{"id":"https://openalex.org/W7225616210","doi":"https://doi.org/10.64898/2026.11.06.764943","title":"Overlapping enhancer activity robustly regulates rax expression during ocular development in zebrafish","display_name":"Overlapping enhancer activity robustly regulates rax expression during ocular development in zebrafish","publication_year":2026,"publication_date":"2026-11-09","ids":{"openalex":"https://openalex.org/W7225616210","doi":"https://doi.org/10.64898/2026.11.06.764943"},"language":"en","primary_location":{"id":"doi:10.64898/2026.11.06.764943","doi":"https://doi.org/10.64898/2026.11.06.764943","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.06.764943","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/09/2026.11.06.764943.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/09/2026.11.06.764943.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5161330735","display_name":"Dwon A Jordana","orcid":"https://orcid.org/0009-0007-6454-4479","observed_orcids":["https://orcid.org/0009-0007-6454-4479"]},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Dwon A Jordana","raw_affiliation_strings":["University of Pittsburgh, United States"],"raw_orcid":"https://orcid.org/0009-0007-6454-4479","affiliations":[{"raw_affiliation_string":"University of Pittsburgh, United States","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064931312","display_name":"Nathan L Clark","orcid":"https://orcid.org/0000-0003-0006-8374","observed_orcids":["https://orcid.org/0000-0003-0006-8374"]},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nathan L. Clark","raw_affiliation_strings":["University of Pittsburgh, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Pittsburgh, United States","institution_ids":["https://openalex.org/I170201317"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5161330735"],"corresponding_institution_ids":["https://openalex.org/I170201317"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12989","display_name":"Ocular Disorders and Treatments","score":0.70169997215271,"subfield":{"id":"https://openalex.org/subfields/2731","display_name":"Ophthalmology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T12989","display_name":"Ocular Disorders and Treatments","score":0.70169997215271,"subfield":{"id":"https://openalex.org/subfields/2731","display_name":"Ophthalmology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10268","display_name":"Developmental Biology and Gene Regulation","score":0.17069999873638153,"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/T10691","display_name":"Retinal Development and Disorders","score":0.10100000351667404,"subfield":{"id":"https://openalex.org/subfields/2731","display_name":"Ophthalmology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/rax","display_name":"RAX","score":0.875},{"id":"https://openalex.org/keywords/eye-development","display_name":"eye development","score":0.765999972820282},{"id":"https://openalex.org/keywords/cis-regulatory-elements","display_name":"cis-regulatory elements","score":0.8550000190734863},{"id":"https://openalex.org/keywords/gene-regulatory-networks","display_name":"gene regulatory networks","score":0.7129999995231628},{"id":"https://openalex.org/keywords/microphthalmia","display_name":"microphthalmia","score":0.7459999918937683},{"id":"https://openalex.org/keywords/anophthalmia","display_name":"anophthalmia","score":1.0},{"id":"https://openalex.org/keywords/congenital-eye-disease","display_name":"congenital eye disease","score":0.8119999766349792},{"id":"https://openalex.org/keywords/zebrafish","display_name":"zebrafish","score":0.6890000104904175}],"concepts":[{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.9180999994277954},{"id":"https://openalex.org/C2776878037","wikidata":"https://www.wikidata.org/wiki/Q169444","display_name":"Zebrafish","level":3,"score":0.8878999948501587},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7699000239372253},{"id":"https://openalex.org/C2780384893","wikidata":"https://www.wikidata.org/wiki/Q901804","display_name":"Danio","level":4,"score":0.7062000036239624},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.6424000263214111},{"id":"https://openalex.org/C114696181","wikidata":"https://www.wikidata.org/wiki/Q5422650","display_name":"Eye development","level":4,"score":0.6391000151634216},{"id":"https://openalex.org/C2777329699","wikidata":"https://www.wikidata.org/wiki/Q760262","display_name":"Optic vesicle","level":5,"score":0.5360000133514404},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4848000109195709},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4512999951839447},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.45080000162124634},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.4397999942302704},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.43140000104904175},{"id":"https://openalex.org/C2778085061","wikidata":"https://www.wikidata.org/wiki/Q1557239","display_name":"Microphthalmia","level":3,"score":0.4253999888896942},{"id":"https://openalex.org/C21784809","wikidata":"https://www.wikidata.org/wiki/Q17119097","display_name":"Enhancer RNAs","level":5,"score":0.4154999852180481},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.39320001006126404},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.3700000047683716},{"id":"https://openalex.org/C2778961482","wikidata":"https://www.wikidata.org/wiki/Q25241","display_name":"Vertebrate","level":3,"score":0.329800009727478},{"id":"https://openalex.org/C96021297","wikidata":"https://www.wikidata.org/wiki/Q7098791","display_name":"Optic cup (embryology)","level":5,"score":0.31630000472068787},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.30649998784065247},{"id":"https://openalex.org/C21592294","wikidata":"https://www.wikidata.org/wiki/Q3238407","display_name":"Regulatory sequence","level":4,"score":0.29760000109672546},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.2750000059604645},{"id":"https://openalex.org/C2910732395","wikidata":"https://www.wikidata.org/wiki/Q430024","display_name":"Eye Proteins","level":3,"score":0.26649999618530273},{"id":"https://openalex.org/C19843653","wikidata":"https://www.wikidata.org/wiki/Q213907","display_name":"Model organism","level":3,"score":0.2635999917984009},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.26249998807907104}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.11.06.764943","doi":"https://doi.org/10.64898/2026.11.06.764943","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.06.764943","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/09/2026.11.06.764943.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.11.06.764943","doi":"https://doi.org/10.64898/2026.11.06.764943","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.06.764943","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/09/2026.11.06.764943.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7225616210.pdf","grobid_xml":"https://content.openalex.org/works/W7225616210.grobid-xml"},"referenced_works_count":75,"referenced_works":["https://openalex.org/W168984702","https://openalex.org/W1522475122","https://openalex.org/W1965425724","https://openalex.org/W1969264427","https://openalex.org/W1971720358","https://openalex.org/W1973260880","https://openalex.org/W1978529094","https://openalex.org/W1983132229","https://openalex.org/W1983961485","https://openalex.org/W1985984310","https://openalex.org/W1993737707","https://openalex.org/W1993910987","https://openalex.org/W1999967392","https://openalex.org/W2005943162","https://openalex.org/W2011341845","https://openalex.org/W2020592877","https://openalex.org/W2033679207","https://openalex.org/W2041468806","https://openalex.org/W2046228536","https://openalex.org/W2050690946","https://openalex.org/W2058576991","https://openalex.org/W2065532397","https://openalex.org/W2072170174","https://openalex.org/W2074941707","https://openalex.org/W2076018100","https://openalex.org/W2090015650","https://openalex.org/W2103606346","https://openalex.org/W2103884152","https://openalex.org/W2125349610","https://openalex.org/W2133094292","https://openalex.org/W2142459397","https://openalex.org/W2145679031","https://openalex.org/W2148684568","https://openalex.org/W2154160956","https://openalex.org/W2161533644","https://openalex.org/W2163811581","https://openalex.org/W2165737607","https://openalex.org/W2168130841","https://openalex.org/W2168655854","https://openalex.org/W2176307841","https://openalex.org/W2194390873","https://openalex.org/W2286751849","https://openalex.org/W2422644017","https://openalex.org/W2511047441","https://openalex.org/W2527710608","https://openalex.org/W2558474650","https://openalex.org/W2560810409","https://openalex.org/W2786174959","https://openalex.org/W2798040129","https://openalex.org/W2943559908","https://openalex.org/W2945038365","https://openalex.org/W2949193645","https://openalex.org/W2982487710","https://openalex.org/W2984395420","https://openalex.org/W2987688991","https://openalex.org/W2996507128","https://openalex.org/W3119327744","https://openalex.org/W3130364234","https://openalex.org/W3133716533","https://openalex.org/W3152375288","https://openalex.org/W4205914585","https://openalex.org/W4206397882","https://openalex.org/W4213365970","https://openalex.org/W4283789731","https://openalex.org/W4313544375","https://openalex.org/W4378781551","https://openalex.org/W4380290590","https://openalex.org/W4383341110","https://openalex.org/W4386241823","https://openalex.org/W4388686809","https://openalex.org/W4395457790","https://openalex.org/W4400656999","https://openalex.org/W4404297735","https://openalex.org/W4411823517","https://openalex.org/W7099666281"],"related_works":["https://openalex.org/W2624628661","https://openalex.org/W2085183296","https://openalex.org/W1985984310","https://openalex.org/W1983961485","https://openalex.org/W1618384235","https://openalex.org/W2070218981","https://openalex.org/W2094866815","https://openalex.org/W304886385","https://openalex.org/W2092195641","https://openalex.org/W6959042987"],"abstract_inverted_index":{"Vertebrate":[0],"eye":[1,14,38,117,217],"development":[2],"relies":[3],"on":[4],"the":[5,24,35,61,64,70,78,144,154,192,202],"tightly":[6],"regulated":[7],"yet":[8],"highly":[9],"dynamic":[10],"spatiotemporal":[11,107],"expression":[12,85,108,139,161],"of":[13,26,73,116,125,146,173,194,204,214],"field":[15,39],"transcription":[16,40,52],"factors":[17,41],"that":[18,54,82,103,130,153],"coordinate":[19],"developmental":[20,71,196],"programs":[21],"required":[22],"for":[23,57],"formation":[25],"a":[27,51],"functional":[28],"eye.":[29],"The":[30],"gene":[31,155],"rax":[32,74,111,138,160,180],"is":[33,43,55,162],"among":[34],"earliest":[36],"expressed":[37],"and":[42,67,101,128,167,186,208],"specifically":[44],"associated":[45],"with":[46,136],"ocular-fated":[47],"tissue.":[48],"It":[49],"encodes":[50],"factor":[53],"essential":[56],"optic":[58,65],"vesicle":[59],"evagination,":[60],"precursor":[62],"to":[63,165,199],"cup":[66],"retina.":[68],"Although":[69],"functions":[72,203],"are":[75],"well":[76],"characterized,":[77],"cis":[79],"-regulatory":[80],"elements":[81],"control":[83],"its":[84],"remain":[86],"poorly":[87],"understood.":[88],"Using":[89],"zebrafish":[90],"(":[91],"Danio":[92],"rerio":[93],"),":[94],"I":[95,120,150],"identified":[96],"five":[97],"novel":[98],"ocular":[99,182,197],"enhancers":[100,127,198],"demonstrate":[102,129,152],"they":[104,131],"drive":[105],"similar":[106],"patterns":[109],"as":[110],"at":[112],"three":[113],"key":[114],"stages":[115],"development.":[118,141],"Furthermore,":[119],"performed":[121],"an":[122],"in-depth":[123],"characterization":[124],"two":[126],"exhibit":[132],"substantial":[133],"transcript-level":[134],"overlap":[135],"endogenous":[137],"during":[140],"Additionally,":[142],"through":[143],"generation":[145],"enhancer":[147,169],"deletion":[148],"lines,":[149],"further":[151],"regulatory":[156,175],"network":[157,176],"(GRN)":[158],"controlling":[159],"largely":[163],"robust":[164],"individual":[166],"combinatorial":[168],"perturbations.":[170],"However,":[171],"perturbation":[172],"this":[174],"can":[177],"result":[178],"in":[179],"-associated":[181],"abnormalities,":[183],"including":[184],"microphthalmia":[185],"anophthalmia.":[187],"Together,":[188],"these":[189],"findings":[190],"highlight":[191],"importance":[193],"studying":[195],"better":[200],"understand":[201],"noncoding":[205],"genomic":[206],"regions":[207],"provide":[209],"insight":[210],"into":[211],"potential":[212],"causes":[213],"unexplained":[215],"congenital":[216],"disease.":[218]},"counts_by_year":[],"updated_date":"2026-11-11T12:16:26.678958","created_date":"2026-11-10T00:00:00"}