Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2018-12

AUTHORS

Ramya Raviram, Pedro P. Rocha, Vincent M. Luo, Emily Swanzey, Emily R. Miraldi, Edward B. Chuong, Cédric Feschotte, Richard Bonneau, Jane A. Skok

ABSTRACT

BACKGROUND: The organization of chromatin in the nucleus plays an essential role in gene regulation. About half of the mammalian genome comprises transposable elements. Given their repetitive nature, reads associated with these elements are generally discarded or randomly distributed among elements of the same type in genome-wide analyses. Thus, it is challenging to identify the activities and properties of individual transposons. As a result, we only have a partial understanding of how transposons contribute to chromatin folding and how they impact gene regulation. RESULTS: Using PCR and Capture-based chromosome conformation capture (3C) approaches, collectively called 4Tran, we take advantage of the repetitive nature of transposons to capture interactions from multiple copies of endogenous retrovirus (ERVs) in the human and mouse genomes. With 4Tran-PCR, reads are selectively mapped to unique regions in the genome. This enables the identification of transposable element interaction profiles for individual ERV families and integration events specific to particular genomes. With this approach, we demonstrate that transposons engage in long-range intra-chromosomal interactions guided by the separation of chromosomes into A and B compartments as well as topologically associated domains (TADs). In contrast to 4Tran-PCR, Capture-4Tran can uniquely identify both ends of an interaction that involve retroviral repeat sequences, providing a powerful tool for uncovering the individual transposable element insertions that interact with and potentially regulate target genes. CONCLUSIONS: 4Tran provides new insight into the manner in which transposons contribute to chromosome architecture and identifies target genes that transposable elements can potentially control. More... »

PAGES

216

References to SciGraph publications

  • 2017-03-28. Functional cis-regulatory modules encoded by mouse-specific endogenous retrovirus in NATURE COMMUNICATIONS
  • 2016-12. Genome-wide mapping and analysis of chromosome architecture in NATURE REVIEWS MOLECULAR CELL BIOLOGY
  • 2016-12. Regulation of disease-associated gene expression in the 3D genome in NATURE REVIEWS MOLECULAR CELL BIOLOGY
  • 2008-11. Endogenous retroviruses in CELLULAR AND MOLECULAR LIFE SCIENCES
  • 2017-10. LINE-1 activation after fertilization regulates global chromatin accessibility in the early mouse embryo in NATURE GENETICS
  • 2016-12. CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data in GENOME BIOLOGY
  • 2016-01. Multiplexed analysis of chromosome conformation at vastly improved sensitivity in NATURE METHODS
  • 2015-12. Repbase Update, a database of repetitive elements in eukaryotic genomes in MOBILE DNA
  • 2011-09. Mouse genomic variation and its effect on phenotypes and gene regulation in NATURE
  • 2014-08. Enhancer loops appear stable during development and are associated with paused polymerase in NATURE
  • 2012-10. Robust 4C-seq data analysis to screen for regulatory DNA interactions in NATURE METHODS
  • 2016. Retrotransposon Capture Sequencing (RC-Seq): A Targeted, High-Throughput Approach to Resolve Somatic L1 Retrotransposition in Humans in TRANSPOSONS AND RETROTRANSPOSONS
  • 1998-05. The impact of L1 retrotransposons on the human genome in NATURE GENETICS
  • 2015-06. Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells in NATURE
  • 2012-04. Fast gapped-read alignment with Bowtie 2 in NATURE METHODS
  • 2017-06-09. Transposable elements in cancer in NATURE REVIEWS CANCER
  • 2012-06. The genomic landscape shaped by selection on transposable elements across 18 mouse strains in GENOME BIOLOGY
  • 2013-11. A high-resolution map of the three-dimensional chromatin interactome in human cells in NATURE
  • 2016-11. Organization and function of the 3D genome in NATURE REVIEWS GENETICS
  • 2012-01. Repetitive DNA and next-generation sequencing: computational challenges and solutions in NATURE REVIEWS GENETICS
  • 2012-12. C-GATE - catalogue of genes affected by transposable elements in MOBILE DNA
  • 2015-12. Retrotransposons shape species-specific embryonic stem cell gene expression in RETROVIROLOGY
  • 2017-02. Regulatory activities of transposable elements: from conflicts to benefits in NATURE REVIEWS GENETICS
  • 2012-07. Embryonic stem cell potency fluctuates with endogenous retrovirus activity in NATURE
  • 2012-09. An integrated encyclopedia of DNA elements in the human genome in NATURE
  • 2012-04-11. Topological domains in mammalian genomes identified by analysis of chromatin interactions in NATURE
  • 2017-10. Lineage-specific dynamic and pre-established enhancer–promoter contacts cooperate in terminal differentiation in NATURE GENETICS
  • 2015-06. Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C in NATURE GENETICS
  • 2017-08. Tissue-specific CTCF-cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo in NATURE CELL BIOLOGY
  • 2016-12. Endogenous retroviral promoter exaptation in human cancer in MOBILE DNA
  • 2016-12. Genomic analysis of mouse VL30 retrotransposons in MOBILE DNA
  • 2016-01-08. Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells in NATURE COMMUNICATIONS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/s13059-018-1598-7

    DOI

    http://dx.doi.org/10.1186/s13059-018-1598-7

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1110518208

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/30541598


    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/2008/0604", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Genetics", 
            "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": "Animals", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "DNA Transposable Elements", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Endogenous Retroviruses", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Gene Expression Regulation", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Genomics", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Humans", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Mice", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Polymorphism, Genetic", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Ludwig Cancer Research", 
              "id": "https://www.grid.ac/institutes/grid.1052.6", 
              "name": [
                "Department of Pathology, New York University School of Medicine, 10016, New York, NY, USA", 
                "Department of Biology, New York University, 10003, New York, NY, USA", 
                "Ludwig Institute for Cancer Research, La Jolla, CA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Raviram", 
            "givenName": "Ramya", 
            "id": "sg:person.01324614605.41", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01324614605.41"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "New York University", 
              "id": "https://www.grid.ac/institutes/grid.137628.9", 
              "name": [
                "Department of Pathology, New York University School of Medicine, 10016, New York, NY, USA", 
                "Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, 20892, Bethesda, MD, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Rocha", 
            "givenName": "Pedro P.", 
            "id": "sg:person.01270211632.48", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01270211632.48"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "New York University", 
              "id": "https://www.grid.ac/institutes/grid.137628.9", 
              "name": [
                "Department of Pathology, New York University School of Medicine, 10016, New York, NY, USA", 
                "Department of Biology, New York University, 10003, New York, NY, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Luo", 
            "givenName": "Vincent M.", 
            "id": "sg:person.01167602433.97", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01167602433.97"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "New York University", 
              "id": "https://www.grid.ac/institutes/grid.137628.9", 
              "name": [
                "Department of Developmental Genetics, New York University School of Medicine, 10016, New York, NY, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Swanzey", 
            "givenName": "Emily", 
            "id": "sg:person.01336664426.47", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01336664426.47"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Cincinnati Children's Hospital Medical Center", 
              "id": "https://www.grid.ac/institutes/grid.239573.9", 
              "name": [
                "Department of Biology, New York University, 10003, New York, NY, USA", 
                "Department of Computer Science, Courant Institute of Mathematical Sciences, 10003, New York, NY, USA", 
                "Simons Center for Data Analysis, 10010, New York, NY, USA", 
                "Divisions of Immunobiology and Biomedical Informatics, Cincinnati Children\u2019s Hospital, 45229, Cincinnati, OH, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Miraldi", 
            "givenName": "Emily R.", 
            "id": "sg:person.01201773404.00", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01201773404.00"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "University of Colorado Boulder", 
              "id": "https://www.grid.ac/institutes/grid.266190.a", 
              "name": [
                "BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, 80309, Boulder, CO, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Chuong", 
            "givenName": "Edward B.", 
            "id": "sg:person.0766027552.14", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0766027552.14"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Cornell University", 
              "id": "https://www.grid.ac/institutes/grid.5386.8", 
              "name": [
                "Department of Molecular Biology and Genetics, Cornell University, 14850, Ithaca, NY, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Feschotte", 
            "givenName": "C\u00e9dric", 
            "id": "sg:person.0713321274.37", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0713321274.37"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Courant Institute of Mathematical Sciences", 
              "id": "https://www.grid.ac/institutes/grid.482020.c", 
              "name": [
                "Department of Biology, New York University, 10003, New York, NY, USA", 
                "Department of Computer Science, Courant Institute of Mathematical Sciences, 10003, New York, NY, USA", 
                "Simons Center for Data Analysis, 10010, New York, NY, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Bonneau", 
            "givenName": "Richard", 
            "id": "sg:person.01122465213.75", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01122465213.75"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "New York University", 
              "id": "https://www.grid.ac/institutes/grid.137628.9", 
              "name": [
                "Department of Pathology, New York University School of Medicine, 10016, New York, NY, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Skok", 
            "givenName": "Jane A.", 
            "id": "sg:person.01045755265.19", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01045755265.19"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "https://doi.org/10.1016/j.cell.2015.03.026", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1000014161"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13059-016-0992-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1001813860", 
              "https://doi.org/10.1186/s13059-016-0992-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13059-016-0992-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1001813860", 
              "https://doi.org/10.1186/s13059-016-0992-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13100-015-0041-9", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1001871370", 
              "https://doi.org/10.1186/s13100-015-0041-9"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13100-015-0041-9", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1001871370", 
              "https://doi.org/10.1186/s13100-015-0041-9"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.molcel.2012.06.036", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1003248902"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.2217/epi.15.25", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1003650579"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ncomms10286", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1003990800", 
              "https://doi.org/10.1038/ncomms10286"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/978-1-4939-3372-3_4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1005170688", 
              "https://doi.org/10.1007/978-1-4939-3372-3_4"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmeth.2173", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1005179498", 
              "https://doi.org/10.1038/nmeth.2173"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1146/annurev-genet-110711-155621", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1005304003"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1128/mmbr.00006-15", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1005334022"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1126/science.1262088", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1005794148"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmeth.1923", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1006541515", 
              "https://doi.org/10.1038/nmeth.1923"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmeth.3664", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1006820435", 
              "https://doi.org/10.1038/nmeth.3664"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.cell.2016.02.007", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007042188"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.cell.2016.02.007", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007042188"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.cell.2011.11.058", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007206139"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s12977-015-0173-5", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007254095", 
              "https://doi.org/10.1186/s12977-015-0173-5"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1126/science.1181369", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007401642"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1126/science.1181369", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007401642"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.celrep.2016.05.073", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007711681"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1371/journal.pgen.1000007", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007821853"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature11244", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1008081317", 
              "https://doi.org/10.1038/nature11244"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1371/journal.pgen.1003504", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1008980180"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1126/science.aad5497", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1009168436"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.gde.2016.01.001", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1009992306"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1146/annurev-genet-110711-155616", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1011581093"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1371/journal.pcbi.1004780", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1013294334"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkv1292", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1013890795"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1101/gad.281964.116", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1014991788"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.ceb.2014.04.004", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015713715"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1759-8753-3-9", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1016399170", 
              "https://doi.org/10.1186/1759-8753-3-9"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.12688/f1000research.7334.1", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1018290070"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.molcel.2014.05.029", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1019663782"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature12644", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1019700652", 
              "https://doi.org/10.1038/nature12644"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrm.2016.138", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1020179702", 
              "https://doi.org/10.1038/nrm.2016.138"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.tig.2016.01.003", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1021158236"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.devcel.2016.10.015", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1022845668"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrm.2016.104", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1022853135", 
              "https://doi.org/10.1038/nrm.2016.104"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1002/bies.201300040", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1026314952"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng.3286", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1026830910", 
              "https://doi.org/10.1038/ng.3286"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.15252/embr.201642743", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1026979293"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1101/gr.168872.113", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1027255605"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1101/gr.168872.113", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1027255605"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00018-008-8497-0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1028172451", 
              "https://doi.org/10.1007/s00018-008-8497-0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature13417", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1028426876", 
              "https://doi.org/10.1038/nature13417"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1073/pnas.0611223104", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1028702517"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/b978-0-12-391938-0.00004-5", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1028902320"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature11247", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1029065430", 
              "https://doi.org/10.1038/nature11247"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrg.2016.112", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1029513141", 
              "https://doi.org/10.1038/nrg.2016.112"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.15252/embr.201642198", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1030041082"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.stem.2016.08.004", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1030363937"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13100-016-0066-8", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1031964740", 
              "https://doi.org/10.1186/s13100-016-0066-8"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng0598-19", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1033511786", 
              "https://doi.org/10.1038/ng0598-19"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrg.2016.139", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1034466564", 
              "https://doi.org/10.1038/nrg.2016.139"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.7554/elife.10565", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1034880122"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.cell.2016.09.037", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1035198067"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1073/pnas.1422187112", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1035485185"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13100-016-0080-x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1035783267", 
              "https://doi.org/10.1186/s13100-016-0080-x"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13100-016-0080-x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1035783267", 
              "https://doi.org/10.1186/s13100-016-0080-x"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.7554/elife.13926", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1036550736"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.stem.2015.01.005", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1036578494"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1101/gr.080663.108", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1036971575"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.gde.2016.01.002", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1037393696"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature11082", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1040271530", 
              "https://doi.org/10.1038/nature11082"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature10413", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1041325874", 
              "https://doi.org/10.1038/nature10413"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrg3117", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1044335233", 
              "https://doi.org/10.1038/nrg3117"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature14308", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1046099015", 
              "https://doi.org/10.1038/nature14308"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1146/annurev-cellbio-100814-125514", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1047796989"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.cell.2014.11.021", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1047951603"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1126/science.1260419", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1048221082"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.cell.2016.10.024", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1050913498"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1083/jcb.200305013", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1053392919"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/gb-2012-13-6-r45", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1053645706", 
              "https://doi.org/10.1186/gb-2012-13-6-r45"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1101/sqb.1951.016.01.004", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1060403039"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1101/sqb.1956.021.01.017", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1060403222"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1158/0008-5472.can-15-3502", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1063216115"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://app.dimensions.ai/details/publication/pub.1079412165", 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ncomms14550", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1084128814", 
              "https://doi.org/10.1038/ncomms14550"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.7554/elife.21926", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1084485295"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.ymeth.2017.04.004", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1084902556"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.ymeth.2017.04.004", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1084902556"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.molcel.2017.04.010", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1085155625"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrc.2017.35", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1085935508", 
              "https://doi.org/10.1038/nrc.2017.35"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ncb3573", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1090880206", 
              "https://doi.org/10.1038/ncb3573"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ncb3573", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1090880206", 
              "https://doi.org/10.1038/ncb3573"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/molbev/msx219", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1091132065"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng.3935", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1091217074", 
              "https://doi.org/10.1038/ng.3935"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng.3935", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1091217074", 
              "https://doi.org/10.1038/ng.3935"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng.3945", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1091371366", 
              "https://doi.org/10.1038/ng.3945"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng.3945", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1091371366", 
              "https://doi.org/10.1038/ng.3945"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1101/gr.218149.116", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1091435105"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.molcel.2017.08.006", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1091505048"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.chom.2017.09.007", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1092185178"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.cell.2017.09.043", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1092293106"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1002/bies.201700155", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1095860783"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.2217/epi-2017-0157", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1101782717"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.2217/epi-2017-0157", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1101782717"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.2217/epi-2017-0157", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1101782717"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2018-12", 
        "datePublishedReg": "2018-12-01", 
        "description": "BACKGROUND: The organization of chromatin in the nucleus plays an essential role in gene regulation. About half of the mammalian genome comprises transposable elements. Given their repetitive nature, reads associated with these elements are generally discarded or randomly distributed among elements of the same type in genome-wide analyses. Thus, it is challenging to identify the activities and properties of individual transposons. As a result, we only have a partial understanding of how transposons contribute to chromatin folding and how they impact gene regulation.\nRESULTS: Using PCR and Capture-based chromosome conformation capture (3C) approaches, collectively called 4Tran, we take advantage of the repetitive nature of transposons to capture interactions from multiple copies of endogenous retrovirus (ERVs) in the human and mouse genomes. With 4Tran-PCR, reads are selectively mapped to unique regions in the genome. This enables the identification of transposable element interaction profiles for individual ERV families and integration events specific to particular genomes. With this approach, we demonstrate that transposons engage in long-range intra-chromosomal interactions guided by the separation of chromosomes into A and B compartments as well as topologically associated domains (TADs). In contrast to 4Tran-PCR, Capture-4Tran can uniquely identify both ends of an interaction that involve retroviral repeat sequences, providing a powerful tool for uncovering the individual transposable element insertions that interact with and potentially regulate target genes.\nCONCLUSIONS: 4Tran provides new insight into the manner in which transposons contribute to chromosome architecture and identifies target genes that transposable elements can potentially control.", 
        "genre": "research_article", 
        "id": "sg:pub.10.1186/s13059-018-1598-7", 
        "inLanguage": [
          "en"
        ], 
        "isAccessibleForFree": true, 
        "isFundedItemOf": [
          {
            "id": "sg:grant.6664426", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.2682595", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.4898521", 
            "type": "MonetaryGrant"
          }
        ], 
        "isPartOf": [
          {
            "id": "sg:journal.1023439", 
            "issn": [
              "1474-760X", 
              "1465-6906"
            ], 
            "name": "Genome Biology", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "1", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "19"
          }
        ], 
        "name": "Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate", 
        "pagination": "216", 
        "productId": [
          {
            "name": "readcube_id", 
            "type": "PropertyValue", 
            "value": [
              "1552e13eea78e882b556884e3d197dcae61653b9bf6b1ea6c6e39bbd812c512d"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "30541598"
            ]
          }, 
          {
            "name": "nlm_unique_id", 
            "type": "PropertyValue", 
            "value": [
              "100960660"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1186/s13059-018-1598-7"
            ]
          }, 
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1110518208"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1186/s13059-018-1598-7", 
          "https://app.dimensions.ai/details/publication/pub.1110518208"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2019-04-11T11:13", 
        "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/v90/0000000353_0000000353/records_45366_00000002.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://link.springer.com/10.1186%2Fs13059-018-1598-7"
      }
    ]
     

    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.10.1186/s13059-018-1598-7'

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

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/s13059-018-1598-7'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/s13059-018-1598-7'

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

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/s13059-018-1598-7'


     

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

    483 TRIPLES      21 PREDICATES      125 URIs      29 LITERALS      17 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1186/s13059-018-1598-7 schema:about N06c88d9b153f498d9eda98cea109c5ab
    2 N758042c9c7574bef9668cdb20bb23a28
    3 N92a13a32b8614da6a376bc70509dd9a3
    4 N956d0430c76e413e96b00789d30faaa6
    5 N9ba25b79a3ce4cb1a9faae24450e66ec
    6 Nb1fe2762e82841158b6742f56e9965dd
    7 Ncbc7e4e0d643489da7329c82b17066f8
    8 Nf54f1a44a08747d68dfd4818af3b47bd
    9 anzsrc-for:06
    10 anzsrc-for:0604
    11 schema:author N30b7c1bd62af471baf5ff386e26fbb90
    12 schema:citation sg:pub.10.1007/978-1-4939-3372-3_4
    13 sg:pub.10.1007/s00018-008-8497-0
    14 sg:pub.10.1038/nature10413
    15 sg:pub.10.1038/nature11082
    16 sg:pub.10.1038/nature11244
    17 sg:pub.10.1038/nature11247
    18 sg:pub.10.1038/nature12644
    19 sg:pub.10.1038/nature13417
    20 sg:pub.10.1038/nature14308
    21 sg:pub.10.1038/ncb3573
    22 sg:pub.10.1038/ncomms10286
    23 sg:pub.10.1038/ncomms14550
    24 sg:pub.10.1038/ng.3286
    25 sg:pub.10.1038/ng.3935
    26 sg:pub.10.1038/ng.3945
    27 sg:pub.10.1038/ng0598-19
    28 sg:pub.10.1038/nmeth.1923
    29 sg:pub.10.1038/nmeth.2173
    30 sg:pub.10.1038/nmeth.3664
    31 sg:pub.10.1038/nrc.2017.35
    32 sg:pub.10.1038/nrg.2016.112
    33 sg:pub.10.1038/nrg.2016.139
    34 sg:pub.10.1038/nrg3117
    35 sg:pub.10.1038/nrm.2016.104
    36 sg:pub.10.1038/nrm.2016.138
    37 sg:pub.10.1186/1759-8753-3-9
    38 sg:pub.10.1186/gb-2012-13-6-r45
    39 sg:pub.10.1186/s12977-015-0173-5
    40 sg:pub.10.1186/s13059-016-0992-2
    41 sg:pub.10.1186/s13100-015-0041-9
    42 sg:pub.10.1186/s13100-016-0066-8
    43 sg:pub.10.1186/s13100-016-0080-x
    44 https://app.dimensions.ai/details/publication/pub.1079412165
    45 https://doi.org/10.1002/bies.201300040
    46 https://doi.org/10.1002/bies.201700155
    47 https://doi.org/10.1016/b978-0-12-391938-0.00004-5
    48 https://doi.org/10.1016/j.ceb.2014.04.004
    49 https://doi.org/10.1016/j.cell.2011.11.058
    50 https://doi.org/10.1016/j.cell.2014.11.021
    51 https://doi.org/10.1016/j.cell.2015.03.026
    52 https://doi.org/10.1016/j.cell.2016.02.007
    53 https://doi.org/10.1016/j.cell.2016.09.037
    54 https://doi.org/10.1016/j.cell.2016.10.024
    55 https://doi.org/10.1016/j.cell.2017.09.043
    56 https://doi.org/10.1016/j.celrep.2016.05.073
    57 https://doi.org/10.1016/j.chom.2017.09.007
    58 https://doi.org/10.1016/j.devcel.2016.10.015
    59 https://doi.org/10.1016/j.gde.2016.01.001
    60 https://doi.org/10.1016/j.gde.2016.01.002
    61 https://doi.org/10.1016/j.molcel.2012.06.036
    62 https://doi.org/10.1016/j.molcel.2014.05.029
    63 https://doi.org/10.1016/j.molcel.2017.04.010
    64 https://doi.org/10.1016/j.molcel.2017.08.006
    65 https://doi.org/10.1016/j.stem.2015.01.005
    66 https://doi.org/10.1016/j.stem.2016.08.004
    67 https://doi.org/10.1016/j.tig.2016.01.003
    68 https://doi.org/10.1016/j.ymeth.2017.04.004
    69 https://doi.org/10.1073/pnas.0611223104
    70 https://doi.org/10.1073/pnas.1422187112
    71 https://doi.org/10.1083/jcb.200305013
    72 https://doi.org/10.1093/molbev/msx219
    73 https://doi.org/10.1093/nar/gkv1292
    74 https://doi.org/10.1101/gad.281964.116
    75 https://doi.org/10.1101/gr.080663.108
    76 https://doi.org/10.1101/gr.168872.113
    77 https://doi.org/10.1101/gr.218149.116
    78 https://doi.org/10.1101/sqb.1951.016.01.004
    79 https://doi.org/10.1101/sqb.1956.021.01.017
    80 https://doi.org/10.1126/science.1181369
    81 https://doi.org/10.1126/science.1260419
    82 https://doi.org/10.1126/science.1262088
    83 https://doi.org/10.1126/science.aad5497
    84 https://doi.org/10.1128/mmbr.00006-15
    85 https://doi.org/10.1146/annurev-cellbio-100814-125514
    86 https://doi.org/10.1146/annurev-genet-110711-155616
    87 https://doi.org/10.1146/annurev-genet-110711-155621
    88 https://doi.org/10.1158/0008-5472.can-15-3502
    89 https://doi.org/10.12688/f1000research.7334.1
    90 https://doi.org/10.1371/journal.pcbi.1004780
    91 https://doi.org/10.1371/journal.pgen.1000007
    92 https://doi.org/10.1371/journal.pgen.1003504
    93 https://doi.org/10.15252/embr.201642198
    94 https://doi.org/10.15252/embr.201642743
    95 https://doi.org/10.2217/epi-2017-0157
    96 https://doi.org/10.2217/epi.15.25
    97 https://doi.org/10.7554/elife.10565
    98 https://doi.org/10.7554/elife.13926
    99 https://doi.org/10.7554/elife.21926
    100 schema:datePublished 2018-12
    101 schema:datePublishedReg 2018-12-01
    102 schema:description BACKGROUND: The organization of chromatin in the nucleus plays an essential role in gene regulation. About half of the mammalian genome comprises transposable elements. Given their repetitive nature, reads associated with these elements are generally discarded or randomly distributed among elements of the same type in genome-wide analyses. Thus, it is challenging to identify the activities and properties of individual transposons. As a result, we only have a partial understanding of how transposons contribute to chromatin folding and how they impact gene regulation. RESULTS: Using PCR and Capture-based chromosome conformation capture (3C) approaches, collectively called 4Tran, we take advantage of the repetitive nature of transposons to capture interactions from multiple copies of endogenous retrovirus (ERVs) in the human and mouse genomes. With 4Tran-PCR, reads are selectively mapped to unique regions in the genome. This enables the identification of transposable element interaction profiles for individual ERV families and integration events specific to particular genomes. With this approach, we demonstrate that transposons engage in long-range intra-chromosomal interactions guided by the separation of chromosomes into A and B compartments as well as topologically associated domains (TADs). In contrast to 4Tran-PCR, Capture-4Tran can uniquely identify both ends of an interaction that involve retroviral repeat sequences, providing a powerful tool for uncovering the individual transposable element insertions that interact with and potentially regulate target genes. CONCLUSIONS: 4Tran provides new insight into the manner in which transposons contribute to chromosome architecture and identifies target genes that transposable elements can potentially control.
    103 schema:genre research_article
    104 schema:inLanguage en
    105 schema:isAccessibleForFree true
    106 schema:isPartOf N0c5d504c6cdf44f19c2bff2cbd4be5b1
    107 N1a9c982e769a49588f310f9c80871e7c
    108 sg:journal.1023439
    109 schema:name Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate
    110 schema:pagination 216
    111 schema:productId N15bc1abc420f445cb459aad1205cf4c9
    112 N54ac334878404131991ec4d0897f0956
    113 N7d935b30b89f41b7b7b004c6151ae601
    114 N8c9cf1720f3240dbad24aaebe325b525
    115 Nb6232b53d1ec4b2492baf1fd4fa2d23b
    116 schema:sameAs https://app.dimensions.ai/details/publication/pub.1110518208
    117 https://doi.org/10.1186/s13059-018-1598-7
    118 schema:sdDatePublished 2019-04-11T11:13
    119 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    120 schema:sdPublisher Nfe2bd6211a1d44bea2df16a49567bfcf
    121 schema:url https://link.springer.com/10.1186%2Fs13059-018-1598-7
    122 sgo:license sg:explorer/license/
    123 sgo:sdDataset articles
    124 rdf:type schema:ScholarlyArticle
    125 N02bb9d35848047e8bcf3c9f32c47b5da rdf:first sg:person.0766027552.14
    126 rdf:rest Nd2690966e05c484aa0088f9db694981f
    127 N06c88d9b153f498d9eda98cea109c5ab schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    128 schema:name Endogenous Retroviruses
    129 rdf:type schema:DefinedTerm
    130 N0c5d504c6cdf44f19c2bff2cbd4be5b1 schema:volumeNumber 19
    131 rdf:type schema:PublicationVolume
    132 N15bc1abc420f445cb459aad1205cf4c9 schema:name pubmed_id
    133 schema:value 30541598
    134 rdf:type schema:PropertyValue
    135 N1a9c982e769a49588f310f9c80871e7c schema:issueNumber 1
    136 rdf:type schema:PublicationIssue
    137 N30b7c1bd62af471baf5ff386e26fbb90 rdf:first sg:person.01324614605.41
    138 rdf:rest Ncb4ad1debf5b46a09acdeb61e411bbe9
    139 N3334b308028e466c8bb3419279622cb1 rdf:first sg:person.01045755265.19
    140 rdf:rest rdf:nil
    141 N54ac334878404131991ec4d0897f0956 schema:name doi
    142 schema:value 10.1186/s13059-018-1598-7
    143 rdf:type schema:PropertyValue
    144 N758042c9c7574bef9668cdb20bb23a28 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    145 schema:name Humans
    146 rdf:type schema:DefinedTerm
    147 N7d935b30b89f41b7b7b004c6151ae601 schema:name readcube_id
    148 schema:value 1552e13eea78e882b556884e3d197dcae61653b9bf6b1ea6c6e39bbd812c512d
    149 rdf:type schema:PropertyValue
    150 N86e0464a9f7845a996bde7db188c384f rdf:first sg:person.01201773404.00
    151 rdf:rest N02bb9d35848047e8bcf3c9f32c47b5da
    152 N8c9cf1720f3240dbad24aaebe325b525 schema:name nlm_unique_id
    153 schema:value 100960660
    154 rdf:type schema:PropertyValue
    155 N92a13a32b8614da6a376bc70509dd9a3 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    156 schema:name Genomics
    157 rdf:type schema:DefinedTerm
    158 N956d0430c76e413e96b00789d30faaa6 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    159 schema:name DNA Transposable Elements
    160 rdf:type schema:DefinedTerm
    161 N9995934ad2e04e3989e12bdac42d8760 rdf:first sg:person.01167602433.97
    162 rdf:rest Nd0afeb520a964746b240c2e59f5a02ba
    163 N9ba25b79a3ce4cb1a9faae24450e66ec schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    164 schema:name Polymorphism, Genetic
    165 rdf:type schema:DefinedTerm
    166 Nb1fe2762e82841158b6742f56e9965dd schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    167 schema:name Animals
    168 rdf:type schema:DefinedTerm
    169 Nb6232b53d1ec4b2492baf1fd4fa2d23b schema:name dimensions_id
    170 schema:value pub.1110518208
    171 rdf:type schema:PropertyValue
    172 Ncb4ad1debf5b46a09acdeb61e411bbe9 rdf:first sg:person.01270211632.48
    173 rdf:rest N9995934ad2e04e3989e12bdac42d8760
    174 Ncbc7e4e0d643489da7329c82b17066f8 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    175 schema:name Gene Expression Regulation
    176 rdf:type schema:DefinedTerm
    177 Nd0afeb520a964746b240c2e59f5a02ba rdf:first sg:person.01336664426.47
    178 rdf:rest N86e0464a9f7845a996bde7db188c384f
    179 Nd2690966e05c484aa0088f9db694981f rdf:first sg:person.0713321274.37
    180 rdf:rest Ndd8e06aad7a94ac59aa575ce667e555f
    181 Ndd8e06aad7a94ac59aa575ce667e555f rdf:first sg:person.01122465213.75
    182 rdf:rest N3334b308028e466c8bb3419279622cb1
    183 Nf54f1a44a08747d68dfd4818af3b47bd schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    184 schema:name Mice
    185 rdf:type schema:DefinedTerm
    186 Nfe2bd6211a1d44bea2df16a49567bfcf schema:name Springer Nature - SN SciGraph project
    187 rdf:type schema:Organization
    188 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    189 schema:name Biological Sciences
    190 rdf:type schema:DefinedTerm
    191 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
    192 schema:name Genetics
    193 rdf:type schema:DefinedTerm
    194 sg:grant.2682595 http://pending.schema.org/fundedItem sg:pub.10.1186/s13059-018-1598-7
    195 rdf:type schema:MonetaryGrant
    196 sg:grant.4898521 http://pending.schema.org/fundedItem sg:pub.10.1186/s13059-018-1598-7
    197 rdf:type schema:MonetaryGrant
    198 sg:grant.6664426 http://pending.schema.org/fundedItem sg:pub.10.1186/s13059-018-1598-7
    199 rdf:type schema:MonetaryGrant
    200 sg:journal.1023439 schema:issn 1465-6906
    201 1474-760X
    202 schema:name Genome Biology
    203 rdf:type schema:Periodical
    204 sg:person.01045755265.19 schema:affiliation https://www.grid.ac/institutes/grid.137628.9
    205 schema:familyName Skok
    206 schema:givenName Jane A.
    207 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01045755265.19
    208 rdf:type schema:Person
    209 sg:person.01122465213.75 schema:affiliation https://www.grid.ac/institutes/grid.482020.c
    210 schema:familyName Bonneau
    211 schema:givenName Richard
    212 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01122465213.75
    213 rdf:type schema:Person
    214 sg:person.01167602433.97 schema:affiliation https://www.grid.ac/institutes/grid.137628.9
    215 schema:familyName Luo
    216 schema:givenName Vincent M.
    217 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01167602433.97
    218 rdf:type schema:Person
    219 sg:person.01201773404.00 schema:affiliation https://www.grid.ac/institutes/grid.239573.9
    220 schema:familyName Miraldi
    221 schema:givenName Emily R.
    222 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01201773404.00
    223 rdf:type schema:Person
    224 sg:person.01270211632.48 schema:affiliation https://www.grid.ac/institutes/grid.137628.9
    225 schema:familyName Rocha
    226 schema:givenName Pedro P.
    227 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01270211632.48
    228 rdf:type schema:Person
    229 sg:person.01324614605.41 schema:affiliation https://www.grid.ac/institutes/grid.1052.6
    230 schema:familyName Raviram
    231 schema:givenName Ramya
    232 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01324614605.41
    233 rdf:type schema:Person
    234 sg:person.01336664426.47 schema:affiliation https://www.grid.ac/institutes/grid.137628.9
    235 schema:familyName Swanzey
    236 schema:givenName Emily
    237 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01336664426.47
    238 rdf:type schema:Person
    239 sg:person.0713321274.37 schema:affiliation https://www.grid.ac/institutes/grid.5386.8
    240 schema:familyName Feschotte
    241 schema:givenName Cédric
    242 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0713321274.37
    243 rdf:type schema:Person
    244 sg:person.0766027552.14 schema:affiliation https://www.grid.ac/institutes/grid.266190.a
    245 schema:familyName Chuong
    246 schema:givenName Edward B.
    247 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0766027552.14
    248 rdf:type schema:Person
    249 sg:pub.10.1007/978-1-4939-3372-3_4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005170688
    250 https://doi.org/10.1007/978-1-4939-3372-3_4
    251 rdf:type schema:CreativeWork
    252 sg:pub.10.1007/s00018-008-8497-0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028172451
    253 https://doi.org/10.1007/s00018-008-8497-0
    254 rdf:type schema:CreativeWork
    255 sg:pub.10.1038/nature10413 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041325874
    256 https://doi.org/10.1038/nature10413
    257 rdf:type schema:CreativeWork
    258 sg:pub.10.1038/nature11082 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040271530
    259 https://doi.org/10.1038/nature11082
    260 rdf:type schema:CreativeWork
    261 sg:pub.10.1038/nature11244 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008081317
    262 https://doi.org/10.1038/nature11244
    263 rdf:type schema:CreativeWork
    264 sg:pub.10.1038/nature11247 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029065430
    265 https://doi.org/10.1038/nature11247
    266 rdf:type schema:CreativeWork
    267 sg:pub.10.1038/nature12644 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019700652
    268 https://doi.org/10.1038/nature12644
    269 rdf:type schema:CreativeWork
    270 sg:pub.10.1038/nature13417 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028426876
    271 https://doi.org/10.1038/nature13417
    272 rdf:type schema:CreativeWork
    273 sg:pub.10.1038/nature14308 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046099015
    274 https://doi.org/10.1038/nature14308
    275 rdf:type schema:CreativeWork
    276 sg:pub.10.1038/ncb3573 schema:sameAs https://app.dimensions.ai/details/publication/pub.1090880206
    277 https://doi.org/10.1038/ncb3573
    278 rdf:type schema:CreativeWork
    279 sg:pub.10.1038/ncomms10286 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003990800
    280 https://doi.org/10.1038/ncomms10286
    281 rdf:type schema:CreativeWork
    282 sg:pub.10.1038/ncomms14550 schema:sameAs https://app.dimensions.ai/details/publication/pub.1084128814
    283 https://doi.org/10.1038/ncomms14550
    284 rdf:type schema:CreativeWork
    285 sg:pub.10.1038/ng.3286 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026830910
    286 https://doi.org/10.1038/ng.3286
    287 rdf:type schema:CreativeWork
    288 sg:pub.10.1038/ng.3935 schema:sameAs https://app.dimensions.ai/details/publication/pub.1091217074
    289 https://doi.org/10.1038/ng.3935
    290 rdf:type schema:CreativeWork
    291 sg:pub.10.1038/ng.3945 schema:sameAs https://app.dimensions.ai/details/publication/pub.1091371366
    292 https://doi.org/10.1038/ng.3945
    293 rdf:type schema:CreativeWork
    294 sg:pub.10.1038/ng0598-19 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033511786
    295 https://doi.org/10.1038/ng0598-19
    296 rdf:type schema:CreativeWork
    297 sg:pub.10.1038/nmeth.1923 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006541515
    298 https://doi.org/10.1038/nmeth.1923
    299 rdf:type schema:CreativeWork
    300 sg:pub.10.1038/nmeth.2173 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005179498
    301 https://doi.org/10.1038/nmeth.2173
    302 rdf:type schema:CreativeWork
    303 sg:pub.10.1038/nmeth.3664 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006820435
    304 https://doi.org/10.1038/nmeth.3664
    305 rdf:type schema:CreativeWork
    306 sg:pub.10.1038/nrc.2017.35 schema:sameAs https://app.dimensions.ai/details/publication/pub.1085935508
    307 https://doi.org/10.1038/nrc.2017.35
    308 rdf:type schema:CreativeWork
    309 sg:pub.10.1038/nrg.2016.112 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029513141
    310 https://doi.org/10.1038/nrg.2016.112
    311 rdf:type schema:CreativeWork
    312 sg:pub.10.1038/nrg.2016.139 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034466564
    313 https://doi.org/10.1038/nrg.2016.139
    314 rdf:type schema:CreativeWork
    315 sg:pub.10.1038/nrg3117 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044335233
    316 https://doi.org/10.1038/nrg3117
    317 rdf:type schema:CreativeWork
    318 sg:pub.10.1038/nrm.2016.104 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022853135
    319 https://doi.org/10.1038/nrm.2016.104
    320 rdf:type schema:CreativeWork
    321 sg:pub.10.1038/nrm.2016.138 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020179702
    322 https://doi.org/10.1038/nrm.2016.138
    323 rdf:type schema:CreativeWork
    324 sg:pub.10.1186/1759-8753-3-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016399170
    325 https://doi.org/10.1186/1759-8753-3-9
    326 rdf:type schema:CreativeWork
    327 sg:pub.10.1186/gb-2012-13-6-r45 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053645706
    328 https://doi.org/10.1186/gb-2012-13-6-r45
    329 rdf:type schema:CreativeWork
    330 sg:pub.10.1186/s12977-015-0173-5 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007254095
    331 https://doi.org/10.1186/s12977-015-0173-5
    332 rdf:type schema:CreativeWork
    333 sg:pub.10.1186/s13059-016-0992-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001813860
    334 https://doi.org/10.1186/s13059-016-0992-2
    335 rdf:type schema:CreativeWork
    336 sg:pub.10.1186/s13100-015-0041-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001871370
    337 https://doi.org/10.1186/s13100-015-0041-9
    338 rdf:type schema:CreativeWork
    339 sg:pub.10.1186/s13100-016-0066-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031964740
    340 https://doi.org/10.1186/s13100-016-0066-8
    341 rdf:type schema:CreativeWork
    342 sg:pub.10.1186/s13100-016-0080-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1035783267
    343 https://doi.org/10.1186/s13100-016-0080-x
    344 rdf:type schema:CreativeWork
    345 https://app.dimensions.ai/details/publication/pub.1079412165 schema:CreativeWork
    346 https://doi.org/10.1002/bies.201300040 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026314952
    347 rdf:type schema:CreativeWork
    348 https://doi.org/10.1002/bies.201700155 schema:sameAs https://app.dimensions.ai/details/publication/pub.1095860783
    349 rdf:type schema:CreativeWork
    350 https://doi.org/10.1016/b978-0-12-391938-0.00004-5 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028902320
    351 rdf:type schema:CreativeWork
    352 https://doi.org/10.1016/j.ceb.2014.04.004 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015713715
    353 rdf:type schema:CreativeWork
    354 https://doi.org/10.1016/j.cell.2011.11.058 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007206139
    355 rdf:type schema:CreativeWork
    356 https://doi.org/10.1016/j.cell.2014.11.021 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047951603
    357 rdf:type schema:CreativeWork
    358 https://doi.org/10.1016/j.cell.2015.03.026 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000014161
    359 rdf:type schema:CreativeWork
    360 https://doi.org/10.1016/j.cell.2016.02.007 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007042188
    361 rdf:type schema:CreativeWork
    362 https://doi.org/10.1016/j.cell.2016.09.037 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035198067
    363 rdf:type schema:CreativeWork
    364 https://doi.org/10.1016/j.cell.2016.10.024 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050913498
    365 rdf:type schema:CreativeWork
    366 https://doi.org/10.1016/j.cell.2017.09.043 schema:sameAs https://app.dimensions.ai/details/publication/pub.1092293106
    367 rdf:type schema:CreativeWork
    368 https://doi.org/10.1016/j.celrep.2016.05.073 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007711681
    369 rdf:type schema:CreativeWork
    370 https://doi.org/10.1016/j.chom.2017.09.007 schema:sameAs https://app.dimensions.ai/details/publication/pub.1092185178
    371 rdf:type schema:CreativeWork
    372 https://doi.org/10.1016/j.devcel.2016.10.015 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022845668
    373 rdf:type schema:CreativeWork
    374 https://doi.org/10.1016/j.gde.2016.01.001 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009992306
    375 rdf:type schema:CreativeWork
    376 https://doi.org/10.1016/j.gde.2016.01.002 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037393696
    377 rdf:type schema:CreativeWork
    378 https://doi.org/10.1016/j.molcel.2012.06.036 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003248902
    379 rdf:type schema:CreativeWork
    380 https://doi.org/10.1016/j.molcel.2014.05.029 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019663782
    381 rdf:type schema:CreativeWork
    382 https://doi.org/10.1016/j.molcel.2017.04.010 schema:sameAs https://app.dimensions.ai/details/publication/pub.1085155625
    383 rdf:type schema:CreativeWork
    384 https://doi.org/10.1016/j.molcel.2017.08.006 schema:sameAs https://app.dimensions.ai/details/publication/pub.1091505048
    385 rdf:type schema:CreativeWork
    386 https://doi.org/10.1016/j.stem.2015.01.005 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036578494
    387 rdf:type schema:CreativeWork
    388 https://doi.org/10.1016/j.stem.2016.08.004 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030363937
    389 rdf:type schema:CreativeWork
    390 https://doi.org/10.1016/j.tig.2016.01.003 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021158236
    391 rdf:type schema:CreativeWork
    392 https://doi.org/10.1016/j.ymeth.2017.04.004 schema:sameAs https://app.dimensions.ai/details/publication/pub.1084902556
    393 rdf:type schema:CreativeWork
    394 https://doi.org/10.1073/pnas.0611223104 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028702517
    395 rdf:type schema:CreativeWork
    396 https://doi.org/10.1073/pnas.1422187112 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035485185
    397 rdf:type schema:CreativeWork
    398 https://doi.org/10.1083/jcb.200305013 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053392919
    399 rdf:type schema:CreativeWork
    400 https://doi.org/10.1093/molbev/msx219 schema:sameAs https://app.dimensions.ai/details/publication/pub.1091132065
    401 rdf:type schema:CreativeWork
    402 https://doi.org/10.1093/nar/gkv1292 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013890795
    403 rdf:type schema:CreativeWork
    404 https://doi.org/10.1101/gad.281964.116 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014991788
    405 rdf:type schema:CreativeWork
    406 https://doi.org/10.1101/gr.080663.108 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036971575
    407 rdf:type schema:CreativeWork
    408 https://doi.org/10.1101/gr.168872.113 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027255605
    409 rdf:type schema:CreativeWork
    410 https://doi.org/10.1101/gr.218149.116 schema:sameAs https://app.dimensions.ai/details/publication/pub.1091435105
    411 rdf:type schema:CreativeWork
    412 https://doi.org/10.1101/sqb.1951.016.01.004 schema:sameAs https://app.dimensions.ai/details/publication/pub.1060403039
    413 rdf:type schema:CreativeWork
    414 https://doi.org/10.1101/sqb.1956.021.01.017 schema:sameAs https://app.dimensions.ai/details/publication/pub.1060403222
    415 rdf:type schema:CreativeWork
    416 https://doi.org/10.1126/science.1181369 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007401642
    417 rdf:type schema:CreativeWork
    418 https://doi.org/10.1126/science.1260419 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048221082
    419 rdf:type schema:CreativeWork
    420 https://doi.org/10.1126/science.1262088 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005794148
    421 rdf:type schema:CreativeWork
    422 https://doi.org/10.1126/science.aad5497 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009168436
    423 rdf:type schema:CreativeWork
    424 https://doi.org/10.1128/mmbr.00006-15 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005334022
    425 rdf:type schema:CreativeWork
    426 https://doi.org/10.1146/annurev-cellbio-100814-125514 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047796989
    427 rdf:type schema:CreativeWork
    428 https://doi.org/10.1146/annurev-genet-110711-155616 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011581093
    429 rdf:type schema:CreativeWork
    430 https://doi.org/10.1146/annurev-genet-110711-155621 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005304003
    431 rdf:type schema:CreativeWork
    432 https://doi.org/10.1158/0008-5472.can-15-3502 schema:sameAs https://app.dimensions.ai/details/publication/pub.1063216115
    433 rdf:type schema:CreativeWork
    434 https://doi.org/10.12688/f1000research.7334.1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018290070
    435 rdf:type schema:CreativeWork
    436 https://doi.org/10.1371/journal.pcbi.1004780 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013294334
    437 rdf:type schema:CreativeWork
    438 https://doi.org/10.1371/journal.pgen.1000007 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007821853
    439 rdf:type schema:CreativeWork
    440 https://doi.org/10.1371/journal.pgen.1003504 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008980180
    441 rdf:type schema:CreativeWork
    442 https://doi.org/10.15252/embr.201642198 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030041082
    443 rdf:type schema:CreativeWork
    444 https://doi.org/10.15252/embr.201642743 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026979293
    445 rdf:type schema:CreativeWork
    446 https://doi.org/10.2217/epi-2017-0157 schema:sameAs https://app.dimensions.ai/details/publication/pub.1101782717
    447 rdf:type schema:CreativeWork
    448 https://doi.org/10.2217/epi.15.25 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003650579
    449 rdf:type schema:CreativeWork
    450 https://doi.org/10.7554/elife.10565 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034880122
    451 rdf:type schema:CreativeWork
    452 https://doi.org/10.7554/elife.13926 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036550736
    453 rdf:type schema:CreativeWork
    454 https://doi.org/10.7554/elife.21926 schema:sameAs https://app.dimensions.ai/details/publication/pub.1084485295
    455 rdf:type schema:CreativeWork
    456 https://www.grid.ac/institutes/grid.1052.6 schema:alternateName Ludwig Cancer Research
    457 schema:name Department of Biology, New York University, 10003, New York, NY, USA
    458 Department of Pathology, New York University School of Medicine, 10016, New York, NY, USA
    459 Ludwig Institute for Cancer Research, La Jolla, CA, USA
    460 rdf:type schema:Organization
    461 https://www.grid.ac/institutes/grid.137628.9 schema:alternateName New York University
    462 schema:name Department of Biology, New York University, 10003, New York, NY, USA
    463 Department of Developmental Genetics, New York University School of Medicine, 10016, New York, NY, USA
    464 Department of Pathology, New York University School of Medicine, 10016, New York, NY, USA
    465 Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, 20892, Bethesda, MD, USA
    466 rdf:type schema:Organization
    467 https://www.grid.ac/institutes/grid.239573.9 schema:alternateName Cincinnati Children's Hospital Medical Center
    468 schema:name Department of Biology, New York University, 10003, New York, NY, USA
    469 Department of Computer Science, Courant Institute of Mathematical Sciences, 10003, New York, NY, USA
    470 Divisions of Immunobiology and Biomedical Informatics, Cincinnati Children’s Hospital, 45229, Cincinnati, OH, USA
    471 Simons Center for Data Analysis, 10010, New York, NY, USA
    472 rdf:type schema:Organization
    473 https://www.grid.ac/institutes/grid.266190.a schema:alternateName University of Colorado Boulder
    474 schema:name BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, 80309, Boulder, CO, USA
    475 rdf:type schema:Organization
    476 https://www.grid.ac/institutes/grid.482020.c schema:alternateName Courant Institute of Mathematical Sciences
    477 schema:name Department of Biology, New York University, 10003, New York, NY, USA
    478 Department of Computer Science, Courant Institute of Mathematical Sciences, 10003, New York, NY, USA
    479 Simons Center for Data Analysis, 10010, New York, NY, USA
    480 rdf:type schema:Organization
    481 https://www.grid.ac/institutes/grid.5386.8 schema:alternateName Cornell University
    482 schema:name Department of Molecular Biology and Genetics, Cornell University, 14850, Ithaca, NY, USA
    483 rdf:type schema:Organization
     




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


    ...