{"id":"https://openalex.org/W4377115378","doi":"https://doi.org/10.1371/journal.pcbi.1011071","title":"Shadow enhancers mediate trade-offs between transcriptional noise and fidelity","display_name":"Shadow enhancers mediate trade-offs between transcriptional noise and fidelity","publication_year":2023,"publication_date":"2023-05-19","ids":{"openalex":"https://openalex.org/W4377115378","doi":"https://doi.org/10.1371/journal.pcbi.1011071","pmid":"https://pubmed.ncbi.nlm.nih.gov/37205714"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1011071","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011071","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1011071","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027076623","display_name":"Alvaro Fletcher","orcid":null},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Alvaro Fletcher","raw_affiliation_strings":["Mathematical, Computational, and Systems Biology, University of California, Irvine, Irvine, CA, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mathematical, Computational, and Systems Biology, University of California, Irvine, Irvine, CA, United States of America","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053074876","display_name":"Zeba Wunderlich","orcid":"https://orcid.org/0000-0003-4491-5715"},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Zeba Wunderlich","raw_affiliation_strings":["Biological Design Center, Boston University, Boston, MA, United States of America","Department of Biology, Boston University, Boston, MA, United States of America"],"raw_orcid":"https://orcid.org/0000-0003-4491-5715","affiliations":[{"raw_affiliation_string":"Biological Design Center, Boston University, Boston, MA, United States of America","institution_ids":["https://openalex.org/I111088046"]},{"raw_affiliation_string":"Department of Biology, Boston University, Boston, MA, United States of America","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032028160","display_name":"Germ\u00e1n Enciso","orcid":"https://orcid.org/0000-0001-8908-9539"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"German Enciso","raw_affiliation_strings":["Department of Mathematics, University of California, Irvine, Irvine, CA, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-8908-9539","affiliations":[{"raw_affiliation_string":"Department of Mathematics, University of California, Irvine, Irvine, CA, United States of America","institution_ids":["https://openalex.org/I204250578"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5027076623","https://openalex.org/A5032028160","https://openalex.org/A5053074876"],"corresponding_institution_ids":["https://openalex.org/I111088046","https://openalex.org/I204250578"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.7268,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.71708593,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"19","issue":"5","first_page":"e1011071","last_page":"e1011071"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9991000294685364,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9991000294685364,"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":0.9987999796867371,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.998199999332428,"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/enhancer","display_name":"Enhancer","score":0.9572615623474121},{"id":"https://openalex.org/keywords/enhancer-rnas","display_name":"Enhancer RNAs","score":0.7055611610412598},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5841567516326904},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5027143955230713},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.4733217656612396},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.44366374611854553},{"id":"https://openalex.org/keywords/noise","display_name":"Noise (video)","score":0.43298590183258057},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.40083229541778564},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.32607609033584595},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.2323494553565979}],"concepts":[{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.9572615623474121},{"id":"https://openalex.org/C21784809","wikidata":"https://www.wikidata.org/wiki/Q17119097","display_name":"Enhancer RNAs","level":5,"score":0.7055611610412598},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5841567516326904},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5027143955230713},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.4733217656612396},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.44366374611854553},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.43298590183258057},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.40083229541778564},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.32607609033584595},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2323494553565979},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1011071","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011071","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:37205714","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37205714","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,"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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt11m0524t","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/11m0524t","pdf_url":"https://escholarship.org/content/qt11m0524t/qt11m0524t.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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":"PLOS Computational Biology, vol 19, iss 5","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10234526","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10234526","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10234526/pdf/pcbi.1011071.pdf","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,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:ark:/13030/qt11m0524t","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:doaj.org/article:f681706b22b44780973026bf9dc8aa81","is_oa":true,"landing_page_url":"https://doaj.org/article/f681706b22b44780973026bf9dc8aa81","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 19, Iss 5, p e1011071 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1011071","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011071","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2318624699","display_name":null,"funder_award_id":"594598","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2625477140","display_name":null,"funder_award_id":"DMS1616233","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3205510348","display_name":null,"funder_award_id":"DMS1763272","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6070842970","display_name":null,"funder_award_id":"R01HD095246","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8673606761","display_name":null,"funder_award_id":"DMS1763272","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G986754019","display_name":null,"funder_award_id":"594598","funder_id":"https://openalex.org/F4320306164","funder_display_name":"Simons Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306164","display_name":"Simons Foundation","ror":"https://ror.org/01cmst727"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":48,"referenced_works":["https://openalex.org/W1675962022","https://openalex.org/W1921421686","https://openalex.org/W1946157893","https://openalex.org/W1972013835","https://openalex.org/W1981014384","https://openalex.org/W1983430442","https://openalex.org/W1991342096","https://openalex.org/W2006824094","https://openalex.org/W2015845481","https://openalex.org/W2021373833","https://openalex.org/W2039307657","https://openalex.org/W2042086471","https://openalex.org/W2045362835","https://openalex.org/W2058999737","https://openalex.org/W2077154296","https://openalex.org/W2095125040","https://openalex.org/W2102130285","https://openalex.org/W2104573545","https://openalex.org/W2106777560","https://openalex.org/W2110927099","https://openalex.org/W2123907240","https://openalex.org/W2136088963","https://openalex.org/W2138897185","https://openalex.org/W2141340108","https://openalex.org/W2155202381","https://openalex.org/W2167154952","https://openalex.org/W2194390873","https://openalex.org/W2265281604","https://openalex.org/W2338264726","https://openalex.org/W2560810409","https://openalex.org/W2581583549","https://openalex.org/W2615153446","https://openalex.org/W2758109932","https://openalex.org/W2786174959","https://openalex.org/W2886353134","https://openalex.org/W2887216660","https://openalex.org/W2917637208","https://openalex.org/W2920631785","https://openalex.org/W2946654177","https://openalex.org/W2976185077","https://openalex.org/W2996507128","https://openalex.org/W3045946041","https://openalex.org/W3101653330","https://openalex.org/W3103757230","https://openalex.org/W3108040874","https://openalex.org/W3119327744","https://openalex.org/W4224883181","https://openalex.org/W6788048921"],"related_works":["https://openalex.org/W2113330652","https://openalex.org/W3098554796","https://openalex.org/W2567553314","https://openalex.org/W3069949010","https://openalex.org/W2146648243","https://openalex.org/W2010420636","https://openalex.org/W4236711043","https://openalex.org/W3014787543","https://openalex.org/W2980673092","https://openalex.org/W4303699336"],"abstract_inverted_index":{"Enhancers":[0],"are":[1,21,37,66],"stretches":[2],"of":[3,15,90,117,165,174,182,195,209,231,234],"regulatory":[4],"DNA":[5],"that":[6,26,121,179,217],"bind":[7],"transcription":[8,51,237],"factors":[9],"(TFs)":[10],"and":[11,34,36,94,111,131,139,145,163,177,187,240],"regulate":[12,27],"the":[13,28,106,161,172,180,192,229],"expression":[14],"a":[16,74,81,166],"target":[17,30],"gene.":[18],"Shadow":[19],"enhancers":[20,25,70,125,142,176,183],"two":[22,113],"or":[23,228],"more":[24,49],"same":[29],"gene":[31],"in":[32,108,129],"space":[33],"time":[35],"associated":[38],"with":[39,87,101],"most":[40],"animal":[41],"developmental":[42],"genes.":[43],"These":[44],"multi-enhancer":[45],"systems":[46,86,220],"can":[47,184],"drive":[48],"consistent":[50],"than":[52,72],"single":[53,75,135,151,167],"enhancer":[54,62,136,168,203,219],"systems.":[55],"Nevertheless,":[56],"it":[57],"remains":[58],"unclear":[59],"why":[60],"shadow":[61,124,141,175,218],"TF":[63,91],"binding":[64,92],"sites":[65,93],"distributed":[67],"across":[68],"multiple":[69],"rather":[71],"within":[73],"large":[76],"enhancer.":[77],"Here,":[78],"we":[79],"use":[80,155],"computational":[82,157],"approach":[83,158],"to":[84,104,150,159],"study":[85],"varying":[88],"numbers":[89],"enhancers.":[95,118,152],"We":[96,153],"employ":[97],"chemical":[98],"reaction":[99],"networks":[100],"stochastic":[102],"dynamics":[103],"determine":[105],"trends":[107],"transcriptional":[109],"noise":[110,130,144,186,239],"fidelity,":[112,189,238],"key":[114,232],"performance":[115],"objectives":[116],"This":[119],"reveals":[120],"while":[122],"additive":[123],"do":[126],"not":[127,148],"differ":[128],"fidelity":[132,146],"from":[133],"their":[134],"counterparts,":[137],"sub-":[138],"superadditive":[140],"have":[143],"trade-offs":[147],"available":[149],"also":[154],"our":[156],"compare":[160],"duplication":[162,181],"splitting":[164],"as":[169],"mechanisms":[170],"for":[171,202,223],"generation":[173],"find":[178],"decrease":[185],"increase":[188],"although":[190],"at":[191],"metabolic":[193],"cost":[194],"increased":[196],"RNA":[197],"production.":[198],"A":[199],"saturation":[200],"mechanism":[201],"interactions":[204],"similarly":[205],"improves":[206],"on":[207],"both":[208],"these":[210],"metrics.":[211],"Taken":[212],"together,":[213],"this":[214],"work":[215],"highlights":[216],"may":[221],"exist":[222],"several":[224],"reasons:":[225],"genetic":[226],"drift":[227],"tuning":[230],"functions":[233],"enhancers,":[235],"including":[236],"output.":[241]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
