{"id":"https://openalex.org/W7214997134","doi":"https://doi.org/10.64898/2026.09.24.754217","title":"Transcriptional adaptation influences buffering among essential paralog gene families","display_name":"Transcriptional adaptation influences buffering among essential paralog gene families","publication_year":2026,"publication_date":"2026-09-29","ids":{"openalex":"https://openalex.org/W7214997134","doi":"https://doi.org/10.64898/2026.09.24.754217","pmid":"https://pubmed.ncbi.nlm.nih.gov/42856160","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/13648420"},"language":"en","primary_location":{"id":"doi:10.64898/2026.09.24.754217","doi":"https://doi.org/10.64898/2026.09.24.754217","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.24.754217","pdf_url":null,"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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","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","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.64898/2026.09.24.754217","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5035006305","display_name":"Siobhan O\u2019Brien","orcid":"https://orcid.org/0000-0003-4958-1080","observed_orcids":["https://orcid.org/0000-0003-4958-1080"]},"institutions":[{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Siobhan O\u2019Brien","raw_affiliation_strings":["Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA"],"raw_orcid":"https://orcid.org/0000-0003-4958-1080","affiliations":[{"raw_affiliation_string":"Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA","institution_ids":["https://openalex.org/I4210089486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5132861611","display_name":"Marissa Fujimoto","orcid":"https://orcid.org/0009-0003-1288-7067","observed_orcids":["https://orcid.org/0009-0003-1288-7067"]},"institutions":[{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marissa H. Fujimoto","raw_affiliation_strings":["Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA"],"raw_orcid":"https://orcid.org/0009-0003-1288-7067","affiliations":[{"raw_affiliation_string":"Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA","institution_ids":["https://openalex.org/I4210089486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5132913204","display_name":"Amy R. Lowe","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Amy R. Lowe","raw_affiliation_strings":["Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA","institution_ids":["https://openalex.org/I4210089486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011108891","display_name":"Alice H. Berger","orcid":"https://orcid.org/0000-0002-6538-2658","observed_orcids":["https://orcid.org/0000-0002-6538-2658"]},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Alice H. Berger","raw_affiliation_strings":["Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA","Herbold Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA","Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA"],"raw_orcid":"https://orcid.org/0000-0002-6538-2658","affiliations":[{"raw_affiliation_string":"Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Herbold Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA","institution_ids":["https://openalex.org/I4210089486"]},{"raw_affiliation_string":"Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA","institution_ids":["https://openalex.org/I4210089486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5011108891"],"corresponding_institution_ids":["https://openalex.org/I201448701","https://openalex.org/I4210089486"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"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/T10604","display_name":"RNA Research and Splicing","score":0.7148000001907349,"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/T10604","display_name":"RNA Research and Splicing","score":0.7148000001907349,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.08240000158548355,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.03620000183582306,"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/transcriptional-adaptation","display_name":"transcriptional adaptation","score":0.878000020980835},{"id":"https://openalex.org/keywords/genetic-redundancy","display_name":"gene redundancy","score":0.4860000014305115},{"id":"https://openalex.org/keywords/compensatory-gene-expression","display_name":"compensatory gene expression","score":0.8569999933242798},{"id":"https://openalex.org/keywords/perturb-seq","display_name":"Perturb-seq","score":0.9100000262260437},{"id":"https://openalex.org/keywords/tia-1","display_name":"TIA-1","score":0.9900000095367432},{"id":"https://openalex.org/keywords/nonsense-mediated-mrna-decay","display_name":"nonsense-mediated mRNA decay","score":0.9860000014305115}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7684000134468079},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.7200000286102295},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6485000252723694},{"id":"https://openalex.org/C7602840","wikidata":"https://www.wikidata.org/wiki/Q746284","display_name":"Gene duplication","level":3,"score":0.5199999809265137},{"id":"https://openalex.org/C2779922708","wikidata":"https://www.wikidata.org/wiki/Q7631143","display_name":"Subfunctionalization","level":5,"score":0.4964999854564667},{"id":"https://openalex.org/C5911399","wikidata":"https://www.wikidata.org/wiki/Q2278983","display_name":"Gene family","level":4,"score":0.487199991941452},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.47940000891685486},{"id":"https://openalex.org/C139807058","wikidata":"https://www.wikidata.org/wiki/Q352374","display_name":"Adaptation (eye)","level":2,"score":0.46880000829696655},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.45329999923706055},{"id":"https://openalex.org/C27153228","wikidata":"https://www.wikidata.org/wiki/Q3787274","display_name":"Transcriptional regulation","level":4,"score":0.4417000114917755},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4023999869823456},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.40130001306533813},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.35749998688697815},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.3379000127315521},{"id":"https://openalex.org/C167683757","wikidata":"https://www.wikidata.org/wiki/Q5937774","display_name":"Human evolutionary genetics","level":4,"score":0.31779998540878296},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.3147999942302704},{"id":"https://openalex.org/C186310378","wikidata":"https://www.wikidata.org/wiki/Q941796","display_name":"Psychological repression","level":4,"score":0.303600013256073},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3012000024318695},{"id":"https://openalex.org/C92509807","wikidata":"https://www.wikidata.org/wiki/Q13417137","display_name":"Dosage compensation","level":4,"score":0.29409998655319214},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.28700000047683716},{"id":"https://openalex.org/C103077935","wikidata":"https://www.wikidata.org/wiki/Q5508811","display_name":"Functional divergence","level":5,"score":0.266400009393692},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.2653999924659729},{"id":"https://openalex.org/C178809742","wikidata":"https://www.wikidata.org/wiki/Q3455913","display_name":"Post-transcriptional regulation","level":4,"score":0.262800008058548}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.64898/2026.09.24.754217","doi":"https://doi.org/10.64898/2026.09.24.754217","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.24.754217","pdf_url":null,"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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:42856160","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42856160","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":"bioRxiv : the preprint server for biology","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13648420","doi":null,"is_oa":true,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42856160/","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"bioRxiv","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.64898/2026.09.24.754217","doi":"https://doi.org/10.64898/2026.09.24.754217","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.24.754217","pdf_url":null,"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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G9000876452","display_name":"University of Washington Genomics Research Training for Data Scientists","funder_award_id":"R25HG012337","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G9000880613","display_name":"Cancer Center Support Grant","funder_award_id":"P30CA015704","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G9000905326","display_name":"Expanding the cancer paralog genetic interaction map to enable precision oncology","funder_award_id":"R01CA262556","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":43,"referenced_works":["https://openalex.org/W1686333409","https://openalex.org/W1820845817","https://openalex.org/W1934704664","https://openalex.org/W1977848450","https://openalex.org/W1978028702","https://openalex.org/W1990607957","https://openalex.org/W2013482681","https://openalex.org/W2022589976","https://openalex.org/W2035622034","https://openalex.org/W2077151220","https://openalex.org/W2099540110","https://openalex.org/W2100122648","https://openalex.org/W2100212753","https://openalex.org/W2121767159","https://openalex.org/W2146308072","https://openalex.org/W2241763745","https://openalex.org/W2289798003","https://openalex.org/W2340295145","https://openalex.org/W2414247940","https://openalex.org/W2520188071","https://openalex.org/W2561754210","https://openalex.org/W2562947047","https://openalex.org/W2580679631","https://openalex.org/W2803271184","https://openalex.org/W2934310150","https://openalex.org/W2947792257","https://openalex.org/W2981480342","https://openalex.org/W3091008282","https://openalex.org/W3093464230","https://openalex.org/W3122724845","https://openalex.org/W3132758757","https://openalex.org/W3197950762","https://openalex.org/W3217729113","https://openalex.org/W4281716291","https://openalex.org/W4285818540","https://openalex.org/W4322766934","https://openalex.org/W4377940798","https://openalex.org/W4378212544","https://openalex.org/W4392641728","https://openalex.org/W4395695320","https://openalex.org/W4407392474","https://openalex.org/W4411881974","https://openalex.org/W7128674588"],"related_works":["https://openalex.org/W2941613566","https://openalex.org/W2026590765","https://openalex.org/W4401516941","https://openalex.org/W3049611888","https://openalex.org/W1566143784","https://openalex.org/W4214589029","https://openalex.org/W2078798531","https://openalex.org/W2420744007","https://openalex.org/W4378363414","https://openalex.org/W2800098072"],"abstract_inverted_index":{"Abstract":[0],"Buffering":[1],"among":[2,18,44,75,147],"paralogous":[3,148],"genes":[4,31],"is":[5,142],"a":[6,22,56,93,131],"well-described":[7],"phenomenon":[8],"in":[9,40,58,102],"which":[10],"genetic":[11,14],"redundancy":[12],"provides":[13],"robustness.":[15],"Shared":[16],"function":[17],"paralogs":[19,76],"allows":[20],"for":[21],"compensation":[23],"effect":[24],"when":[25],"one":[26,100],"or":[27],"more":[28],"paralog":[29,59,66,89,101,114],"family":[30],"are":[32],"inactivated.":[33],"Considering":[34],"the":[35,81,103,109,125],"role":[36,57],"of":[37,64,99,111,134],"transcriptional":[38,53,94,135,140],"adaptation":[39,54,95,136,141],"influencing":[41],"gene":[42,67,72],"expression":[43,73],"highly":[45],"homologous":[46],"genes,":[47],"we":[48,106],"sought":[49],"to":[50],"identify":[51],"whether":[52],"has":[55],"buffering.":[60],"We":[61],"performed":[62],"Perturb-seq":[63],"110":[65],"knockouts":[68],"and":[69,120,137],"assessed":[70],"compensatory":[71],"effects":[74],"as":[77,79],"well":[78],"at":[80],"whole":[82],"transcriptome":[83],"level.":[84],"This":[85],"analysis":[86],"identified":[87],"six":[88],"pairs":[90],"that":[91,108,139],"undergo":[92],"following":[96,113],"CRISPR-mediated":[97],"loss":[98,116],"pair.":[104],"Further,":[105],"found":[107],"upregulation":[110],"TIA1":[112],"TIAL1":[115],"requires":[117],"nonsense-mediated":[118],"decay,":[119],"active":[121],"nuclear":[122],"import":[123],"via":[124],"importin":[126],"IPO8.":[127],"These":[128],"data":[129],"provide":[130],"comprehensive":[132],"evaluation":[133],"show":[138],"recurrent":[143],"but":[144],"not":[145],"pervasive":[146],"human":[149],"genes.":[150]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-10-01T00:00:00"}