{"id":"https://openalex.org/W2126742226","doi":"https://doi.org/10.1074/jbc.m109.007948","title":"Gene Looping Is Conferred by Activator-dependent Interaction of Transcription Initiation and Termination Machineries","display_name":"Gene Looping Is Conferred by Activator-dependent Interaction of Transcription Initiation and Termination Machineries","publication_year":2009,"publication_date":"2009-07-14","ids":{"openalex":"https://openalex.org/W2126742226","doi":"https://doi.org/10.1074/jbc.m109.007948","mag":"2126742226","pmid":"https://pubmed.ncbi.nlm.nih.gov/19602510","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/2757206"},"language":"en","primary_location":{"id":"doi:10.1074/jbc.m109.007948","doi":"https://doi.org/10.1074/jbc.m109.007948","is_oa":true,"landing_page_url":"https://doi.org/10.1074/jbc.m109.007948","pdf_url":"http://www.jbc.org/article/S0021925820305913/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","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"http://www.jbc.org/article/S0021925820305913/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5069660757","display_name":"Belal El Kaderi","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Belal El Kaderi","raw_affiliation_strings":["Department of Biological Science, Wayne State University, Detroit, Michigan 48202, USA","Department of Biological Science, Wayne State University, Detroit, Michigan 48202"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Science, Wayne State University, Detroit, Michigan 48202, USA","institution_ids":["https://openalex.org/I185443292"]},{"raw_affiliation_string":"Department of Biological Science, Wayne State University, Detroit, Michigan 48202","institution_ids":["https://openalex.org/I185443292"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048572637","display_name":"Scott Medler","orcid":"https://orcid.org/0000-0002-7778-0928","observed_orcids":["https://orcid.org/0000-0002-7778-0928"]},"institutions":[{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Scott Medler","raw_affiliation_strings":["Department of Biological Science, Wayne State University, Detroit, Michigan 48202"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Science, Wayne State University, Detroit, Michigan 48202","institution_ids":["https://openalex.org/I185443292"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082883913","display_name":"Sarita Raghunayakula","orcid":"https://orcid.org/0009-0002-0896-8545","observed_orcids":["https://orcid.org/0009-0002-0896-8545"]},"institutions":[{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sarita Raghunayakula","raw_affiliation_strings":["Department of Biological Science, Wayne State University, Detroit, Michigan 48202"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Science, Wayne State University, Detroit, Michigan 48202","institution_ids":["https://openalex.org/I185443292"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044716428","display_name":"Athar Ansari","orcid":"https://orcid.org/0000-0003-2806-421X","observed_orcids":["https://orcid.org/0000-0003-2806-421X"]},"institutions":[{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Athar Ansari","raw_affiliation_strings":["Department of Biological Science, Wayne State University, Detroit, Michigan 48202"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Science, Wayne State University, Detroit, Michigan 48202","institution_ids":["https://openalex.org/I185443292"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5044716428"],"corresponding_institution_ids":["https://openalex.org/I185443292"],"apc_list":{"value":3430,"currency":"USD","value_usd":3430},"apc_paid":{"value":3430,"currency":"USD","value_usd":3430},"fwci":3.1248,"has_fulltext":true,"cited_by_count":82,"citation_normalized_percentile":{"value":0.92682927,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":88,"max":99},"biblio":{"volume":"284","issue":"37","first_page":"25015","last_page":"25025"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9980000257492065,"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":0.9980000257492065,"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/T10497","display_name":"Fungal and yeast genetics research","score":0.0006000000284984708,"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":0.00019999999494757503,"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/transcription-initiation","display_name":"transcription initiation","score":0.6140000224113464},{"id":"https://openalex.org/keywords/transcription-termination","display_name":"transcription termination","score":0.9279999732971191},{"id":"https://openalex.org/keywords/rna-polymerase-ii","display_name":"RNA polymerase II","score":0.8130000233650208},{"id":"https://openalex.org/keywords/transcriptional-activator","display_name":"transcriptional activator","score":0.843999981880188},{"id":"https://openalex.org/keywords/tfiib","display_name":"TFIIB","score":0.9679999947547913},{"id":"https://openalex.org/keywords/3-end-processing","display_name":"3' end processing","score":0.9210000038146973},{"id":"https://openalex.org/keywords/ino1","display_name":"INO1","score":0.9769999980926514},{"id":"https://openalex.org/keywords/saccharomyces-cerevisiae","display_name":"Saccharomyces cerevisiae","score":0.8560000061988831}],"concepts":[{"id":"https://openalex.org/C88045685","wikidata":"https://www.wikidata.org/wiki/Q174576","display_name":"Activator (genetics)","level":3,"score":0.6129207611083984},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.5931002497673035},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.5562157034873962},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.49130430817604065},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4252665042877197},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3602028489112854},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3539385497570038},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005800","descriptor_name":"Genes, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012319","descriptor_name":"RNA Polymerase II","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015966","descriptor_name":"Gene Expression Regulation, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020133","descriptor_name":"Reverse Transcriptase Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D035581","descriptor_name":"Transcription Factor TFIIB","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D039221","descriptor_name":"mRNA Cleavage and Polyadenylation Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1074/jbc.m109.007948","doi":"https://doi.org/10.1074/jbc.m109.007948","is_oa":true,"landing_page_url":"https://doi.org/10.1074/jbc.m109.007948","pdf_url":"http://www.jbc.org/article/S0021925820305913/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":"pmh:oai:pubmedcentral.nih.gov:2757206","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2757206","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"J Biol Chem","raw_type":"Text"},{"id":"pmid:19602510","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19602510","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.m109.007948","doi":"https://doi.org/10.1074/jbc.m109.007948","is_oa":true,"landing_page_url":"https://doi.org/10.1074/jbc.m109.007948","pdf_url":"http://www.jbc.org/article/S0021925820305913/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":[],"funders":[{"id":"https://openalex.org/F4320309272","display_name":"Wayne State University","ror":"https://ror.org/01070mq45"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2126742226.pdf","grobid_xml":"https://content.openalex.org/works/W2126742226.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W914334466","https://openalex.org/W1588445101","https://openalex.org/W1601315441","https://openalex.org/W1817418355","https://openalex.org/W1835640804","https://openalex.org/W1966072209","https://openalex.org/W1969670694","https://openalex.org/W1973498182","https://openalex.org/W1984783168","https://openalex.org/W2019348861","https://openalex.org/W2026592511","https://openalex.org/W2038424676","https://openalex.org/W2046186543","https://openalex.org/W2054603310","https://openalex.org/W2071984045","https://openalex.org/W2073026107","https://openalex.org/W2088454058","https://openalex.org/W2088772708","https://openalex.org/W2094184203","https://openalex.org/W2094972443","https://openalex.org/W2100057937","https://openalex.org/W2106448802","https://openalex.org/W2113086697","https://openalex.org/W2119722433","https://openalex.org/W2124458647","https://openalex.org/W2133912711","https://openalex.org/W2142379668","https://openalex.org/W2143462761","https://openalex.org/W2166760304","https://openalex.org/W2268730793","https://openalex.org/W2281470818"],"related_works":["https://openalex.org/W1973498182","https://openalex.org/W1983412356","https://openalex.org/W44186889","https://openalex.org/W284306532","https://openalex.org/W7098887497","https://openalex.org/W2166760304","https://openalex.org/W2768638443","https://openalex.org/W2974660015","https://openalex.org/W2078076994","https://openalex.org/W3211679876"],"abstract_inverted_index":{"Gene":[0],"looping":[1,32,190],"juxtaposes":[2],"the":[3,58,111,115,122,128,141,144,148,160,165,186],"promoter":[4,142],"and":[5,15,27,42,65,70,132,143],"terminator":[6,145,161],"regions":[7,146],"of":[8,24,60,67,114,152,157,168,179,199],"RNA":[9],"polymerase":[10],"II-transcribed":[11],"genes":[12,129],"in":[13,33,45,57,77,92,133],"yeast":[14],"mammalian":[16],"cells.":[17],"Here":[18],"we":[19],"report":[20],"an":[21,87,108],"activator-dependent":[22],"interaction":[23,109,178,193],"transcription":[25,61,78,124],"initiation":[26],"termination":[28],"factors":[29],"during":[30,50,147,196],"gene":[31,93,189],"budding":[34],"yeast.":[35],"Chromatin":[36],"analysis":[37],"revealed":[38,175],"that":[39,185],"MET16,":[40,68],"INO1,":[41,69],"GAL1p-BUD3":[43,71],"are":[44],"a":[46,134,153,176],"stable":[47],"looped":[48,135],"configuration":[49],"activated":[51,131,150],"transcription.":[52],"Looping":[53],"was":[54,79,162],"nearly":[55],"abolished":[56],"absence":[59],"activators":[62,91,96,118,187],"Met28,":[63],"Ino2,":[64],"Gal4":[66],"genes,":[72],"respectively.":[73],"The":[74,95,155],"activator-independent":[75],"increase":[76],"not":[80,98,106],"accompanied":[81],"by":[82],"loop":[83,100],"formation,":[84],"thereby":[85],"suggesting":[86],"essential":[88],"role":[89],"for":[90],"looping.":[94],"did":[97,105],"facilitate":[99,188],"formation":[101],"directly":[102],"because":[103],"they":[104],"exhibit":[107],"with":[110,121,181,194],"3'":[112,170],"end":[113,171],"genes.":[116,200],"Instead,":[117],"physically":[119],"interacted":[120],"general":[123],"factor":[125],"TFIIB":[126,137,158,195],"when":[127],"were":[130],"configuration.":[136],"cross-linked":[138],"to":[139],"both":[140],"transcriptionally":[149],"state":[151],"gene.":[154],"presence":[156],"on":[159,164],"dependent":[163],"Rna15":[166,180],"component":[167],"CF1":[169],"processing":[172],"complex.":[173],"Coimmunoprecipitation":[174],"physical":[177],"TFIIB.":[182],"We":[183],"propose":[184],"through":[191],"their":[192],"transcriptional":[197],"activation":[198]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":9},{"year":2012,"cited_by_count":12}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}