.67", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011044425553.67"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan", 
              "id": "http://www.grid.ac/institutes/grid.26999.3d", 
              "name": [
                "Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Oshima", 
            "givenName": "Motohiko", 
            "id": "sg:person.0634641424.80", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0634641424.80"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan", 
              "id": "http://www.grid.ac/institutes/grid.26999.3d", 
              "name": [
                "Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Koide", 
            "givenName": "Shuhei", 
            "id": "sg:person.01043542146.49", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01043542146.49"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Regenerative Medicine, Chiba University Graduate School of Medicine, Chiba, Japan", 
              "id": "http://www.grid.ac/institutes/grid.136304.3", 
              "name": [
                "Department of Regenerative Medicine, Chiba University Graduate School of Medicine, Chiba, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Takayama", 
            "givenName": "Naoya", 
            "id": "sg:person.01134747604.40", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01134747604.40"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan", 
              "id": "http://www.grid.ac/institutes/grid.26999.3d", 
              "name": [
                "Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan", 
                "Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Kuribayashi", 
            "givenName": "Wakako", 
            "id": "sg:person.014317266111.04", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014317266111.04"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan", 
              "id": "http://www.grid.ac/institutes/grid.26999.3d", 
              "name": [
                "Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Nakajima-Takagi", 
            "givenName": "Yaeko", 
            "id": "sg:person.01125434330.40", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01125434330.40"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan", 
              "id": "http://www.grid.ac/institutes/grid.26999.3d", 
              "name": [
                "Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan", 
                "Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Aoyama", 
            "givenName": "Kazumasa", 
            "id": "sg:person.01342605152.20", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01342605152.20"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Laboratory of Stem Cell Therapy, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan", 
              "id": "http://www.grid.ac/institutes/grid.20515.33", 
              "name": [
                "Division of Stem Cell Biology, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan", 
                "Laboratory of Stem Cell Therapy, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Yamazaki", 
            "givenName": "Satoshi", 
            "id": "sg:person.0630743167.55", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0630743167.55"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan", 
              "id": "http://www.grid.ac/institutes/grid.26999.3d", 
              "name": [
                "Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Yamaguchi", 
            "givenName": "Kiyoshi", 
            "id": "sg:person.016457707452.82", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016457707452.82"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan", 
              "id": "http://www.grid.ac/institutes/grid.26999.3d", 
              "name": [
                "Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Furukawa", 
            "givenName": "Yoichi", 
            "id": "sg:person.01161610300.37", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01161610300.37"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan", 
              "id": "http://www.grid.ac/institutes/grid.258799.8", 
              "name": [
                "Department of Regenerative Medicine, Chiba University Graduate School of Medicine, Chiba, Japan", 
                "Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Eto", 
            "givenName": "Koji", 
            "id": "sg:person.01062427654.09", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01062427654.09"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Laboratoty of Cellular and Molecular Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan", 
              "id": "http://www.grid.ac/institutes/grid.26999.3d", 
              "name": [
                "Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan", 
                "Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan", 
                "Laboratoty of Cellular and Molecular Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Iwama", 
            "givenName": "Atsushi", 
            "id": "sg:person.0614375646.43", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0614375646.43"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1038/s41375-019-0617-3", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1122202837", 
              "https://doi.org/10.1038/s41375-019-0617-3"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41580-019-0103-9", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1112059803", 
              "https://doi.org/10.1038/s41580-019-0103-9"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41577-019-0236-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1122669105", 
              "https://doi.org/10.1038/s41577-019-0236-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrc3343", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1042261597", 
              "https://doi.org/10.1038/nrc3343"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s41232-020-00138-3", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1132317411", 
              "https://doi.org/10.1186/s41232-020-00138-3"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s12185-019-02600-6", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1111822249", 
              "https://doi.org/10.1007/s12185-019-02600-6"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41591-018-0030-x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1103817446", 
              "https://doi.org/10.1038/s41591-018-0030-x"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41577-020-0285-6", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1125343614", 
              "https://doi.org/10.1038/s41577-020-0285-6"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nm0996-1011", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1045465259", 
              "https://doi.org/10.1038/nm0996-1011"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41698-019-0079-0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1112580757", 
              "https://doi.org/10.1038/s41698-019-0079-0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13059-014-0550-8", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015222646", 
              "https://doi.org/10.1186/s13059-014-0550-8"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41575-020-0273-0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1125770720", 
              "https://doi.org/10.1038/s41575-020-0273-0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature17638", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1044080541", 
              "https://doi.org/10.1038/nature17638"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng.3646", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1014039410", 
              "https://doi.org/10.1038/ng.3646"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2022-05-16", 
        "datePublishedReg": "2022-05-16", 
        "description": "Hematopoietic stem cells (HSCs) exhibit considerable cell-intrinsic changes with age. Here, we present an integrated analysis of transcriptome and chromatin accessibility of aged HSCs and downstream progenitors. Alterations in chromatin accessibility preferentially take place in HSCs with aging, which gradually resolve with differentiation. Differentially open accessible regions (open DARs) in aged HSCs are enriched for enhancers and show enrichment of binding motifs of the STAT, ATF, and CNC family transcription factors that are activated in response to external stresses. Genes linked to open DARs show significantly higher levels of basal expression and their expression reaches significantly higher peaks after cytokine stimulation in aged HSCs than in young HSCs, suggesting that open DARs contribute to augmented transcriptional responses under stress conditions. However, a short-term stress challenge that mimics infection is not sufficient to induce persistent chromatin accessibility changes in young HSCs. These results indicate that the ongoing and/or history of exposure to external stresses may be epigenetically inscribed in HSCs to augment their responses to external stimuli.", 
        "genre": "article", 
        "id": "sg:pub.10.1038/s41467-022-30440-2", 
        "isAccessibleForFree": true, 
        "isFundedItemOf": [
          {
            "id": "sg:grant.8535065", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.8534972", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.6127776", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.12844243", 
            "type": "MonetaryGrant"
          }
        ], 
        "isPartOf": [
          {
            "id": "sg:journal.1043282", 
            "issn": [
              "2041-1723"
            ], 
            "name": "Nature Communications", 
            "publisher": "Springer Nature", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "1", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "13"
          }
        ], 
        "keywords": [
          "aged hematopoietic stem cells", 
          "hematopoietic stem cells", 
          "chromatin accessibility", 
          "young hematopoietic stem cells", 
          "chromatin accessibility changes", 
          "family transcription factors", 
          "stem cells", 
          "cell-intrinsic changes", 
          "transcriptional response", 
          "transcription factors", 
          "epigenetic traits", 
          "downstream progenitors", 
          "stress conditions", 
          "accessibility changes", 
          "basal expression", 
          "integrated analysis", 
          "cytokine stimulation", 
          "accessible regions", 
          "external stress", 
          "stress challenge", 
          "expression", 
          "transcriptome", 
          "cells", 
          "external stimuli", 
          "genes", 
          "traits", 
          "progenitors", 
          "STAT", 
          "motif", 
          "enhancer", 
          "differentiation", 
          "ATF", 
          "high levels", 
          "stress", 
          "response", 
          "enrichment", 
          "accessibility", 
          "alterations", 
          "changes", 
          "region", 
          "mimics infection", 
          "stimulation", 
          "levels", 
          "stimuli", 
          "factors", 
          "infection", 
          "exposure", 
          "DAR", 
          "analysis", 
          "history of exposure", 
          "conditions", 
          "results", 
          "high peak", 
          "history", 
          "challenges", 
          "place", 
          "peak", 
          "age"
        ], 
        "name": "Epigenetic traits inscribed in chromatin accessibility in aged hematopoietic stem cells", 
        "pagination": "2691", 
        "productId": [
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1147893610"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1038/s41467-022-30440-2"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "35577813"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1038/s41467-022-30440-2", 
          "https://app.dimensions.ai/details/publication/pub.1147893610"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2022-09-02T16:07", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-springernature-scigraph/baseset/20220902/entities/gbq_results/article/article_941.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://doi.org/10.1038/s41467-022-30440-2"
      }
    ]
     

    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/s41467-022-30440-2'

    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/s41467-022-30440-2'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/s41467-022-30440-2'

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

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/s41467-022-30440-2'


     

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

    295 TRIPLES      21 PREDICATES      102 URIs      80 LITERALS      12 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1038/s41467-022-30440-2 schema:about N2b1233f127bc474da7f785b1bc2fc9ab
    2 N4102aaec3e684022b360e4d2dcf60198
    3 N4a9b084d70a34ecdb0d9228aa6d2b20f
    4 Nbc12ff4a586240b599fc8b669eeccc37
    5 Nfd9ac48bb7e343d9b201ad1d8af57c18
    6 anzsrc-for:06
    7 anzsrc-for:0604
    8 schema:author Nd5655e5754a9474e85183b53b42b0720
    9 schema:citation sg:pub.10.1007/s12185-019-02600-6
    10 sg:pub.10.1038/nature17638
    11 sg:pub.10.1038/ng.3646
    12 sg:pub.10.1038/nm0996-1011
    13 sg:pub.10.1038/nrc3343
    14 sg:pub.10.1038/s41375-019-0617-3
    15 sg:pub.10.1038/s41575-020-0273-0
    16 sg:pub.10.1038/s41577-019-0236-2
    17 sg:pub.10.1038/s41577-020-0285-6
    18 sg:pub.10.1038/s41580-019-0103-9
    19 sg:pub.10.1038/s41591-018-0030-x
    20 sg:pub.10.1038/s41698-019-0079-0
    21 sg:pub.10.1186/s13059-014-0550-8
    22 sg:pub.10.1186/s41232-020-00138-3
    23 schema:datePublished 2022-05-16
    24 schema:datePublishedReg 2022-05-16
    25 schema:description Hematopoietic stem cells (HSCs) exhibit considerable cell-intrinsic changes with age. Here, we present an integrated analysis of transcriptome and chromatin accessibility of aged HSCs and downstream progenitors. Alterations in chromatin accessibility preferentially take place in HSCs with aging, which gradually resolve with differentiation. Differentially open accessible regions (open DARs) in aged HSCs are enriched for enhancers and show enrichment of binding motifs of the STAT, ATF, and CNC family transcription factors that are activated in response to external stresses. Genes linked to open DARs show significantly higher levels of basal expression and their expression reaches significantly higher peaks after cytokine stimulation in aged HSCs than in young HSCs, suggesting that open DARs contribute to augmented transcriptional responses under stress conditions. However, a short-term stress challenge that mimics infection is not sufficient to induce persistent chromatin accessibility changes in young HSCs. These results indicate that the ongoing and/or history of exposure to external stresses may be epigenetically inscribed in HSCs to augment their responses to external stimuli.
    26 schema:genre article
    27 schema:isAccessibleForFree true
    28 schema:isPartOf N380ed2f102bd4e60a7a91a5b120fd51f
    29 Nca0660a18aeb4e36b21eb8458d8bf0dc
    30 sg:journal.1043282
    31 schema:keywords ATF
    32 DAR
    33 STAT
    34 accessibility
    35 accessibility changes
    36 accessible regions
    37 age
    38 aged hematopoietic stem cells
    39 alterations
    40 analysis
    41 basal expression
    42 cell-intrinsic changes
    43 cells
    44 challenges
    45 changes
    46 chromatin accessibility
    47 chromatin accessibility changes
    48 conditions
    49 cytokine stimulation
    50 differentiation
    51 downstream progenitors
    52 enhancer
    53 enrichment
    54 epigenetic traits
    55 exposure
    56 expression
    57 external stimuli
    58 external stress
    59 factors
    60 family transcription factors
    61 genes
    62 hematopoietic stem cells
    63 high levels
    64 high peak
    65 history
    66 history of exposure
    67 infection
    68 integrated analysis
    69 levels
    70 mimics infection
    71 motif
    72 peak
    73 place
    74 progenitors
    75 region
    76 response
    77 results
    78 stem cells
    79 stimulation
    80 stimuli
    81 stress
    82 stress challenge
    83 stress conditions
    84 traits
    85 transcription factors
    86 transcriptional response
    87 transcriptome
    88 young hematopoietic stem cells
    89 schema:name Epigenetic traits inscribed in chromatin accessibility in aged hematopoietic stem cells
    90 schema:pagination 2691
    91 schema:productId N1e7425eb0d57469d8439a24362872e57
    92 Nca9632aee4b541ebbf68eeb57e9dca00
    93 Neb261271bdc647aca25aa3beb3973ef1
    94 schema:sameAs https://app.dimensions.ai/details/publication/pub.1147893610
    95 https://doi.org/10.1038/s41467-022-30440-2
    96 schema:sdDatePublished 2022-09-02T16:07
    97 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    98 schema:sdPublisher N58a45ad79a274c3c83d98359274ab1e3
    99 schema:url https://doi.org/10.1038/s41467-022-30440-2
    100 sgo:license sg:explorer/license/
    101 sgo:sdDataset articles
    102 rdf:type schema:ScholarlyArticle
    103 N1e21d4fb2c9248cb9cb666fea0778d7e rdf:first sg:person.01043542146.49
    104 rdf:rest Na0d4f3790f804ce6a28f78a08b57ab59
    105 N1e7425eb0d57469d8439a24362872e57 schema:name dimensions_id
    106 schema:value pub.1147893610
    107 rdf:type schema:PropertyValue
    108 N2b1233f127bc474da7f785b1bc2fc9ab schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    109 schema:name Chromatin
    110 rdf:type schema:DefinedTerm
    111 N380ed2f102bd4e60a7a91a5b120fd51f schema:issueNumber 1
    112 rdf:type schema:PublicationIssue
    113 N4102aaec3e684022b360e4d2dcf60198 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    114 schema:name Epigenesis, Genetic
    115 rdf:type schema:DefinedTerm
    116 N4a9b084d70a34ecdb0d9228aa6d2b20f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    117 schema:name Cell Differentiation
    118 rdf:type schema:DefinedTerm
    119 N5710a62f026f488ca5d7793db7105359 rdf:first sg:person.01062427654.09
    120 rdf:rest Ne65a06726b0041d4980ab6d1127c8184
    121 N58a45ad79a274c3c83d98359274ab1e3 schema:name Springer Nature - SN SciGraph project
    122 rdf:type schema:Organization
    123 N5d9ca79040d64b32b087f23f56771439 rdf:first sg:person.0630743167.55
    124 rdf:rest Nffd41238665b43ac91005cb371d2e922
    125 N6b96aaaa419744c5b6514f0014970273 rdf:first sg:person.01125434330.40
    126 rdf:rest N81c0bb8987654cd68c2c8803e423739f
    127 N81c0bb8987654cd68c2c8803e423739f rdf:first sg:person.01342605152.20
    128 rdf:rest N5d9ca79040d64b32b087f23f56771439
    129 Na0d4f3790f804ce6a28f78a08b57ab59 rdf:first sg:person.01134747604.40
    130 rdf:rest Ne14a3d16ce1c471e8135bf37f2fba475
    131 Naf526bb8a94049739f318736352f6e10 rdf:first sg:person.01161610300.37
    132 rdf:rest N5710a62f026f488ca5d7793db7105359
    133 Nb1357d5b89cd415caba2c5641e4608ca rdf:first sg:person.0634641424.80
    134 rdf:rest N1e21d4fb2c9248cb9cb666fea0778d7e
    135 Nbc12ff4a586240b599fc8b669eeccc37 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    136 schema:name Hematopoietic Stem Cells
    137 rdf:type schema:DefinedTerm
    138 Nca0660a18aeb4e36b21eb8458d8bf0dc schema:volumeNumber 13
    139 rdf:type schema:PublicationVolume
    140 Nca9632aee4b541ebbf68eeb57e9dca00 schema:name pubmed_id
    141 schema:value 35577813
    142 rdf:type schema:PropertyValue
    143 Nd5655e5754a9474e85183b53b42b0720 rdf:first sg:person.011044425553.67
    144 rdf:rest Nb1357d5b89cd415caba2c5641e4608ca
    145 Ne14a3d16ce1c471e8135bf37f2fba475 rdf:first sg:person.014317266111.04
    146 rdf:rest N6b96aaaa419744c5b6514f0014970273
    147 Ne65a06726b0041d4980ab6d1127c8184 rdf:first sg:person.0614375646.43
    148 rdf:rest rdf:nil
    149 Neb261271bdc647aca25aa3beb3973ef1 schema:name doi
    150 schema:value 10.1038/s41467-022-30440-2
    151 rdf:type schema:PropertyValue
    152 Nfd9ac48bb7e343d9b201ad1d8af57c18 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    153 schema:name Epigenomics
    154 rdf:type schema:DefinedTerm
    155 Nffd41238665b43ac91005cb371d2e922 rdf:first sg:person.016457707452.82
    156 rdf:rest Naf526bb8a94049739f318736352f6e10
    157 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    158 schema:name Biological Sciences
    159 rdf:type schema:DefinedTerm
    160 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
    161 schema:name Genetics
    162 rdf:type schema:DefinedTerm
    163 sg:grant.12844243 http://pending.schema.org/fundedItem sg:pub.10.1038/s41467-022-30440-2
    164 rdf:type schema:MonetaryGrant
    165 sg:grant.6127776 http://pending.schema.org/fundedItem sg:pub.10.1038/s41467-022-30440-2
    166 rdf:type schema:MonetaryGrant
    167 sg:grant.8534972 http://pending.schema.org/fundedItem sg:pub.10.1038/s41467-022-30440-2
    168 rdf:type schema:MonetaryGrant
    169 sg:grant.8535065 http://pending.schema.org/fundedItem sg:pub.10.1038/s41467-022-30440-2
    170 rdf:type schema:MonetaryGrant
    171 sg:journal.1043282 schema:issn 2041-1723
    172 schema:name Nature Communications
    173 schema:publisher Springer Nature
    174 rdf:type schema:Periodical
    175 sg:person.01043542146.49 schema:affiliation grid-institutes:grid.26999.3d
    176 schema:familyName Koide
    177 schema:givenName Shuhei
    178 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01043542146.49
    179 rdf:type schema:Person
    180 sg:person.01062427654.09 schema:affiliation grid-institutes:grid.258799.8
    181 schema:familyName Eto
    182 schema:givenName Koji
    183 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01062427654.09
    184 rdf:type schema:Person
    185 sg:person.011044425553.67 schema:affiliation grid-institutes:grid.26999.3d
    186 schema:familyName Itokawa
    187 schema:givenName Naoki
    188 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011044425553.67
    189 rdf:type schema:Person
    190 sg:person.01125434330.40 schema:affiliation grid-institutes:grid.26999.3d
    191 schema:familyName Nakajima-Takagi
    192 schema:givenName Yaeko
    193 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01125434330.40
    194 rdf:type schema:Person
    195 sg:person.01134747604.40 schema:affiliation grid-institutes:grid.136304.3
    196 schema:familyName Takayama
    197 schema:givenName Naoya
    198 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01134747604.40
    199 rdf:type schema:Person
    200 sg:person.01161610300.37 schema:affiliation grid-institutes:grid.26999.3d
    201 schema:familyName Furukawa
    202 schema:givenName Yoichi
    203 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01161610300.37
    204 rdf:type schema:Person
    205 sg:person.01342605152.20 schema:affiliation grid-institutes:grid.26999.3d
    206 schema:familyName Aoyama
    207 schema:givenName Kazumasa
    208 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01342605152.20
    209 rdf:type schema:Person
    210 sg:person.014317266111.04 schema:affiliation grid-institutes:grid.26999.3d
    211 schema:familyName Kuribayashi
    212 schema:givenName Wakako
    213 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014317266111.04
    214 rdf:type schema:Person
    215 sg:person.016457707452.82 schema:affiliation grid-institutes:grid.26999.3d
    216 schema:familyName Yamaguchi
    217 schema:givenName Kiyoshi
    218 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016457707452.82
    219 rdf:type schema:Person
    220 sg:person.0614375646.43 schema:affiliation grid-institutes:grid.26999.3d
    221 schema:familyName Iwama
    222 schema:givenName Atsushi
    223 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0614375646.43
    224 rdf:type schema:Person
    225 sg:person.0630743167.55 schema:affiliation grid-institutes:grid.20515.33
    226 schema:familyName Yamazaki
    227 schema:givenName Satoshi
    228 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0630743167.55
    229 rdf:type schema:Person
    230 sg:person.0634641424.80 schema:affiliation grid-institutes:grid.26999.3d
    231 schema:familyName Oshima
    232 schema:givenName Motohiko
    233 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0634641424.80
    234 rdf:type schema:Person
    235 sg:pub.10.1007/s12185-019-02600-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1111822249
    236 https://doi.org/10.1007/s12185-019-02600-6
    237 rdf:type schema:CreativeWork
    238 sg:pub.10.1038/nature17638 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044080541
    239 https://doi.org/10.1038/nature17638
    240 rdf:type schema:CreativeWork
    241 sg:pub.10.1038/ng.3646 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014039410
    242 https://doi.org/10.1038/ng.3646
    243 rdf:type schema:CreativeWork
    244 sg:pub.10.1038/nm0996-1011 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045465259
    245 https://doi.org/10.1038/nm0996-1011
    246 rdf:type schema:CreativeWork
    247 sg:pub.10.1038/nrc3343 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042261597
    248 https://doi.org/10.1038/nrc3343
    249 rdf:type schema:CreativeWork
    250 sg:pub.10.1038/s41375-019-0617-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1122202837
    251 https://doi.org/10.1038/s41375-019-0617-3
    252 rdf:type schema:CreativeWork
    253 sg:pub.10.1038/s41575-020-0273-0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1125770720
    254 https://doi.org/10.1038/s41575-020-0273-0
    255 rdf:type schema:CreativeWork
    256 sg:pub.10.1038/s41577-019-0236-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1122669105
    257 https://doi.org/10.1038/s41577-019-0236-2
    258 rdf:type schema:CreativeWork
    259 sg:pub.10.1038/s41577-020-0285-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1125343614
    260 https://doi.org/10.1038/s41577-020-0285-6
    261 rdf:type schema:CreativeWork
    262 sg:pub.10.1038/s41580-019-0103-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1112059803
    263 https://doi.org/10.1038/s41580-019-0103-9
    264 rdf:type schema:CreativeWork
    265 sg:pub.10.1038/s41591-018-0030-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1103817446
    266 https://doi.org/10.1038/s41591-018-0030-x
    267 rdf:type schema:CreativeWork
    268 sg:pub.10.1038/s41698-019-0079-0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1112580757
    269 https://doi.org/10.1038/s41698-019-0079-0
    270 rdf:type schema:CreativeWork
    271 sg:pub.10.1186/s13059-014-0550-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015222646
    272 https://doi.org/10.1186/s13059-014-0550-8
    273 rdf:type schema:CreativeWork
    274 sg:pub.10.1186/s41232-020-00138-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1132317411
    275 https://doi.org/10.1186/s41232-020-00138-3
    276 rdf:type schema:CreativeWork
    277 grid-institutes:grid.136304.3 schema:alternateName Department of Regenerative Medicine, Chiba University Graduate School of Medicine, Chiba, Japan
    278 schema:name Department of Regenerative Medicine, Chiba University Graduate School of Medicine, Chiba, Japan
    279 rdf:type schema:Organization
    280 grid-institutes:grid.20515.33 schema:alternateName Laboratory of Stem Cell Therapy, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
    281 schema:name Division of Stem Cell Biology, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
    282 Laboratory of Stem Cell Therapy, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
    283 rdf:type schema:Organization
    284 grid-institutes:grid.258799.8 schema:alternateName Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
    285 schema:name Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
    286 Department of Regenerative Medicine, Chiba University Graduate School of Medicine, Chiba, Japan
    287 rdf:type schema:Organization
    288 grid-institutes:grid.26999.3d schema:alternateName Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
    289 Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
    290 Laboratoty of Cellular and Molecular Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
    291 schema:name Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
    292 Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
    293 Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
    294 Laboratoty of Cellular and Molecular Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
    295 rdf:type schema:Organization
     




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


    ...