{"id":"https://openalex.org/W7223456782","doi":"https://doi.org/10.64898/2026.10.22.760879","title":"Nonsense-mediated decay constrains transposable element-driven evolutionary innovation","display_name":"Nonsense-mediated decay constrains transposable element-driven evolutionary innovation","publication_year":2026,"publication_date":"2026-10-23","ids":{"openalex":"https://openalex.org/W7223456782","doi":"https://doi.org/10.64898/2026.10.22.760879"},"language":"en","primary_location":{"id":"doi:10.64898/2026.10.22.760879","doi":"https://doi.org/10.64898/2026.10.22.760879","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.22.760879","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/23/2026.10.22.760879.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"acceptedVersion","is_accepted":true,"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/2026/10/23/2026.10.22.760879.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5087013197","display_name":"Tobias Plowman","orcid":"https://orcid.org/0000-0002-0413-0975","observed_orcids":["https://orcid.org/0000-0002-0413-0975"]},"institutions":[{"id":"https://openalex.org/I2801081054","display_name":"The Francis Crick Institute","ror":"https://ror.org/04tnbqb63","country_code":"GB","type":"facility","lineage":["https://openalex.org/I2801081054"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Tobias Plowman","raw_affiliation_strings":["Retroviral Immunology Laboratory, The Francis Crick Institute, London NW1 1AT, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Retroviral Immunology Laboratory, The Francis Crick Institute, London NW1 1AT, UK","institution_ids":["https://openalex.org/I2801081054"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058020166","display_name":"George Kassiotis","orcid":"https://orcid.org/0000-0002-8457-2633","observed_orcids":["https://orcid.org/0000-0002-8457-2633","https://orcid.org/0000-0002-1203-588X"]},"institutions":[{"id":"https://openalex.org/I2801081054","display_name":"The Francis Crick Institute","ror":"https://ror.org/04tnbqb63","country_code":"GB","type":"facility","lineage":["https://openalex.org/I2801081054"]},{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"George Kassiotis","raw_affiliation_strings":["Department of Infectious Disease, Imperial College London, London W2 1NY, UK","Retroviral Immunology Laboratory, The Francis Crick Institute, London NW1 1AT, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Infectious Disease, Imperial College London, London W2 1NY, UK","institution_ids":["https://openalex.org/I47508984"]},{"raw_affiliation_string":"Retroviral Immunology Laboratory, The Francis Crick Institute, London NW1 1AT, UK","institution_ids":["https://openalex.org/I2801081054"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5058020166"],"corresponding_institution_ids":["https://openalex.org/I2801081054","https://openalex.org/I47508984"],"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/T10604","display_name":"RNA Research and Splicing","score":0.9779999852180481,"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":0.9779999852180481,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.019500000402331352,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.000699999975040555,"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/nonsense-mediated-mrna-decay","display_name":"nonsense-mediated mRNA decay","score":1.0},{"id":"https://openalex.org/keywords/transposable-elements","display_name":"transposable elements","score":0.9959999918937683},{"id":"https://openalex.org/keywords/long-terminal-repeat","display_name":"long terminal repeat","score":0.6309999823570251},{"id":"https://openalex.org/keywords/premature-termination-codon","display_name":"premature stop codon","score":0.8389999866485596},{"id":"https://openalex.org/keywords/alternative-splicing","display_name":"alternative splicing","score":0.7609999775886536},{"id":"https://openalex.org/keywords/protein-isoforms","display_name":"protein isoforms","score":0.6859999895095825},{"id":"https://openalex.org/keywords/transcriptome-assembly","display_name":"transcriptome assembly","score":0.6909999847412109},{"id":"https://openalex.org/keywords/lung-cancer","display_name":"lung cancer","score":0.6079999804496765},{"id":"https://openalex.org/keywords/lung-squamous-cell-carcinoma","display_name":"lung squamous cell carcinoma","score":0.9779999852180481},{"id":"https://openalex.org/keywords/alu-elements","display_name":"Alu elements","score":0.7770000100135803},{"id":"https://openalex.org/keywords/neil3","display_name":"NEIL3","score":0.9909999966621399},{"id":"https://openalex.org/keywords/setdb1","display_name":"SETDB1","score":0.9919999837875366},{"id":"https://openalex.org/keywords/evolutionary-novelty","display_name":"evolutionary innovation","score":0.5569999814033508}],"concepts":[{"id":"https://openalex.org/C4918238","wikidata":"https://www.wikidata.org/wiki/Q121438","display_name":"Transposable element","level":4,"score":0.8327999711036682},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7756999731063843},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.7032999992370605},{"id":"https://openalex.org/C53345823","wikidata":"https://www.wikidata.org/wiki/Q5531554","display_name":"Gene isoform","level":3,"score":0.5633999705314636},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5361999869346619},{"id":"https://openalex.org/C194583182","wikidata":"https://www.wikidata.org/wiki/Q21114084","display_name":"Alternative splicing","level":4,"score":0.5291000008583069},{"id":"https://openalex.org/C161078062","wikidata":"https://www.wikidata.org/wiki/Q1068690","display_name":"Functional genomics","level":5,"score":0.45719999074935913},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.445499986410141},{"id":"https://openalex.org/C54458228","wikidata":"https://www.wikidata.org/wiki/Q237218","display_name":"RNA splicing","level":4,"score":0.4424999952316284},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.43790000677108765},{"id":"https://openalex.org/C2780989783","wikidata":"https://www.wikidata.org/wiki/Q7578557","display_name":"splice","level":3,"score":0.429500013589859},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4156000018119812},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.396699994802475},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.38690000772476196},{"id":"https://openalex.org/C19843653","wikidata":"https://www.wikidata.org/wiki/Q213907","display_name":"Model organism","level":3,"score":0.36489999294281006},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.3441999852657318},{"id":"https://openalex.org/C36823959","wikidata":"https://www.wikidata.org/wiki/Q373027","display_name":"Exon","level":3,"score":0.336899995803833},{"id":"https://openalex.org/C199216141","wikidata":"https://www.wikidata.org/wiki/Q4995178","display_name":"Conserved sequence","level":4,"score":0.3057999908924103},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.305400013923645},{"id":"https://openalex.org/C166703698","wikidata":"https://www.wikidata.org/wiki/Q201993","display_name":"RNA interference","level":4,"score":0.29829999804496765},{"id":"https://openalex.org/C178169997","wikidata":"https://www.wikidata.org/wiki/Q2892636","display_name":"Genome instability","level":4,"score":0.29649999737739563},{"id":"https://openalex.org/C174510640","wikidata":"https://www.wikidata.org/wiki/Q489618","display_name":"HEK 293 cells","level":3,"score":0.273499995470047},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.27309998869895935},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.27129998803138733},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.27090001106262207},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.2702000141143799},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.26919999718666077},{"id":"https://openalex.org/C119056186","wikidata":"https://www.wikidata.org/wiki/Q1431332","display_name":"Gene silencing","level":3,"score":0.2619999945163727},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.25920000672340393}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.10.22.760879","doi":"https://doi.org/10.64898/2026.10.22.760879","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.22.760879","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/23/2026.10.22.760879.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.10.22.760879","doi":"https://doi.org/10.64898/2026.10.22.760879","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.22.760879","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/23/2026.10.22.760879.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G2310770258","display_name":null,"funder_award_id":"CC2088","funder_id":"https://openalex.org/F4320312060","funder_display_name":"Francis Crick Institute"},{"id":"https://openalex.org/G7131719142","display_name":null,"funder_award_id":"CC2088","funder_id":"https://openalex.org/F4320319985","funder_display_name":"Cancer Research UK"}],"funders":[{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320312060","display_name":"Francis Crick Institute","ror":"https://ror.org/04tnbqb63"},{"id":"https://openalex.org/F4320319985","display_name":"Cancer Research UK","ror":"https://ror.org/054225q67"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7223456782.pdf","grobid_xml":"https://content.openalex.org/works/W7223456782.grobid-xml"},"referenced_works_count":59,"referenced_works":["https://openalex.org/W1528634627","https://openalex.org/W1571581410","https://openalex.org/W1871517579","https://openalex.org/W1965074434","https://openalex.org/W1979031804","https://openalex.org/W1986512768","https://openalex.org/W1999676455","https://openalex.org/W2016910640","https://openalex.org/W2031616673","https://openalex.org/W2033013069","https://openalex.org/W2040891039","https://openalex.org/W2059919630","https://openalex.org/W2085963663","https://openalex.org/W2123785598","https://openalex.org/W2123957786","https://openalex.org/W2136942244","https://openalex.org/W2141327598","https://openalex.org/W2142912355","https://openalex.org/W2151627051","https://openalex.org/W2152974197","https://openalex.org/W2158482911","https://openalex.org/W2168909179","https://openalex.org/W2212235774","https://openalex.org/W2270023616","https://openalex.org/W2318777795","https://openalex.org/W2520188071","https://openalex.org/W2525711566","https://openalex.org/W2550329754","https://openalex.org/W2725192529","https://openalex.org/W2739782708","https://openalex.org/W2775351627","https://openalex.org/W2794480084","https://openalex.org/W2797495365","https://openalex.org/W2939923831","https://openalex.org/W2974901045","https://openalex.org/W2981514644","https://openalex.org/W3081765743","https://openalex.org/W3082610805","https://openalex.org/W3112685079","https://openalex.org/W3159958642","https://openalex.org/W3187141080","https://openalex.org/W3191162099","https://openalex.org/W3212761873","https://openalex.org/W3217281179","https://openalex.org/W4298326878","https://openalex.org/W4372288016","https://openalex.org/W4382011890","https://openalex.org/W4386486827","https://openalex.org/W4396708531","https://openalex.org/W4401667829","https://openalex.org/W4405288351","https://openalex.org/W4405319369","https://openalex.org/W4410159286","https://openalex.org/W4410369895","https://openalex.org/W4412021907","https://openalex.org/W4413421809","https://openalex.org/W7128075054","https://openalex.org/W7152114278","https://openalex.org/W7220852053"],"related_works":["https://openalex.org/W2605103176","https://openalex.org/W2064036807","https://openalex.org/W4318480549","https://openalex.org/W2108420406","https://openalex.org/W1999130532","https://openalex.org/W2887522795","https://openalex.org/W1993315210","https://openalex.org/W3038481672","https://openalex.org/W1512503552","https://openalex.org/W2150075314"],"abstract_inverted_index":{"Abstract":[0],"Nonsense-mediated":[1],"decay":[2],"(NMD)":[3],"degrades":[4],"transcripts":[5,41],"carrying":[6],"premature":[7],"termination":[8],"codons,":[9],"but":[10],"its":[11],"role":[12],"in":[13,44,99,107,115],"controlling":[14,149],"transposable":[15],"element-derived":[16],"transcript":[17],"diversity":[18],"is":[19],"unclear.":[20],"We":[21,120],"assembled":[22],"an":[23],"NMD-extended":[24],"transcriptome":[25],"(\u223c217,000":[26],"transcripts,":[27],"\u223c80%":[28],"unannotated)":[29],"from":[30],"long-read":[31],"RNA":[32],"sequencing":[33],"of":[34,48,64,129,152],"cell":[35,118],"lines":[36],"after":[37],"NMD":[38,97,103],"inhibition.":[39],"NMD-regulated":[40,124],"were":[42,73],"enriched":[43],"TE":[45],"exonization,":[46],"particularly":[47],"long":[49,54],"terminal":[50],"repeat":[51],"(LTR)":[52],"and":[53,84,110,133],"interspersed":[55],"nuclear":[56],"element":[57],"(LINE)":[58],"integrations,":[59],"largely":[60],"as":[61],"alternative":[62],"isoforms":[63,91,128],"annotated":[65],"genes.":[66],"Comparative":[67],"genomics":[68],"showed":[69],"that":[70,123],"NMD-silenced":[71],"TEs":[72,94],"evolutionarily":[74],"younger,":[75,79],"more":[76,85],"diverged,":[77],"contained":[78],"less":[80],"conserved":[81],"splice":[82],"sites,":[83],"often":[86],"encoded":[87],"functionally":[88],"distinct":[89,139],"protein":[90],"compared":[92],"to":[93],"tuned":[95],"by":[96],"or":[98],"stably":[100],"expressed":[101],"transcripts.":[102],"activity":[104,141],"was":[105],"elevated":[106],"lung":[108,116],"cancer":[109],"associated":[111],"with":[112,138],"improved":[113],"survival":[114],"squamous":[117],"carcinoma.":[119],"further":[121],"show":[122],"primate-specific":[125],"Alu":[126],"-exonizing":[127],"DDX49":[130],",":[131],"NEIL3":[132],"SETDB1":[134],"produced":[135],"stable":[136],"proteins":[137],"biological":[140],"effects.":[142],"NMD,":[143],"thus,":[144],"buffers":[145],"TE-driven":[146],"transcriptomic":[147],"innovation,":[148],"the":[150],"reservoir":[151],"evolutionary":[153],"novelty.":[154]},"counts_by_year":[],"updated_date":"2026-11-08T12:12:28.789561","created_date":"2026-10-25T00:00:00"}