{"id":"https://openalex.org/W1998433561","doi":"https://doi.org/10.1074/jbc.m610584200","title":"The Core Histone Tail Domains Contribute to Sequence-dependent Nucleosome Positioning","display_name":"The Core Histone Tail Domains Contribute to Sequence-dependent Nucleosome Positioning","publication_year":2007,"publication_date":"2007-01-19","ids":{"openalex":"https://openalex.org/W1998433561","doi":"https://doi.org/10.1074/jbc.m610584200","mag":"1998433561","pmid":"https://pubmed.ncbi.nlm.nih.gov/17234628"},"language":"en","primary_location":{"id":"doi:10.1074/jbc.m610584200","doi":"https://doi.org/10.1074/jbc.m610584200","is_oa":true,"landing_page_url":"https://doi.org/10.1074/jbc.m610584200","pdf_url":"http://www.jbc.org/article/S0021925820638005/pdf","source":{"id":"https://openalex.org/S140251998","display_name":"Journal of Biological Chemistry","issn_l":"0021-9258","issn":["0021-9258","1067-8816","1083-351X"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-b","doyens","jufo-2","ki-jl-2","medline","norway-2","poland-100","vabb-shw"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biological Chemistry","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"http://www.jbc.org/article/S0021925820638005/pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103475459","display_name":"Zungyoon Yang","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I5388228","display_name":"University of Rochester","ror":"https://ror.org/022kthw22","country_code":"US","type":"education","lineage":["https://openalex.org/I5388228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zungyoon Yang","raw_affiliation_strings":["Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642, USA","institution_ids":["https://openalex.org/I5388228"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100858799","display_name":"Chunyang Y. Zheng","orcid":"https://orcid.org/0000-0003-4850-3320","observed_orcids":["https://orcid.org/0000-0003-4850-3320"]},"institutions":[{"id":"https://openalex.org/I5388228","display_name":"University of Rochester","ror":"https://ror.org/022kthw22","country_code":"US","type":"education","lineage":["https://openalex.org/I5388228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chunyang Zheng","raw_affiliation_strings":["Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642","institution_ids":["https://openalex.org/I5388228"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5018233941","display_name":"Jeffrey J. Hayes","orcid":"https://orcid.org/0000-0001-6981-1803","observed_orcids":["https://orcid.org/0000-0001-6981-1803"]},"institutions":[{"id":"https://openalex.org/I5388228","display_name":"University of Rochester","ror":"https://ror.org/022kthw22","country_code":"US","type":"education","lineage":["https://openalex.org/I5388228"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jeffrey J. Hayes","raw_affiliation_strings":["Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642","institution_ids":["https://openalex.org/I5388228"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5018233941"],"corresponding_institution_ids":["https://openalex.org/I5388228"],"apc_list":{"value":3430,"currency":"USD","value_usd":3430},"apc_paid":{"value":3430,"currency":"USD","value_usd":3430},"fwci":1.066,"has_fulltext":true,"cited_by_count":37,"citation_normalized_percentile":{"value":0.71794131,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":97},"biblio":{"volume":"282","issue":"11","first_page":"7930","last_page":"7938"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9994999766349792,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9994999766349792,"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/T11841","display_name":"Nuclear Structure and Function","score":9.999999747378752e-05,"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":9.999999747378752e-05,"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-positioning","display_name":"nucleosome positioning","score":0.9750000238418579},{"id":"https://openalex.org/keywords/histone-n-terminal-tails","display_name":"histone N-terminal tails","score":0.902999997138977},{"id":"https://openalex.org/keywords/histone-dna-interactions","display_name":"histone-DNA interactions","score":0.8019999861717224},{"id":"https://openalex.org/keywords/nucleosome-reconstitution","display_name":"nucleosome reconstitution","score":0.8299999833106995},{"id":"https://openalex.org/keywords/5s-rna-gene","display_name":"5S RNA gene","score":0.7730000019073486},{"id":"https://openalex.org/keywords/chromatin","display_name":"chromatin","score":0.48100000619888306},{"id":"https://openalex.org/keywords/gene-expression-regulation","display_name":"gene expression regulation","score":0.7379999756813049}],"concepts":[{"id":"https://openalex.org/C84772758","wikidata":"https://www.wikidata.org/wiki/Q271794","display_name":"Nucleosome","level":4,"score":0.893251895904541},{"id":"https://openalex.org/C64927066","wikidata":"https://www.wikidata.org/wiki/Q36293","display_name":"Histone","level":3,"score":0.6713228821754456},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5876731872558594},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5683000087738037},{"id":"https://openalex.org/C173681060","wikidata":"https://www.wikidata.org/wiki/Q5773169","display_name":"Histone octamer","level":5,"score":0.535532534122467},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.43947482109069824},{"id":"https://openalex.org/C10058791","wikidata":"https://www.wikidata.org/wiki/Q910897","display_name":"Histone code","level":5,"score":0.4260827898979187},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.42500174045562744}],"mesh":[{"descriptor_ui":"D000426","descriptor_name":"Alcohol Dehydrogenase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006657","descriptor_name":"Histones","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D009707","descriptor_name":"Nucleosomes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D009707","descriptor_name":"Nucleosomes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012341","descriptor_name":"RNA, Ribosomal, 5S","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014176","descriptor_name":"Protein Biosynthesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014357","descriptor_name":"Trypsin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014981","descriptor_name":"Xenopus","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053938","descriptor_name":"DNA Fragmentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1074/jbc.m610584200","doi":"https://doi.org/10.1074/jbc.m610584200","is_oa":true,"landing_page_url":"https://doi.org/10.1074/jbc.m610584200","pdf_url":"http://www.jbc.org/article/S0021925820638005/pdf","source":{"id":"https://openalex.org/S140251998","display_name":"Journal of Biological Chemistry","issn_l":"0021-9258","issn":["0021-9258","1067-8816","1083-351X"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-b","doyens","jufo-2","ki-jl-2","medline","norway-2","poland-100","vabb-shw"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biological Chemistry","raw_type":"journal-article"},{"id":"pmid:17234628","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17234628","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":"The Journal of biological chemistry","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1074/jbc.m610584200","doi":"https://doi.org/10.1074/jbc.m610584200","is_oa":true,"landing_page_url":"https://doi.org/10.1074/jbc.m610584200","pdf_url":"http://www.jbc.org/article/S0021925820638005/pdf","source":{"id":"https://openalex.org/S140251998","display_name":"Journal of Biological Chemistry","issn_l":"0021-9258","issn":["0021-9258","1067-8816","1083-351X"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-b","doyens","jufo-2","ki-jl-2","medline","norway-2","poland-100","vabb-shw"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biological Chemistry","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G7931499147","display_name":"Histone Tall Interactions and Functions in Chromatin","funder_award_id":"R01GM052426","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1998433561.pdf","grobid_xml":"https://content.openalex.org/works/W1998433561.grobid-xml"},"referenced_works_count":68,"referenced_works":["https://openalex.org/W1520588455","https://openalex.org/W1542095362","https://openalex.org/W1573199447","https://openalex.org/W1599540521","https://openalex.org/W1606047558","https://openalex.org/W1637308698","https://openalex.org/W1967769642","https://openalex.org/W1971765644","https://openalex.org/W1972878920","https://openalex.org/W1978569157","https://openalex.org/W1980971292","https://openalex.org/W1983801284","https://openalex.org/W1988997227","https://openalex.org/W1989819265","https://openalex.org/W1998220537","https://openalex.org/W1999141348","https://openalex.org/W1999723663","https://openalex.org/W2003435166","https://openalex.org/W2005374586","https://openalex.org/W2008580418","https://openalex.org/W2013050831","https://openalex.org/W2026669507","https://openalex.org/W2028895538","https://openalex.org/W2029873987","https://openalex.org/W2036316728","https://openalex.org/W2037979189","https://openalex.org/W2041301785","https://openalex.org/W2044495919","https://openalex.org/W2050830515","https://openalex.org/W2054275637","https://openalex.org/W2055698723","https://openalex.org/W2056216005","https://openalex.org/W2057916572","https://openalex.org/W2062104167","https://openalex.org/W2066958696","https://openalex.org/W2070663406","https://openalex.org/W2071478793","https://openalex.org/W2071908010","https://openalex.org/W2075879183","https://openalex.org/W2077657264","https://openalex.org/W2079603002","https://openalex.org/W2079797742","https://openalex.org/W2081830518","https://openalex.org/W2085471818","https://openalex.org/W2086605270","https://openalex.org/W2091386983","https://openalex.org/W2093397699","https://openalex.org/W2094592924","https://openalex.org/W2095774295","https://openalex.org/W2097935140","https://openalex.org/W2100005920","https://openalex.org/W2100928698","https://openalex.org/W2118328473","https://openalex.org/W2118736381","https://openalex.org/W2124409271","https://openalex.org/W2126824096","https://openalex.org/W2129020471","https://openalex.org/W2129314778","https://openalex.org/W2140388293","https://openalex.org/W2141511238","https://openalex.org/W2144792857","https://openalex.org/W2146358743","https://openalex.org/W2153833981","https://openalex.org/W2158930155","https://openalex.org/W2159678021","https://openalex.org/W2159710424","https://openalex.org/W2170562450","https://openalex.org/W2171479687"],"related_works":["https://openalex.org/W4405802000","https://openalex.org/W1529844709","https://openalex.org/W1999141348","https://openalex.org/W1479687765","https://openalex.org/W1990255252","https://openalex.org/W2100787604","https://openalex.org/W4240905746","https://openalex.org/W2067291910","https://openalex.org/W2066204517","https://openalex.org/W2100005920"],"abstract_inverted_index":{"The":[0],"precise":[1],"positioning":[2,29,228,266],"of":[3,12,21,39,55,63,85,120,143,154,172,195,199,222,231,246],"nucleosomes":[4,46,86,144,200],"plays":[5],"a":[6,67,71,75,110,114,121,147,213,232,261],"critical":[7],"role":[8],"in":[9,83,163,212,274,278],"the":[10,17,37,40,88,106,118,135,141,155,164,180,183,193,196,220,223,227,239,244,247],"regulation":[11],"gene":[13,81],"expression":[14],"by":[15,130,170,252,271],"modulating":[16],"DNA":[18,50,72,115,136,148,190,240,256],"binding":[19,157],"activity":[20],"trans-acting":[22],"factors.":[23],"However,":[24,140,219],"molecular":[25],"determinants":[26],"responsible":[27],"for":[28,159],"are":[30,205],"not":[31,168],"well":[32],"understood.":[33],"We":[34],"examined":[35],"whether":[36],"removal":[38,62,171],"core":[41,160,173],"histone":[42,161,174,275],"tail":[43,64,138,175,185],"domains":[44,65,186],"from":[45,66],"reconstituted":[47,112],"with":[48,103,113,146],"specific":[49],"fragments":[51],"led":[52],"to":[53,105,151,188,235],"alteration":[54],"translational":[56,94,127,197,209],"positions.":[57],"Remarkably,":[58],"we":[59],"find":[60],"that":[61,96,182,202,243],"nucleosome":[68,111,233,265],"assembled":[69,145],"on":[70,216,226,238],"fragment":[73,116,149],"containing":[74,117],"Xenopus":[76],"borealis":[77],"somatic-type":[78],"5S":[79,107],"RNA":[80],"results":[82,259],"repositioning":[84],"along":[87,134],"DNA,":[89],"including":[90],"two":[91],"related":[92],"major":[93],"positions":[95,128,142,210],"move":[97],"about":[98,131],"20":[99],"bp":[100,133],"further":[101],"upstream":[102],"respect":[104],"gene.":[108],"In":[109],"promoter":[119],"Drosophila":[122],"alcohol":[123],"dehydrogenase":[124],"gene,":[125],"several":[126],"shifted":[129],"10":[132],"upon":[137],"removal.":[139],"known":[150],"have":[152],"one":[153],"highest":[156],"affinities":[158],"proteins":[162],"mouse":[165],"genome":[166],"were":[167],"altered":[169,270],"domains.":[176],"Our":[177,258],"data":[178],"support":[179],"notion":[181],"basic":[184],"bind":[187],"nucleosomal":[189],"and":[191,201,229],"influence":[192],"selection":[194],"position":[198],"once":[203],"tails":[204,225,248],"removed":[206],"movement":[207,230],"between":[208],"occurs":[211],"facile":[214],"manner":[215],"some":[217],"sequences.":[218,257],"effect":[221],"N-terminal":[224],"appears":[234],"be":[236,250,268],"dependent":[237],"sequence":[241],"such":[242],"contribution":[245],"can":[249,267],"masked":[251],"very":[253],"high":[254],"affinity":[255],"suggest":[260],"mechanism":[262],"whereby":[263],"sequence-dependent":[264],"specifically":[269],"regulated":[272],"changes":[273],"tail-DNA":[276],"interactions":[277],"chromatin.":[279]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":4}],"updated_date":"2026-11-13T13:42:25.865203","created_date":"2016-06-24T00:00:00"}