Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2004-12

AUTHORS

Albin Sandelin, Peter Bailey, Sara Bruce, Pär G Engström, Joanna M Klos, Wyeth W Wasserman, Johan Ericson, Boris Lenhard

ABSTRACT

BACKGROUND: Evolutionarily conserved sequences within or adjoining orthologous genes often serve as critical cis-regulatory regions. Recent studies have identified long, non-coding genomic regions that are perfectly conserved between human and mouse, termed ultra-conserved regions (UCRs). Here, we focus on UCRs that cluster around genes involved in early vertebrate development; genes conserved over 450 million years of vertebrate evolution. RESULTS: Based on a high resolution detection procedure, our UCR set enables novel insights into vertebrate genome organization and regulation of developmentally important genes. We find that the genomic positions of deeply conserved UCRs are strongly associated with the locations of genes encoding key regulators of development, with particularly strong positional correlation to transcription factor-encoding genes. Of particular importance is the observation that most UCRs are clustered into arrays that span hundreds of kilobases around their presumptive target genes. Such a hallmark signature is present around several uncharacterized human genes predicted to encode developmentally important DNA-binding proteins. CONCLUSION: The genomic organization of UCRs, combined with previous findings, suggests that UCRs act as essential long-range modulators of gene expression. The exceptional sequence conservation and clustered structure suggests that UCR-mediated molecular events involve greater complexity than traditional DNA binding by transcription factors. The high-resolution UCR collection presented here provides a wealth of target sequences for future experimental studies to determine the nature of the biochemical mechanisms involved in the preservation of arrays of nearly identical non-coding sequences over the course of vertebrate evolution. More... »

PAGES

99

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2164-5-99

DOI

http://dx.doi.org/10.1186/1471-2164-5-99

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1011003957

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/15613238


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": "Cluster Analysis", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Conserved Sequence", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA-Binding Proteins", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Evolution, Molecular", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Gene Expression Regulation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Gene Expression Regulation, Developmental", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genes, Developmental", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genome", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Humans", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Molecular Sequence Data", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Multigene Family", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Oligonucleotide Array Sequence Analysis", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Protein Binding", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Vertebrates", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Karolinska Institute", 
          "id": "https://www.grid.ac/institutes/grid.4714.6", 
          "name": [
            "Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Sandelin", 
        "givenName": "Albin", 
        "id": "sg:person.01266452163.72", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01266452163.72"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Karolinska Institute", 
          "id": "https://www.grid.ac/institutes/grid.4714.6", 
          "name": [
            "Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Bailey", 
        "givenName": "Peter", 
        "id": "sg:person.016066163407.19", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016066163407.19"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Karolinska Institute", 
          "id": "https://www.grid.ac/institutes/grid.4714.6", 
          "name": [
            "Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden", 
            "Department of Biosciences at Novum, Karolinska Institutet, Stockholm, Sweden"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Bruce", 
        "givenName": "Sara", 
        "id": "sg:person.01243701452.81", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01243701452.81"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Karolinska Institute", 
          "id": "https://www.grid.ac/institutes/grid.4714.6", 
          "name": [
            "Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Engstr\u00f6m", 
        "givenName": "P\u00e4r G", 
        "id": "sg:person.01232124755.17", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01232124755.17"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Karolinska Institute", 
          "id": "https://www.grid.ac/institutes/grid.4714.6", 
          "name": [
            "Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Klos", 
        "givenName": "Joanna M", 
        "id": "sg:person.01360130052.84", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01360130052.84"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of British Columbia", 
          "id": "https://www.grid.ac/institutes/grid.17091.3e", 
          "name": [
            "Centre for Molecular Medicine, Department of Medical Genetics, University of British Columbia, Vancouver, Canada"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Wasserman", 
        "givenName": "Wyeth W", 
        "id": "sg:person.01164162122.26", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01164162122.26"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Karolinska Institute", 
          "id": "https://www.grid.ac/institutes/grid.4714.6", 
          "name": [
            "Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Ericson", 
        "givenName": "Johan", 
        "id": "sg:person.01067613356.30", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01067613356.30"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Karolinska Institute", 
          "id": "https://www.grid.ac/institutes/grid.4714.6", 
          "name": [
            "Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Lenhard", 
        "givenName": "Boris", 
        "id": "sg:person.01064443570.02", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01064443570.02"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1101/gr.668403", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000868941"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkh038", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004852830"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.229202", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006260064"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrg1043", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009331603", 
          "https://doi.org/10.1038/nrg1043"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrg1043", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009331603", 
          "https://doi.org/10.1038/nrg1043"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0092-8674(03)00310-6", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011398902"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.403602", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1012195556"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkg129", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1012203647"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.112212199", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016844565"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2164-5-75", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1020696069", 
          "https://doi.org/10.1186/1471-2164-5-75"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1098119", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022514256"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1006/jmbi.1997.0951", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028174721"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1006/geno.2001.6648", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028638606"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1475-4924-2-13", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1029375403", 
          "https://doi.org/10.1186/1475-4924-2-13"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1088328", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030171389"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.700503", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031202093"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1023/a:1022682505914", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031786484", 
          "https://doi.org/10.1023/a:1022682505914"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0959-4388(00)00172-0", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1032644332"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.716103", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1035294729"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkg046", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1036764063"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0959-437x(02)00317-9", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1041641459"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/25.17.3389", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047265454"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0959-4388(99)00049-5", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049055853"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0945-053x(00)00094-9", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049322817"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrg1350", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049911084", 
          "https://doi.org/10.1038/nrg1350"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrg1350", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049911084", 
          "https://doi.org/10.1038/nrg1350"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1145/6497.214326", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051743138"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2004-12", 
    "datePublishedReg": "2004-12-01", 
    "description": "BACKGROUND: Evolutionarily conserved sequences within or adjoining orthologous genes often serve as critical cis-regulatory regions. Recent studies have identified long, non-coding genomic regions that are perfectly conserved between human and mouse, termed ultra-conserved regions (UCRs). Here, we focus on UCRs that cluster around genes involved in early vertebrate development; genes conserved over 450 million years of vertebrate evolution.\nRESULTS: Based on a high resolution detection procedure, our UCR set enables novel insights into vertebrate genome organization and regulation of developmentally important genes. We find that the genomic positions of deeply conserved UCRs are strongly associated with the locations of genes encoding key regulators of development, with particularly strong positional correlation to transcription factor-encoding genes. Of particular importance is the observation that most UCRs are clustered into arrays that span hundreds of kilobases around their presumptive target genes. Such a hallmark signature is present around several uncharacterized human genes predicted to encode developmentally important DNA-binding proteins.\nCONCLUSION: The genomic organization of UCRs, combined with previous findings, suggests that UCRs act as essential long-range modulators of gene expression. The exceptional sequence conservation and clustered structure suggests that UCR-mediated molecular events involve greater complexity than traditional DNA binding by transcription factors. The high-resolution UCR collection presented here provides a wealth of target sequences for future experimental studies to determine the nature of the biochemical mechanisms involved in the preservation of arrays of nearly identical non-coding sequences over the course of vertebrate evolution.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1186/1471-2164-5-99", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.3754999", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1023790", 
        "issn": [
          "1471-2164"
        ], 
        "name": "BMC Genomics", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "5"
      }
    ], 
    "name": "Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes", 
    "pagination": "99", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "346d65521943d4f645f1d44a08dc3369c1b3b9c93f67e557c329274edb13fcac"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "15613238"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "100965258"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/1471-2164-5-99"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1011003957"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/1471-2164-5-99", 
      "https://app.dimensions.ai/details/publication/pub.1011003957"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-11T01:58", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000001_0000000264/records_8700_00000503.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://link.springer.com/10.1186%2F1471-2164-5-99"
  }
]
 

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.10.1186/1471-2164-5-99'

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

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-5-99'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-5-99'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-5-99'


 

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

268 TRIPLES      21 PREDICATES      70 URIs      37 LITERALS      25 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/1471-2164-5-99 schema:about N0c93954453cc4e81b513be9a7b42054d
2 N11b95b05f7864e089e321eb3bbbb5648
3 N23dbb079348b458e806da8808b50f11f
4 N4ac38a4ecc7a4a89b968a35d8d18201a
5 N654f91b2044f4ad895d67f494d539ac2
6 N700e46b4256b4739866d12153fd0c43a
7 N823d89d450344a029f67c0853c692447
8 Nabef2541094043578e2c701de522e420
9 Nadc1da1293104d3f930268840ed8221e
10 Nb29fb86db17641d4afa2820e5a864cd9
11 Nb7272ae83d0049abb6bf7ebaa1a57119
12 Nc347dfb249ca4c6eae1ac38c0ea0b004
13 Nd99a1525844349be97cb1d74c59dd7f1
14 Neb376e09a83c48d8b35208e0c7ae5854
15 Nf27e48bab06449939fb6d27761d6683e
16 Nf42251ea1a4b4bf9b7db2528e5b0b527
17 anzsrc-for:06
18 anzsrc-for:0604
19 schema:author N6406b8fd8d154d04b16a1b42dca9e3a3
20 schema:citation sg:pub.10.1023/a:1022682505914
21 sg:pub.10.1038/nrg1043
22 sg:pub.10.1038/nrg1350
23 sg:pub.10.1186/1471-2164-5-75
24 sg:pub.10.1186/1475-4924-2-13
25 https://doi.org/10.1006/geno.2001.6648
26 https://doi.org/10.1006/jmbi.1997.0951
27 https://doi.org/10.1016/s0092-8674(03)00310-6
28 https://doi.org/10.1016/s0945-053x(00)00094-9
29 https://doi.org/10.1016/s0959-437x(02)00317-9
30 https://doi.org/10.1016/s0959-4388(00)00172-0
31 https://doi.org/10.1016/s0959-4388(99)00049-5
32 https://doi.org/10.1073/pnas.112212199
33 https://doi.org/10.1093/nar/25.17.3389
34 https://doi.org/10.1093/nar/gkg046
35 https://doi.org/10.1093/nar/gkg129
36 https://doi.org/10.1093/nar/gkh038
37 https://doi.org/10.1101/gr.229202
38 https://doi.org/10.1101/gr.403602
39 https://doi.org/10.1101/gr.668403
40 https://doi.org/10.1101/gr.700503
41 https://doi.org/10.1101/gr.716103
42 https://doi.org/10.1126/science.1088328
43 https://doi.org/10.1126/science.1098119
44 https://doi.org/10.1145/6497.214326
45 schema:datePublished 2004-12
46 schema:datePublishedReg 2004-12-01
47 schema:description BACKGROUND: Evolutionarily conserved sequences within or adjoining orthologous genes often serve as critical cis-regulatory regions. Recent studies have identified long, non-coding genomic regions that are perfectly conserved between human and mouse, termed ultra-conserved regions (UCRs). Here, we focus on UCRs that cluster around genes involved in early vertebrate development; genes conserved over 450 million years of vertebrate evolution. RESULTS: Based on a high resolution detection procedure, our UCR set enables novel insights into vertebrate genome organization and regulation of developmentally important genes. We find that the genomic positions of deeply conserved UCRs are strongly associated with the locations of genes encoding key regulators of development, with particularly strong positional correlation to transcription factor-encoding genes. Of particular importance is the observation that most UCRs are clustered into arrays that span hundreds of kilobases around their presumptive target genes. Such a hallmark signature is present around several uncharacterized human genes predicted to encode developmentally important DNA-binding proteins. CONCLUSION: The genomic organization of UCRs, combined with previous findings, suggests that UCRs act as essential long-range modulators of gene expression. The exceptional sequence conservation and clustered structure suggests that UCR-mediated molecular events involve greater complexity than traditional DNA binding by transcription factors. The high-resolution UCR collection presented here provides a wealth of target sequences for future experimental studies to determine the nature of the biochemical mechanisms involved in the preservation of arrays of nearly identical non-coding sequences over the course of vertebrate evolution.
48 schema:genre research_article
49 schema:inLanguage en
50 schema:isAccessibleForFree true
51 schema:isPartOf N2596995e8f874b3abfd8b0a05bcc09c5
52 Ne1f64e8e4e1e4063a81f3e3e81d04a04
53 sg:journal.1023790
54 schema:name Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes
55 schema:pagination 99
56 schema:productId N8c6e79822b47416bbdf8cd749d90565d
57 Nc8c535ad7d2448e9a6a737008dd7477f
58 Ne85e7373d29a43128ea9f6acbfbbe8e9
59 Nf8305876dc0f4071b148eaee45491c17
60 Nff6ccc1e795b404aa6e961d9e551373b
61 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011003957
62 https://doi.org/10.1186/1471-2164-5-99
63 schema:sdDatePublished 2019-04-11T01:58
64 schema:sdLicense https://scigraph.springernature.com/explorer/license/
65 schema:sdPublisher N3ab8970e2c3246ca9c9904df9b466066
66 schema:url http://link.springer.com/10.1186%2F1471-2164-5-99
67 sgo:license sg:explorer/license/
68 sgo:sdDataset articles
69 rdf:type schema:ScholarlyArticle
70 N0a796defad0441748c48d27c9026b764 rdf:first sg:person.01360130052.84
71 rdf:rest N5ec5e614065f449088ec986484c80eea
72 N0c93954453cc4e81b513be9a7b42054d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
73 schema:name Evolution, Molecular
74 rdf:type schema:DefinedTerm
75 N11b95b05f7864e089e321eb3bbbb5648 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
76 schema:name Oligonucleotide Array Sequence Analysis
77 rdf:type schema:DefinedTerm
78 N23dbb079348b458e806da8808b50f11f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
79 schema:name Genes, Developmental
80 rdf:type schema:DefinedTerm
81 N2596995e8f874b3abfd8b0a05bcc09c5 schema:volumeNumber 5
82 rdf:type schema:PublicationVolume
83 N3ab8970e2c3246ca9c9904df9b466066 schema:name Springer Nature - SN SciGraph project
84 rdf:type schema:Organization
85 N4ac38a4ecc7a4a89b968a35d8d18201a schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
86 schema:name Humans
87 rdf:type schema:DefinedTerm
88 N5ec5e614065f449088ec986484c80eea rdf:first sg:person.01164162122.26
89 rdf:rest Nc9083b76dfe746808e8c22347b3a421c
90 N6351307d1e4e43c8b27d6b293bcc95e2 rdf:first sg:person.01232124755.17
91 rdf:rest N0a796defad0441748c48d27c9026b764
92 N6406b8fd8d154d04b16a1b42dca9e3a3 rdf:first sg:person.01266452163.72
93 rdf:rest N8d7fbb8ad5b34ba282f832bc4d0f3b72
94 N654f91b2044f4ad895d67f494d539ac2 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
95 schema:name Genome
96 rdf:type schema:DefinedTerm
97 N700e46b4256b4739866d12153fd0c43a schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
98 schema:name DNA-Binding Proteins
99 rdf:type schema:DefinedTerm
100 N823d89d450344a029f67c0853c692447 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
101 schema:name Molecular Sequence Data
102 rdf:type schema:DefinedTerm
103 N8c6e79822b47416bbdf8cd749d90565d schema:name doi
104 schema:value 10.1186/1471-2164-5-99
105 rdf:type schema:PropertyValue
106 N8d7fbb8ad5b34ba282f832bc4d0f3b72 rdf:first sg:person.016066163407.19
107 rdf:rest N951bb60b63fa437e82ec309dab92f24a
108 N951bb60b63fa437e82ec309dab92f24a rdf:first sg:person.01243701452.81
109 rdf:rest N6351307d1e4e43c8b27d6b293bcc95e2
110 Nab13e5acc45b43f1b6238a0cc8a5ce4a rdf:first sg:person.01064443570.02
111 rdf:rest rdf:nil
112 Nabef2541094043578e2c701de522e420 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
113 schema:name Cluster Analysis
114 rdf:type schema:DefinedTerm
115 Nadc1da1293104d3f930268840ed8221e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
116 schema:name Conserved Sequence
117 rdf:type schema:DefinedTerm
118 Nb29fb86db17641d4afa2820e5a864cd9 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
119 schema:name DNA
120 rdf:type schema:DefinedTerm
121 Nb7272ae83d0049abb6bf7ebaa1a57119 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
122 schema:name Gene Expression Regulation
123 rdf:type schema:DefinedTerm
124 Nc347dfb249ca4c6eae1ac38c0ea0b004 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
125 schema:name Vertebrates
126 rdf:type schema:DefinedTerm
127 Nc8c535ad7d2448e9a6a737008dd7477f schema:name pubmed_id
128 schema:value 15613238
129 rdf:type schema:PropertyValue
130 Nc9083b76dfe746808e8c22347b3a421c rdf:first sg:person.01067613356.30
131 rdf:rest Nab13e5acc45b43f1b6238a0cc8a5ce4a
132 Nd99a1525844349be97cb1d74c59dd7f1 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
133 schema:name Gene Expression Regulation, Developmental
134 rdf:type schema:DefinedTerm
135 Ne1f64e8e4e1e4063a81f3e3e81d04a04 schema:issueNumber 1
136 rdf:type schema:PublicationIssue
137 Ne85e7373d29a43128ea9f6acbfbbe8e9 schema:name nlm_unique_id
138 schema:value 100965258
139 rdf:type schema:PropertyValue
140 Neb376e09a83c48d8b35208e0c7ae5854 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
141 schema:name Animals
142 rdf:type schema:DefinedTerm
143 Nf27e48bab06449939fb6d27761d6683e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
144 schema:name Protein Binding
145 rdf:type schema:DefinedTerm
146 Nf42251ea1a4b4bf9b7db2528e5b0b527 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
147 schema:name Multigene Family
148 rdf:type schema:DefinedTerm
149 Nf8305876dc0f4071b148eaee45491c17 schema:name readcube_id
150 schema:value 346d65521943d4f645f1d44a08dc3369c1b3b9c93f67e557c329274edb13fcac
151 rdf:type schema:PropertyValue
152 Nff6ccc1e795b404aa6e961d9e551373b schema:name dimensions_id
153 schema:value pub.1011003957
154 rdf:type schema:PropertyValue
155 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
156 schema:name Biological Sciences
157 rdf:type schema:DefinedTerm
158 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
159 schema:name Genetics
160 rdf:type schema:DefinedTerm
161 sg:grant.3754999 http://pending.schema.org/fundedItem sg:pub.10.1186/1471-2164-5-99
162 rdf:type schema:MonetaryGrant
163 sg:journal.1023790 schema:issn 1471-2164
164 schema:name BMC Genomics
165 rdf:type schema:Periodical
166 sg:person.01064443570.02 schema:affiliation https://www.grid.ac/institutes/grid.4714.6
167 schema:familyName Lenhard
168 schema:givenName Boris
169 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01064443570.02
170 rdf:type schema:Person
171 sg:person.01067613356.30 schema:affiliation https://www.grid.ac/institutes/grid.4714.6
172 schema:familyName Ericson
173 schema:givenName Johan
174 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01067613356.30
175 rdf:type schema:Person
176 sg:person.01164162122.26 schema:affiliation https://www.grid.ac/institutes/grid.17091.3e
177 schema:familyName Wasserman
178 schema:givenName Wyeth W
179 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01164162122.26
180 rdf:type schema:Person
181 sg:person.01232124755.17 schema:affiliation https://www.grid.ac/institutes/grid.4714.6
182 schema:familyName Engström
183 schema:givenName Pär G
184 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01232124755.17
185 rdf:type schema:Person
186 sg:person.01243701452.81 schema:affiliation https://www.grid.ac/institutes/grid.4714.6
187 schema:familyName Bruce
188 schema:givenName Sara
189 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01243701452.81
190 rdf:type schema:Person
191 sg:person.01266452163.72 schema:affiliation https://www.grid.ac/institutes/grid.4714.6
192 schema:familyName Sandelin
193 schema:givenName Albin
194 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01266452163.72
195 rdf:type schema:Person
196 sg:person.01360130052.84 schema:affiliation https://www.grid.ac/institutes/grid.4714.6
197 schema:familyName Klos
198 schema:givenName Joanna M
199 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01360130052.84
200 rdf:type schema:Person
201 sg:person.016066163407.19 schema:affiliation https://www.grid.ac/institutes/grid.4714.6
202 schema:familyName Bailey
203 schema:givenName Peter
204 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016066163407.19
205 rdf:type schema:Person
206 sg:pub.10.1023/a:1022682505914 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031786484
207 https://doi.org/10.1023/a:1022682505914
208 rdf:type schema:CreativeWork
209 sg:pub.10.1038/nrg1043 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009331603
210 https://doi.org/10.1038/nrg1043
211 rdf:type schema:CreativeWork
212 sg:pub.10.1038/nrg1350 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049911084
213 https://doi.org/10.1038/nrg1350
214 rdf:type schema:CreativeWork
215 sg:pub.10.1186/1471-2164-5-75 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020696069
216 https://doi.org/10.1186/1471-2164-5-75
217 rdf:type schema:CreativeWork
218 sg:pub.10.1186/1475-4924-2-13 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029375403
219 https://doi.org/10.1186/1475-4924-2-13
220 rdf:type schema:CreativeWork
221 https://doi.org/10.1006/geno.2001.6648 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028638606
222 rdf:type schema:CreativeWork
223 https://doi.org/10.1006/jmbi.1997.0951 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028174721
224 rdf:type schema:CreativeWork
225 https://doi.org/10.1016/s0092-8674(03)00310-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011398902
226 rdf:type schema:CreativeWork
227 https://doi.org/10.1016/s0945-053x(00)00094-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049322817
228 rdf:type schema:CreativeWork
229 https://doi.org/10.1016/s0959-437x(02)00317-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041641459
230 rdf:type schema:CreativeWork
231 https://doi.org/10.1016/s0959-4388(00)00172-0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032644332
232 rdf:type schema:CreativeWork
233 https://doi.org/10.1016/s0959-4388(99)00049-5 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049055853
234 rdf:type schema:CreativeWork
235 https://doi.org/10.1073/pnas.112212199 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016844565
236 rdf:type schema:CreativeWork
237 https://doi.org/10.1093/nar/25.17.3389 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047265454
238 rdf:type schema:CreativeWork
239 https://doi.org/10.1093/nar/gkg046 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036764063
240 rdf:type schema:CreativeWork
241 https://doi.org/10.1093/nar/gkg129 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012203647
242 rdf:type schema:CreativeWork
243 https://doi.org/10.1093/nar/gkh038 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004852830
244 rdf:type schema:CreativeWork
245 https://doi.org/10.1101/gr.229202 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006260064
246 rdf:type schema:CreativeWork
247 https://doi.org/10.1101/gr.403602 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012195556
248 rdf:type schema:CreativeWork
249 https://doi.org/10.1101/gr.668403 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000868941
250 rdf:type schema:CreativeWork
251 https://doi.org/10.1101/gr.700503 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031202093
252 rdf:type schema:CreativeWork
253 https://doi.org/10.1101/gr.716103 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035294729
254 rdf:type schema:CreativeWork
255 https://doi.org/10.1126/science.1088328 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030171389
256 rdf:type schema:CreativeWork
257 https://doi.org/10.1126/science.1098119 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022514256
258 rdf:type schema:CreativeWork
259 https://doi.org/10.1145/6497.214326 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051743138
260 rdf:type schema:CreativeWork
261 https://www.grid.ac/institutes/grid.17091.3e schema:alternateName University of British Columbia
262 schema:name Centre for Molecular Medicine, Department of Medical Genetics, University of British Columbia, Vancouver, Canada
263 rdf:type schema:Organization
264 https://www.grid.ac/institutes/grid.4714.6 schema:alternateName Karolinska Institute
265 schema:name Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden
266 Department of Biosciences at Novum, Karolinska Institutet, Stockholm, Sweden
267 Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
268 rdf:type schema:Organization
 




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


...