{"id":"https://openalex.org/W2052014424","doi":"https://doi.org/10.1101/gr.163485.113","title":"Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer","display_name":"Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer","publication_year":2014,"publication_date":"2014-06-10","ids":{"openalex":"https://openalex.org/W2052014424","doi":"https://doi.org/10.1101/gr.163485.113","mag":"2052014424","pmid":"https://pubmed.ncbi.nlm.nih.gov/24916973","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/4158760"},"language":"en","primary_location":{"id":"doi:10.1101/gr.163485.113","doi":"https://doi.org/10.1101/gr.163485.113","is_oa":true,"landing_page_url":"https://doi.org/10.1101/gr.163485.113","pdf_url":"http://genome.cshlp.org/content/24/9/1421.full.pdf","source":{"id":"https://openalex.org/S43092948","display_name":"Genome Research","issn_l":"1088-9051","issn":["1088-9051","1549-5469"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-a","doyens","jufo-3","ki-jl-2","medline","norway-2","poland-200","russia-white-list-1"],"host_organization":"https://openalex.org/P4310315909","host_organization_name":"Cold Spring Harbor Laboratory Press","host_organization_lineage":["https://openalex.org/P4310315909"],"host_organization_lineage_names":["Cold Spring Harbor Laboratory Press"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genome Research","raw_type":"journal-article"},"volume":null,"type":"preprint","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"http://genome.cshlp.org/content/24/9/1421.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5012025471","display_name":"Phillippa C. Taberlay","orcid":"https://orcid.org/0000-0002-5298-8730","observed_orcids":["https://orcid.org/0000-0002-5298-8730"]},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]},{"id":"https://openalex.org/I136750679","display_name":"Garvan Institute of Medical Research","ror":"https://ror.org/01b3dvp57","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I136750679","https://openalex.org/I4210087284"]},{"id":"https://openalex.org/I31746571","display_name":"UNSW Sydney","ror":"https://ror.org/03r8z3t63","country_code":"AU","type":"education","lineage":["https://openalex.org/I31746571"]},{"id":"https://openalex.org/I4210117038","display_name":"USC Norris Comprehensive Cancer Center","ror":"https://ror.org/01nmyfr60","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2800154431","https://openalex.org/I4210117038"]}],"countries":["AU","US"],"is_corresponding":false,"raw_author_name":"Phillippa C. Taberlay","raw_affiliation_strings":["Epigenetics Research, Cancer Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia; Departments of Biochemistry and Urology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90033, USA; St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, New South Wales 2010, Australia;","1Epigenetics Research, Cancer Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia","2Departments of Biochemistry and Urology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90033, USA","3St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, New South Wales 2010, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Epigenetics Research, Cancer Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia; Departments of Biochemistry and Urology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90033, USA; St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, New South Wales 2010, Australia;","institution_ids":["https://openalex.org/I1174212","https://openalex.org/I136750679","https://openalex.org/I31746571","https://openalex.org/I4210117038"]},{"raw_affiliation_string":"1Epigenetics Research, Cancer Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia","institution_ids":["https://openalex.org/I136750679"]},{"raw_affiliation_string":"2Departments of Biochemistry and Urology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90033, USA","institution_ids":["https://openalex.org/I1174212","https://openalex.org/I4210117038"]},{"raw_affiliation_string":"3St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, New South Wales 2010, Australia","institution_ids":["https://openalex.org/I31746571"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050873859","display_name":"Aaron L. Statham","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I136750679","display_name":"Garvan Institute of Medical Research","ror":"https://ror.org/01b3dvp57","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I136750679","https://openalex.org/I4210087284"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Aaron L. Statham","raw_affiliation_strings":["Epigenetics Research, Cancer Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia;","1Epigenetics Research, Cancer Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Epigenetics Research, Cancer Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia;","institution_ids":["https://openalex.org/I136750679"]},{"raw_affiliation_string":"1Epigenetics Research, Cancer Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia","institution_ids":["https://openalex.org/I136750679"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110559476","display_name":"Theresa Kathleen Kelly","orcid":"https://orcid.org/0000-0001-8845-8777","observed_orcids":["https://orcid.org/0000-0001-8845-8777"]},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]},{"id":"https://openalex.org/I4210117038","display_name":"USC Norris Comprehensive Cancer Center","ror":"https://ror.org/01nmyfr60","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2800154431","https://openalex.org/I4210117038"]},{"id":"https://openalex.org/I4210134854","display_name":"Active Motif (United States)","ror":"https://ror.org/02sdw5w15","country_code":"US","type":"company","lineage":["https://openalex.org/I4210134854"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Theresa K. Kelly","raw_affiliation_strings":["Departments of Biochemistry and Urology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90033, USA; Active Motif, Inc., Carlsbad, California 92008, USA;","2Departments of Biochemistry and Urology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90033, USA","4Active Motif, Inc., Carlsbad, California 92008, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Biochemistry and Urology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90033, USA; Active Motif, Inc., Carlsbad, California 92008, USA;","institution_ids":["https://openalex.org/I1174212","https://openalex.org/I4210117038"]},{"raw_affiliation_string":"2Departments of Biochemistry and Urology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90033, USA","institution_ids":["https://openalex.org/I1174212","https://openalex.org/I4210117038"]},{"raw_affiliation_string":"4Active Motif, Inc., Carlsbad, California 92008, USA","institution_ids":["https://openalex.org/I4210134854"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041095680","display_name":"Susan J. Clark","orcid":"https://orcid.org/0000-0001-5925-5030","observed_orcids":["https://orcid.org/0000-0001-5925-5030"]},"institutions":[{"id":"https://openalex.org/I136750679","display_name":"Garvan Institute of Medical Research","ror":"https://ror.org/01b3dvp57","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I136750679","https://openalex.org/I4210087284"]},{"id":"https://openalex.org/I31746571","display_name":"UNSW Sydney","ror":"https://ror.org/03r8z3t63","country_code":"AU","type":"education","lineage":["https://openalex.org/I31746571"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Susan J. Clark","raw_affiliation_strings":["Epigenetics Research, Cancer Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, New South Wales 2010, Australia; p.jones@med.usc.edu s.clark@garvan.org.au","1Epigenetics Research, Cancer Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia","3St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, New South Wales 2010, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Epigenetics Research, Cancer Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, New South Wales 2010, Australia; p.jones@med.usc.edu s.clark@garvan.org.au","institution_ids":["https://openalex.org/I136750679","https://openalex.org/I31746571"]},{"raw_affiliation_string":"1Epigenetics Research, Cancer Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia","institution_ids":["https://openalex.org/I136750679"]},{"raw_affiliation_string":"3St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, New South Wales 2010, Australia","institution_ids":["https://openalex.org/I31746571"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088347458","display_name":"Peter A. Jones","orcid":"https://orcid.org/0000-0001-8309-4767","observed_orcids":["https://orcid.org/0000-0001-8309-4767"]},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]},{"id":"https://openalex.org/I1317189400","display_name":"Van Andel Institute","ror":"https://ror.org/00wm07d60","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1317189400"]},{"id":"https://openalex.org/I4210117038","display_name":"USC Norris Comprehensive Cancer Center","ror":"https://ror.org/01nmyfr60","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2800154431","https://openalex.org/I4210117038"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Peter A. Jones","raw_affiliation_strings":["Departments of Biochemistry and Urology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90033, USA; Van Andel Research Institute, Grand Rapids, Michigan 49503, USA p.jones@med.usc.edu s.clark@garvan.org.au","2Departments of Biochemistry and Urology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90033, USA","5Van Andel Research Institute, Grand Rapids, Michigan 49503, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Biochemistry and Urology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90033, USA; Van Andel Research Institute, Grand Rapids, Michigan 49503, USA p.jones@med.usc.edu s.clark@garvan.org.au","institution_ids":["https://openalex.org/I1174212","https://openalex.org/I4210117038"]},{"raw_affiliation_string":"2Departments of Biochemistry and Urology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90033, USA","institution_ids":["https://openalex.org/I1174212","https://openalex.org/I4210117038"]},{"raw_affiliation_string":"5Van Andel Research Institute, Grand Rapids, Michigan 49503, USA","institution_ids":["https://openalex.org/I1317189400"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5041095680","https://openalex.org/A5088347458"],"corresponding_institution_ids":["https://openalex.org/I1174212","https://openalex.org/I1317189400","https://openalex.org/I136750679","https://openalex.org/I31746571","https://openalex.org/I4210117038"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":183,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"24","issue":"9","first_page":"1421","last_page":"1432"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.6869999766349792,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.6869999766349792,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.3073999881744385,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12820","display_name":"Chromatin Remodeling and Cancer","score":0.0035000001080334187,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/nucleosome-depleted-regions","display_name":"nucleosome-depleted regions","score":0.9850000143051147},{"id":"https://openalex.org/keywords/nucleosome-occupancy","display_name":"nucleosome occupancy","score":0.8289999961853027},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.9419999718666077},{"id":"https://openalex.org/keywords/enhancers","display_name":"enhancers","score":0.9440000057220459},{"id":"https://openalex.org/keywords/insulation-materials","display_name":"insulators","score":0.8920000195503235},{"id":"https://openalex.org/keywords/distal-regulatory-elements","display_name":"distal regulatory elements","score":0.953000009059906},{"id":"https://openalex.org/keywords/cancer-epigenetics","display_name":"cancer epigenetics","score":0.847000002861023},{"id":"https://openalex.org/keywords/epigenetic-silencing","display_name":"epigenetic silencing","score":0.7860000133514404},{"id":"https://openalex.org/keywords/epigenetic-activation","display_name":"epigenetic activation","score":0.7900000214576721},{"id":"https://openalex.org/keywords/transcription-factor-binding-sites","display_name":"transcription factor binding sites","score":0.890999972820282},{"id":"https://openalex.org/keywords/nucleosome-phasing","display_name":"nucleosome phasing","score":0.7870000004768372},{"id":"https://openalex.org/keywords/prostate-cancer","display_name":"prostate cancer","score":0.8460000157356262},{"id":"https://openalex.org/keywords/breast-cancer","display_name":"breast cancer","score":0.9890000224113464}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8294702768325806},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.7623006701469421},{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.732093095779419},{"id":"https://openalex.org/C84772758","wikidata":"https://www.wikidata.org/wiki/Q271794","display_name":"Nucleosome","level":4,"score":0.6902429461479187},{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.5541656017303467},{"id":"https://openalex.org/C121912465","wikidata":"https://www.wikidata.org/wiki/Q3589153","display_name":"Epigenomics","level":5,"score":0.544004499912262},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5294154286384583},{"id":"https://openalex.org/C64927066","wikidata":"https://www.wikidata.org/wiki/Q36293","display_name":"Histone","level":3,"score":0.49268609285354614},{"id":"https://openalex.org/C37080517","wikidata":"https://www.wikidata.org/wiki/Q18353747","display_name":"Epigenetics of physical exercise","level":5,"score":0.42111936211586},{"id":"https://openalex.org/C140173407","wikidata":"https://www.wikidata.org/wiki/Q1138358","display_name":"CpG site","level":5,"score":0.4207490384578705},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.2841641902923584},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.141148179769516},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.08932158350944519},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07045257091522217}],"mesh":[{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009707","descriptor_name":"Nucleosomes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009707","descriptor_name":"Nucleosomes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015972","descriptor_name":"Gene Expression Regulation, Neoplastic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D038101","descriptor_name":"Insulator Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D061986","descriptor_name":"MCF-7 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1101/gr.163485.113","doi":"https://doi.org/10.1101/gr.163485.113","is_oa":true,"landing_page_url":"https://doi.org/10.1101/gr.163485.113","pdf_url":"http://genome.cshlp.org/content/24/9/1421.full.pdf","source":{"id":"https://openalex.org/S43092948","display_name":"Genome Research","issn_l":"1088-9051","issn":["1088-9051","1549-5469"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-a","doyens","jufo-3","ki-jl-2","medline","norway-2","poland-200","russia-white-list-1"],"host_organization":"https://openalex.org/P4310315909","host_organization_name":"Cold Spring Harbor Laboratory Press","host_organization_lineage":["https://openalex.org/P4310315909"],"host_organization_lineage_names":["Cold Spring Harbor Laboratory Press"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genome Research","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:3133816","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4158760","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:4158760","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4158760","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genome Res","raw_type":"Text"},{"id":"pmid:24916973","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24916973","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genome research","raw_type":"Journal Article"},{"id":"pmh:oai:ecite.utas.edu.au:101260","doi":null,"is_oa":true,"landing_page_url":"http://ecite.utas.edu.au/101260","pdf_url":null,"source":{"id":"https://openalex.org/S4306401569","display_name":"eCite Digital Repository (University of Tasmania)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I129801699","host_organization_name":"University of Tasmania","host_organization_lineage":["https://openalex.org/I129801699"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Refereed Article"},{"id":"pmh:oai:figshare.com:article/22925885","doi":null,"is_oa":true,"landing_page_url":"https://figshare.com/articles/journal_contribution/Reconfiguration_of_Nucleosome_Depleted_Regions_at_Distal_Regulatory_Elements_Accompanies_DNA_Methylation_of_Enhancers_and_Insulators_in_Cancer/22925885","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:genome:24/9/1421","doi":null,"is_oa":false,"landing_page_url":"http://genome.cshlp.org/cgi/content/short/24/9/1421","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1101/gr.163485.113","doi":"https://doi.org/10.1101/gr.163485.113","is_oa":true,"landing_page_url":"https://doi.org/10.1101/gr.163485.113","pdf_url":"http://genome.cshlp.org/content/24/9/1421.full.pdf","source":{"id":"https://openalex.org/S43092948","display_name":"Genome Research","issn_l":"1088-9051","issn":["1088-9051","1549-5469"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-a","doyens","jufo-3","ki-jl-2","medline","norway-2","poland-200","russia-white-list-1"],"host_organization":"https://openalex.org/P4310315909","host_organization_name":"Cold Spring Harbor Laboratory Press","host_organization_lineage":["https://openalex.org/P4310315909"],"host_organization_lineage_names":["Cold Spring Harbor Laboratory Press"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genome Research","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.9391000270843506,"display_name":"Good health and well-being"}],"study_designs":[],"awards":[{"id":"https://openalex.org/G209760903","display_name":null,"funder_award_id":"1070613","funder_id":"https://openalex.org/F4320320549","funder_display_name":"Cure Cancer Australia Foundation"},{"id":"https://openalex.org/G233630718","display_name":null,"funder_award_id":"NIH R01 CA082422","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G2449860646","display_name":"Epigenetic Drivers of Cancer (PQ 10)","funder_award_id":"R01CA170550","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G4356415821","display_name":"Mechanisms of De Novo Methylation in Cancer","funder_award_id":"R01CA082422","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G5520316217","display_name":null,"funder_award_id":"NIH-R01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5888711010","display_name":"BEYOND TRADITIONAL GENE BOUNDARIES","funder_award_id":"1051757","funder_id":"https://openalex.org/F4320334705","funder_display_name":"National Health and Medical Research Council"},{"id":"https://openalex.org/G7103864405","display_name":"Modelling epigenomic change in early breast carcinogenesis","funder_award_id":"1029579","funder_id":"https://openalex.org/F4320334705","funder_display_name":"National Health and Medical Research Council"}],"funders":[{"id":"https://openalex.org/F4320320438","display_name":"National Breast Cancer Foundation","ror":"https://ror.org/0120ky124"},{"id":"https://openalex.org/F4320320501","display_name":"Cancer Australia","ror":"https://ror.org/00510tw04"},{"id":"https://openalex.org/F4320320543","display_name":"Cancer Institute NSW","ror":"https://ror.org/029a54f25"},{"id":"https://openalex.org/F4320320549","display_name":"Cure Cancer Australia Foundation","ror":"https://ror.org/03yqfnv74"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320334705","display_name":"National Health and Medical Research Council","ror":"https://ror.org/011kf5r70"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2052014424.pdf","grobid_xml":"https://content.openalex.org/works/W2052014424.grobid-xml"},"referenced_works_count":71,"referenced_works":["https://openalex.org/W41135433","https://openalex.org/W1595310168","https://openalex.org/W1598350571","https://openalex.org/W1964963969","https://openalex.org/W1965630177","https://openalex.org/W1971584645","https://openalex.org/W1972813594","https://openalex.org/W1979413690","https://openalex.org/W1980971292","https://openalex.org/W1983386103","https://openalex.org/W1983998398","https://openalex.org/W1984562049","https://openalex.org/W1985706594","https://openalex.org/W1995950906","https://openalex.org/W1997614722","https://openalex.org/W1998000745","https://openalex.org/W1998418245","https://openalex.org/W2001528153","https://openalex.org/W2002197756","https://openalex.org/W2006604860","https://openalex.org/W2007576179","https://openalex.org/W2008051478","https://openalex.org/W2012499563","https://openalex.org/W2013624745","https://openalex.org/W2014119967","https://openalex.org/W2014677321","https://openalex.org/W2015416439","https://openalex.org/W2016429792","https://openalex.org/W2029521343","https://openalex.org/W2029873987","https://openalex.org/W2039053594","https://openalex.org/W2041686632","https://openalex.org/W2044826047","https://openalex.org/W2045273474","https://openalex.org/W2049114614","https://openalex.org/W2054936253","https://openalex.org/W2072152932","https://openalex.org/W2077109220","https://openalex.org/W2083174529","https://openalex.org/W2085353149","https://openalex.org/W2088735811","https://openalex.org/W2101491950","https://openalex.org/W2102066411","https://openalex.org/W2108010006","https://openalex.org/W2110312780","https://openalex.org/W2114752404","https://openalex.org/W2114803986","https://openalex.org/W2115219137","https://openalex.org/W2116805270","https://openalex.org/W2117792884","https://openalex.org/W2118608526","https://openalex.org/W2123032740","https://openalex.org/W2123564569","https://openalex.org/W2124985265","https://openalex.org/W2126740719","https://openalex.org/W2127114672","https://openalex.org/W2129759388","https://openalex.org/W2135173446","https://openalex.org/W2141410747","https://openalex.org/W2147734340","https://openalex.org/W2152223521","https://openalex.org/W2152531852","https://openalex.org/W2154109129","https://openalex.org/W2154731166","https://openalex.org/W2156626022","https://openalex.org/W2167674777","https://openalex.org/W2225434408","https://openalex.org/W2418535197","https://openalex.org/W3040797750","https://openalex.org/W4297943700","https://openalex.org/W4298026142"],"related_works":["https://openalex.org/W2165854182","https://openalex.org/W2040921271","https://openalex.org/W2402437477","https://openalex.org/W2077358246","https://openalex.org/W1970225064","https://openalex.org/W6964146002","https://openalex.org/W1986997536","https://openalex.org/W2167996825","https://openalex.org/W2314940824","https://openalex.org/W2108010006"],"abstract_inverted_index":{"It":[0],"is":[1,35,80,124,217],"well":[2],"established":[3],"that":[4,72,145,171,204],"cancer-associated":[5],"epigenetic":[6,27,46,129,140,239],"repression":[7],"occurs":[8],"concomitant":[9],"with":[10,109,126,137],"CpG":[11],"island":[12],"hypermethylation":[13,127,221],"and":[14,26,50,55,66,85,128,132,139,150,193,208,225,238],"loss":[15,134],"of":[16,23,44,63,76,102,113,119,135,162,197,206,223],"nucleosomes":[17,120,136,146],"at":[18,29,48,88,104,121,152,210],"promoters,":[19],"but":[20],"the":[21,42,73,114,160,185],"role":[22],"nucleosome":[24,67,182],"occupancy":[25,68],"reprogramming":[28],"distal":[30,105,155,211],"regulatory":[31,106,156,212],"elements":[32,52,107,213],"in":[33,53,90,159,214,229,241],"cancer":[34,57,94,115,198,215],"still":[36],"poorly":[37],"understood.":[38],"Here,":[39],"we":[40,97,143,169],"evaluate":[41],"scope":[43],"global":[45,100],"alterations":[47],"enhancers":[49,89,224],"insulator":[51,226],"prostate":[54],"breast":[56],"cells":[58,216],"using":[59],"simultaneous":[60],"genome-wide":[61,192,236],"mapping":[62],"DNA":[64,220],"methylation":[65],"(NOMe-seq).":[69],"We":[70],"find":[71,170],"genomic":[74],"location":[75],"nucleosome-depleted":[77],"regions":[78],"(NDRs)":[79],"mostly":[81],"cell":[82],"type":[83],"specific":[84],"preferentially":[86],"found":[87],"normal":[91],"cells.":[92],"In":[93],"cells,":[95],"however,":[96],"observe":[98],"a":[99,110,163],"reconfiguration":[101],"NDRs":[103,123,191,207],"coupled":[108],"substantial":[111],"reorganization":[112],"methylome.":[116],"Aberrant":[117],"acquisition":[118],"enhancer-associated":[122],"associated":[125],"silencing":[130],"marks,":[131],"conversely,":[133],"demethylation":[138],"activation.":[141],"Remarkably,":[142],"show":[144,179],"remain":[147],"strongly":[148],"organized":[149],"phased":[151],"many":[153],"facultative":[154],"elements,":[157,227],"even":[158],"absence":[161],"NDR":[164],"as":[165],"an":[166,234],"anchor.":[167],"Finally,":[168],"key":[172],"transcription":[173],"factor":[174],"(TF)":[175],"binding":[176],"sites":[177],"also":[178],"extensive":[180],"peripheral":[181],"phasing,":[183],"suggesting":[184],"potential":[186],"for":[187],"TFs":[188,209],"to":[189,195,233],"organize":[190],"contribute":[194,232],"deregulation":[196,240],"epigenomes.":[199],"Together,":[200],"our":[201],"findings":[202],"suggest":[203],"\"decommissioning\"":[205],"accompanied":[218],"by":[219],"susceptibility":[222],"which":[228],"turn":[230],"may":[231],"altered":[235],"architecture":[237],"malignancy.":[242]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":11},{"year":2021,"cited_by_count":19},{"year":2020,"cited_by_count":14},{"year":2019,"cited_by_count":28},{"year":2018,"cited_by_count":16},{"year":2017,"cited_by_count":20},{"year":2016,"cited_by_count":30},{"year":2015,"cited_by_count":17},{"year":2014,"cited_by_count":8}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}