{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T13:02:09Z","timestamp":1790600529616,"version":"4.1.0"},"reference-count":141,"publisher":"Elsevier BV","issue":"10","license":[{"start":{"date-parts":[[2025,10,1]],"date-time":"2025-10-01T00:00:00Z","timestamp":1759276800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,10,1]],"date-time":"2025-10-01T00:00:00Z","timestamp":1759276800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,9,2]],"date-time":"2025-09-02T00:00:00Z","timestamp":1756771200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000011","name":"Howard Hughes Medical Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000011","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R35 GM136275"],"award-info":[{"award-number":["R35 GM136275"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell Reports"],"published-print":{"date-parts":[[2025,10]]},"DOI":"10.1016\/j.celrep.2025.116329","type":"journal-article","created":{"date-parts":[[2025,9,24]],"date-time":"2025-09-24T09:25:20Z","timestamp":1758705920000},"page":"116329","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":6,"title":["Defining the roles of the Integrator, NEXT, and nuclear exosome complexes in Drosophila oogenesis"],"prefix":"10.1016","volume":"44","author":[{"given":"Yongjin","family":"Lee","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adriano","family":"Biasini","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cindy","family":"Tipping","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Seong Hyeon","family":"Hong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4505-9618","authenticated-orcid":false,"given":"Phillip D.","family":"Zamore","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.celrep.2025.116329_bib1","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1016\/S1534-5807(02)00134-X","article-title":"Protein and RNA export from the nucleus","volume":"2","author":"Lei","year":"2002","journal-title":"Dev. Cell"},{"key":"10.1016\/j.celrep.2025.116329_bib2","doi-asserted-by":"crossref","DOI":"10.1101\/cshperspect.a000752","article-title":"RNA processing and export","volume":"2","author":"Hocine","year":"2010","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"10.1016\/j.celrep.2025.116329_bib3","doi-asserted-by":"crossref","first-page":"761","DOI":"10.1038\/nrm2255","article-title":"Exporting RNA from the nucleus to the cytoplasm","volume":"8","author":"K\u00f6hler","year":"2007","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.celrep.2025.116329_bib4","doi-asserted-by":"crossref","first-page":"2757","DOI":"10.1093\/nar\/gkp1176","article-title":"Molecular mechanisms of eukaryotic pre-mRNA 3\u2019 end processing regulation","volume":"38","author":"Millevoi","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2025.116329_bib5","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1016\/j.molcel.2020.12.014","article-title":"Integrator is a genome-wide attenuator of non-productive transcription","volume":"81","author":"Lykke-Andersen","year":"2021","journal-title":"Mol. Cell"},{"key":"10.1016\/j.celrep.2025.116329_bib6","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.abe3393","article-title":"Integrator enforces the fidelity of transcriptional termination at protein-coding genes","volume":"7","author":"Dasilva","year":"2021","journal-title":"Sci. Adv."},{"key":"10.1016\/j.celrep.2025.116329_bib7","doi-asserted-by":"crossref","first-page":"502","DOI":"10.1016\/j.molcel.2020.12.002","article-title":"Hyperosmotic stress alters the RNA polymerase II interactome and induces readthrough transcription despite widespread transcriptional repression","volume":"81","author":"Rosa-Mercado","year":"2021","journal-title":"Mol. Cell"},{"key":"10.1016\/j.celrep.2025.116329_bib8","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2020.107917","article-title":"The Human Integrator Complex Facilitates Transcriptional Elongation by Endonucleolytic Cleavage of Nascent Transcripts","volume":"32","author":"Beckedorff","year":"2020","journal-title":"Cell Rep."},{"key":"10.1016\/j.celrep.2025.116329_bib9","doi-asserted-by":"crossref","first-page":"1525","DOI":"10.1101\/gad.330167.119","article-title":"The Integrator complex cleaves nascent mRNAs to attenuate transcription","volume":"33","author":"Tatomer","year":"2019","journal-title":"Genes Dev."},{"key":"10.1016\/j.celrep.2025.116329_bib10","doi-asserted-by":"crossref","first-page":"738","DOI":"10.1016\/j.molcel.2019.10.034","article-title":"The Integrator Complex Attenuates Promoter-Proximal Transcription at Protein-Coding Genes","volume":"76","author":"Elrod","year":"2019","journal-title":"Mol. Cell"},{"key":"10.1016\/j.celrep.2025.116329_bib11","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.aaz9072","article-title":"Integrator restrains paraspeckles assembly by promoting isoform switching of the lncRNA NEAT1","volume":"6","author":"Barra","year":"2020","journal-title":"Sci. Adv."},{"key":"10.1016\/j.celrep.2025.116329_bib12","doi-asserted-by":"crossref","first-page":"1701","DOI":"10.1038\/s41598-018-38297-6","article-title":"Integrator is a key component of human telomerase RNA biogenesis","volume":"9","author":"Rubtsova","year":"2019","journal-title":"Sci. Rep."},{"key":"10.1016\/j.celrep.2025.116329_bib13","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1038\/cr.2015.19","article-title":"The Integrator complex controls the termination of transcription at diverse classes of gene targets","volume":"25","author":"Skaar","year":"2015","journal-title":"Cell Res."},{"key":"10.1016\/j.celrep.2025.116329_bib14","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1038\/nature14906","article-title":"Integrator mediates the biogenesis of enhancer RNAs","volume":"525","author":"Lai","year":"2015","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116329_bib15","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1016\/j.cell.2005.08.019","article-title":"Integrator, a multiprotein mediator of small nuclear RNA processing, associates with the C-terminal repeat of RNA polymerase II","volume":"123","author":"Baillat","year":"2005","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2025.116329_bib16","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1007981","article-title":"Disruption of the Caenorhabditis elegans Integrator complex triggers a non-conventional transcriptional mechanism beyond snRNA genes","volume":"15","author":"G\u00f3mez-Orte","year":"2019","journal-title":"PLoS Genet."},{"key":"10.1016\/j.celrep.2025.116329_bib17","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1007828","article-title":"The Integrator complex regulates differential snRNA processing and fate of adult stem cells in the highly regenerative planarian Schmidtea mediterranea","volume":"14","author":"Schmidt","year":"2018","journal-title":"PLoS Genet."},{"key":"10.1016\/j.celrep.2025.116329_bib18","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1128\/MCB.00943-10","article-title":"A subset of Drosophila integrator proteins is essential for efficient U7 snRNA and spliceosomal snRNA 3\u2032-end formation","volume":"31","author":"Ezzeddine","year":"2011","journal-title":"Mol. Cell Biol."},{"key":"10.1016\/j.celrep.2025.116329_bib19","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1038\/s41586-024-07269-4","article-title":"Structural basis of Integrator-dependent RNA polymerase II termination","volume":"629","author":"Fianu","year":"2024","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116329_bib20","doi-asserted-by":"crossref","first-page":"698","DOI":"10.1093\/procel\/pwad010","article-title":"Structural basis of INTAC-regulated transcription","volume":"14","author":"Zheng","year":"2023","journal-title":"Protein Cell"},{"key":"10.1016\/j.celrep.2025.116329_bib21","doi-asserted-by":"crossref","first-page":"2032","DOI":"10.1093\/hmg\/ddad034","article-title":"Integrator complex subunit 15 controls mRNA splicing and is critical for eye development","volume":"32","author":"Azuma","year":"2023","journal-title":"Hum. Mol. Genet."},{"key":"10.1016\/j.celrep.2025.116329_bib22","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2023.112244","article-title":"A combinatorial approach to uncover an additional Integrator subunit","volume":"42","author":"Offley","year":"2023","journal-title":"Cell Rep."},{"key":"10.1016\/j.celrep.2025.116329_bib23","doi-asserted-by":"crossref","first-page":"2148","DOI":"10.1261\/rna.035725.112","article-title":"An RNAi screen identifies additional members of the Drosophila Integrator complex and a requirement for cyclin C\/Cdk8 in snRNA 3\u2019-end formation","volume":"18","author":"Chen","year":"2012","journal-title":"RNA"},{"key":"10.1016\/j.celrep.2025.116329_bib24","doi-asserted-by":"crossref","first-page":"883","DOI":"10.1126\/science.abk0154","article-title":"Structural basis of Integrator-mediated transcription regulation","volume":"374","author":"Fianu","year":"2021","journal-title":"Science"},{"key":"10.1016\/j.celrep.2025.116329_bib25","doi-asserted-by":"crossref","DOI":"10.1126\/science.abb5872","article-title":"Identification of Integrator-PP2A complex (INTAC), an RNA polymerase II phosphatase","volume":"370","author":"Zheng","year":"2020","journal-title":"Science"},{"key":"10.1016\/j.celrep.2025.116329_bib26","doi-asserted-by":"crossref","first-page":"3422","DOI":"10.1038\/s41467-020-17232-2","article-title":"INTS10-INTS13-INTS14 form a functional module of Integrator that binds nucleic acids and the cleavage module","volume":"11","author":"Sabath","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2025.116329_bib27","doi-asserted-by":"crossref","first-page":"1246","DOI":"10.1016\/j.molcel.2021.01.005","article-title":"Structure of the catalytic core of the Integrator complex","volume":"81","author":"Pfleiderer","year":"2021","journal-title":"Mol. Cell"},{"key":"10.1016\/j.celrep.2025.116329_bib28","doi-asserted-by":"crossref","first-page":"4241","DOI":"10.1093\/nar\/gky100","article-title":"Integrator subunit 4 is a \u2018Symplekin-like\u2019 scaffold that associates with INTS9\/11 to form the Integrator cleavage module","volume":"46","author":"Albrecht","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2025.116329_bib29","doi-asserted-by":"crossref","first-page":"4394","DOI":"10.1073\/pnas.1616605114","article-title":"Molecular basis for the interaction between Integrator subunits IntS9 and IntS11 and its functional importance","volume":"114","author":"Wu","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.celrep.2025.116329_bib30","doi-asserted-by":"crossref","first-page":"1112","DOI":"10.1128\/MCB.06511-11","article-title":"snRNA 3\u2019 end formation requires heterodimeric association of integrator subunits","volume":"32","author":"Albrecht","year":"2012","journal-title":"Mol. Cell Biol."},{"key":"10.1016\/j.celrep.2025.116329_bib31","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/j.cell.2005.08.002","article-title":"The polyadenylation factor CPSF-73 is involved in histone-pre-mRNA processing","volume":"123","author":"Dominski","year":"2005","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2025.116329_bib32","doi-asserted-by":"crossref","first-page":"2882","DOI":"10.1016\/j.molcel.2024.06.032","article-title":"Assembly mechanism of Integrator\u2019s RNA cleavage module","volume":"84","author":"Sabath","year":"2024","journal-title":"Mol. Cell"},{"key":"10.1016\/j.celrep.2025.116329_bib33","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2318740121","article-title":"Neuronal differentiation requires BRAT1 complex to remove REST from chromatin","volume":"121","author":"Dokaneheifard","year":"2024","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.celrep.2025.116329_bib34","doi-asserted-by":"crossref","first-page":"2900","DOI":"10.1016\/j.molcel.2024.06.017","article-title":"Cytoplasmic binding partners of the Integrator endonuclease INTS11 and its paralog CPSF73 are required for their nuclear function","volume":"84","author":"Lin","year":"2024","journal-title":"Mol. Cell"},{"key":"10.1016\/j.celrep.2025.116329_bib35","doi-asserted-by":"crossref","first-page":"5026","DOI":"10.1038\/s41467-022-32763-6","article-title":"BRAT1 links Integrator and defective RNA processing with neurodegeneration","volume":"13","author":"Cihlarova","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2025.116329_bib36","doi-asserted-by":"crossref","first-page":"5388","DOI":"10.1038\/s41598-021-84472-7","article-title":"Disruption of pathways regulated by Integrator complex in Galloway-Mowat syndrome due to WDR73 mutations","volume":"11","author":"Tilley","year":"2021","journal-title":"Sci. Rep."},{"key":"10.1016\/j.celrep.2025.116329_bib37","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1038\/s41586-018-0440-4","article-title":"Structure of activated transcription complex Pol II-DSIF-PAF-SPT6","volume":"560","author":"Vos","year":"2018","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116329_bib38","doi-asserted-by":"crossref","first-page":"41597","DOI":"10.1074\/jbc.M110.144568","article-title":"A tandem SH2 domain in transcription elongation factor Spt6 binds the phosphorylated RNA polymerase II C-terminal repeat domain (CTD)","volume":"285","author":"Sun","year":"2010","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.celrep.2025.116329_bib39","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1016\/j.molcel.2020.08.016","article-title":"Integrator Recruits Protein Phosphatase 2A to Prevent Pause Release and Facilitate Transcription Termination","volume":"80","author":"Huang","year":"2020","journal-title":"Mol. Cell"},{"key":"10.1016\/j.celrep.2025.116329_bib40","doi-asserted-by":"crossref","first-page":"896","DOI":"10.1016\/j.molcel.2019.09.031","article-title":"Control of RNA Pol II Speed by PNUTS-PP1 and Spt5 Dephosphorylation Facilitates Termination by a \u201cSitting Duck Torpedo\u201d Mechanism","volume":"76","author":"Cortazar","year":"2019","journal-title":"Mol. Cell"},{"key":"10.1016\/j.celrep.2025.116329_bib41","doi-asserted-by":"crossref","first-page":"4263","DOI":"10.1038\/ncomms5263","article-title":"DSIF and NELF interact with Integrator to specify the correct post-transcriptional fate of snRNA genes","volume":"5","author":"Yamamoto","year":"2014","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2025.116329_bib42","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1016\/j.molcel.2011.11.006","article-title":"Ser7 phosphorylation of the CTD recruits the RPAP2 Ser5 phosphatase to snRNA genes","volume":"45","author":"Egloff","year":"2012","journal-title":"Mol. Cell"},{"key":"10.1016\/j.celrep.2025.116329_bib43","doi-asserted-by":"crossref","first-page":"20564","DOI":"10.1074\/jbc.M110.132530","article-title":"The integrator complex recognizes a new double mark on the RNA polymerase II carboxyl-terminal domain","volume":"285","author":"Egloff","year":"2010","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.celrep.2025.116329_bib44","doi-asserted-by":"crossref","first-page":"2387","DOI":"10.1016\/j.celrep.2020.01.068","article-title":"A Two-Layered Targeting Mechanism Underlies Nuclear RNA Sorting by the Human Exosome","volume":"30","author":"Wu","year":"2020","journal-title":"Cell Rep."},{"key":"10.1016\/j.celrep.2025.116329_bib45","doi-asserted-by":"crossref","first-page":"520","DOI":"10.1016\/j.molcel.2016.09.025","article-title":"Identification of a Nuclear Exosome Decay Pathway for Processed Transcripts","volume":"64","author":"Meola","year":"2016","journal-title":"Mol. Cell"},{"key":"10.1016\/j.celrep.2025.116329_bib46","doi-asserted-by":"crossref","first-page":"624","DOI":"10.1016\/j.molcel.2011.06.028","article-title":"Interaction profiling identifies the human nuclear exosome targeting complex","volume":"43","author":"Lubas","year":"2011","journal-title":"Mol. Cell"},{"key":"10.1016\/j.celrep.2025.116329_bib47","doi-asserted-by":"crossref","first-page":"2505","DOI":"10.1016\/j.molcel.2022.04.011","article-title":"Structure and regulation of the nuclear exosome targeting complex guides RNA substrates to the exosome","volume":"82","author":"Gerlach","year":"2022","journal-title":"Mol. Cell"},{"key":"10.1016\/j.celrep.2025.116329_bib48","doi-asserted-by":"crossref","first-page":"2132","DOI":"10.1016\/j.cell.2022.04.016","article-title":"Structural basis for RNA surveillance by the human nuclear exosome targeting (NEXT) complex","volume":"185","author":"Puno","year":"2022","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2025.116329_bib49","doi-asserted-by":"crossref","first-page":"E5506","DOI":"10.1073\/pnas.1803530115","article-title":"Structural basis for MTR4-ZCCHC8 interactions that stimulate the MTR4 helicase in the nuclear exosome-targeting complex","volume":"115","author":"Puno","year":"2018","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.celrep.2025.116329_bib50","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms13573","article-title":"Structure of the RBM7-ZCCHC8 core of the NEXT complex reveals connections to splicing factors","volume":"7","author":"Falk","year":"2016","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2025.116329_bib51","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1261\/rna.048090.114","article-title":"p38MAPK\/MK2-mediated phosphorylation of RBM7 regulates the human nuclear exosome targeting complex","volume":"21","author":"Tiedje","year":"2015","journal-title":"RNA"},{"key":"10.1016\/j.celrep.2025.116329_bib52","doi-asserted-by":"crossref","first-page":"4236","DOI":"10.1093\/nar\/gkv240","article-title":"RBM7 subunit of the NEXT complex binds U-rich sequences and targets 3\u2019-end extended forms of snRNAs","volume":"43","author":"Hrossova","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2025.116329_bib53","doi-asserted-by":"crossref","first-page":"1367","DOI":"10.1038\/nsmb.2703","article-title":"The human cap-binding complex is functionally connected to the nuclear RNA exosome","volume":"20","author":"Andersen","year":"2013","journal-title":"Nat. Struct. Mol. Biol."},{"key":"10.1016\/j.celrep.2025.116329_bib54","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1016\/j.molcel.2011.12.020","article-title":"Ars2 promotes proper replication-dependent histone mRNA 3\u2019 end formation","volume":"45","author":"Gruber","year":"2012","journal-title":"Mol. Cell"},{"key":"10.1016\/j.celrep.2025.116329_bib55","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1016\/j.cell.2009.04.045","article-title":"Ars2 regulates both miRNA- and siRNA- dependent silencing and suppresses RNA virus infection in Drosophila","volume":"138","author":"Sabin","year":"2009","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2025.116329_bib56","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1016\/j.cell.2009.04.046","article-title":"Ars2 links the nuclear cap-binding complex to RNA interference and cell proliferation","volume":"138","author":"Gruber","year":"2009","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2025.116329_bib57","doi-asserted-by":"crossref","first-page":"1503","DOI":"10.1128\/MCB.01565-07","article-title":"ARS2 is a conserved eukaryotic gene essential for early mammalian development","volume":"28","author":"Wilson","year":"2008","journal-title":"Mol. Cell Biol."},{"key":"10.1016\/j.celrep.2025.116329_bib58","doi-asserted-by":"crossref","first-page":"818","DOI":"10.1016\/j.cub.2007.04.005","article-title":"Identification of nuclear dicing bodies containing proteins for microRNA biogenesis in living Arabidopsis plants","volume":"17","author":"Fang","year":"2007","journal-title":"Curr. Biol."},{"key":"10.1016\/j.celrep.2025.116329_bib59","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1038\/nrm.2015.15","article-title":"The regulation and functions of the nuclear RNA exosome complex","volume":"17","author":"Kilchert","year":"2016","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.celrep.2025.116329_bib60","doi-asserted-by":"crossref","first-page":"734","DOI":"10.1016\/j.molcel.2016.09.038","article-title":"Nuclear RNA Exosome at 3.1 \u00c5 Reveals Substrate Specificities, RNA Paths, and Allosteric Inhibition of Rrp44\/Dis3","volume":"64","author":"Zinder","year":"2016","journal-title":"Mol. Cell"},{"key":"10.1016\/j.celrep.2025.116329_bib61","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1038\/nature13406","article-title":"Structure of an Rrp6-RNA exosome complex bound to poly(A) RNA","volume":"511","author":"Wasmuth","year":"2014","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116329_bib62","doi-asserted-by":"crossref","first-page":"2876","DOI":"10.1073\/pnas.1221904110","article-title":"Divergent transcription of long noncoding RNA\/mRNA gene pairs in embryonic stem cells","volume":"110","author":"Sigova","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.celrep.2025.116329_bib63","doi-asserted-by":"crossref","first-page":"648","DOI":"10.1016\/j.molcel.2018.01.006","article-title":"Transcriptional Pause Sites Delineate Stable Nucleosome-Associated Premature Polyadenylation Suppressed by U1 snRNP","volume":"69","author":"Chiu","year":"2018","journal-title":"Mol. Cell"},{"key":"10.1016\/j.celrep.2025.116329_bib64","doi-asserted-by":"crossref","first-page":"2779","DOI":"10.1016\/j.celrep.2019.02.012","article-title":"Rapid Depletion of DIS3, EXOSC10, or XRN2 Reveals the Immediate Impact of Exoribonucleolysis on Nuclear RNA Metabolism and Transcriptional Control","volume":"26","author":"Davidson","year":"2019","journal-title":"Cell Rep."},{"key":"10.1016\/j.celrep.2025.116329_bib65","doi-asserted-by":"crossref","first-page":"1396","DOI":"10.1074\/mcp.RA119.001777","article-title":"PolySTest: Robust Statistical Testing of Proteomics Data with Missing Values Improves Detection of Biologically Relevant Features","volume":"19","author":"Schw\u00e4mmle","year":"2020","journal-title":"Mol. Cell. Proteomics"},{"key":"10.1016\/j.celrep.2025.116329_bib66","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1038\/nature05351","article-title":"Crystal structure of a protein phosphatase 2A heterotrimeric holoenzyme","volume":"445","author":"Cho","year":"2007","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116329_bib67","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1038\/s41580-024-00778-0","article-title":"Mechanisms and regulation of substrate degradation by the 26S proteasome","volume":"26","author":"Arkinson","year":"2025","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.celrep.2025.116329_bib68","doi-asserted-by":"crossref","first-page":"6984","DOI":"10.1038\/s41467-021-27306-4","article-title":"Starvation-induced proteasome assemblies in the nucleus link amino acid supply to apoptosis","volume":"12","author":"Uriarte","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2025.116329_bib69","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1146\/annurev-biochem-062917-011931","article-title":"Structure and Function of the 26S Proteasome","volume":"87","author":"Bard","year":"2018","journal-title":"Annu. Rev. Biochem."},{"key":"10.1016\/j.celrep.2025.116329_bib70","doi-asserted-by":"crossref","first-page":"869","DOI":"10.1038\/cr.2016.86","article-title":"The life cycle of the 26S proteasome: from birth, through regulation and function, and onto its death","volume":"26","author":"Livneh","year":"2016","journal-title":"Cell Res."},{"key":"10.1016\/j.celrep.2025.116329_bib71","doi-asserted-by":"crossref","first-page":"6087","DOI":"10.1093\/emboj\/16.20.6087","article-title":"Dynamics of proteasome distribution in living cells","volume":"16","author":"Reits","year":"1997","journal-title":"EMBO J."},{"key":"10.1016\/j.celrep.2025.116329_bib72","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1016\/j.modgep.2003.10.001","article-title":"Tissue- and developmental stage-specific changes in the subcellular localization of the 26S proteasome in the ovary of Drosophila melanogaster","volume":"4","author":"Ad\u00e1m","year":"2004","journal-title":"Gene Expr. Patterns"},{"key":"10.1016\/j.celrep.2025.116329_bib73","article-title":"Protein complex prediction with AlphaFold-Multimer","author":"Evans","year":"2021","journal-title":"bioRxiv"},{"key":"10.1016\/j.celrep.2025.116329_bib74","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116329_bib75","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1186\/1471-2105-12-357","article-title":"An integrative approach to ortholog prediction for disease-focused and other functional studies","volume":"12","author":"Hu","year":"2011","journal-title":"BMC Bioinf."},{"key":"10.1016\/j.celrep.2025.116329_bib76","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2023.113639","article-title":"Structural basis for competitive binding of productive and degradative co-transcriptional effectors to the nuclear cap-binding complex","volume":"43","author":"Dubiez","year":"2024","journal-title":"Cell Rep."},{"key":"10.1016\/j.celrep.2025.116329_bib77","doi-asserted-by":"crossref","first-page":"1358","DOI":"10.1038\/nsmb.2720","article-title":"CBC-ARS2 stimulates 3\u2019-end maturation of multiple RNA families and favors cap-proximal processing","volume":"20","author":"Hallais","year":"2013","journal-title":"Nat. Struct. Mol. Biol."},{"key":"10.1016\/j.celrep.2025.116329_bib78","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2023.113325","article-title":"Dual agonistic and antagonistic roles of ZC3H18 provide for co-activation of distinct nuclear RNA decay pathways","volume":"42","author":"Pol\u00e1k","year":"2023","journal-title":"Cell Rep."},{"key":"10.1016\/j.celrep.2025.116329_bib79","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1016\/j.celrep.2017.12.037","article-title":"Characterizing ZC3H18, a Multi-domain Protein at the Interface of RNA Production and Destruction Decisions","volume":"22","author":"Winczura","year":"2018","journal-title":"Cell Rep."},{"key":"10.1016\/j.celrep.2025.116329_bib80","doi-asserted-by":"crossref","first-page":"1302","DOI":"10.1038\/s41467-017-01402-w","article-title":"Structural basis for mutually exclusive co-transcriptional nuclear cap-binding complexes with either NELF-E or ARS2","volume":"8","author":"Schulze","year":"2017","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2025.116329_bib82","doi-asserted-by":"crossref","first-page":"4855","DOI":"10.1128\/MCB.18.8.4855","article-title":"Premature translation of oskar in oocytes lacking the RNA-binding protein bicaudal-C","volume":"18","author":"Saffman","year":"1998","journal-title":"Mol. Cell Biol."},{"key":"10.1016\/j.celrep.2025.116329_bib83","doi-asserted-by":"crossref","first-page":"1949","DOI":"10.1242\/dev.01078","article-title":"Hrb27C, Sqd and Otu cooperatively regulate gurken RNA localization and mediate nurse cell chromosome dispersion in Drosophila oogenesis","volume":"131","author":"Goodrich","year":"2004","journal-title":"Development"},{"key":"10.1016\/j.celrep.2025.116329_bib84","doi-asserted-by":"crossref","first-page":"2457","DOI":"10.1242\/dev.120.9.2457","article-title":"Dorsoventral axis formation in Drosophila depends on the correct dosage of the gene gurken","volume":"120","author":"Neuman-Silberberg","year":"1994","journal-title":"Development"},{"key":"10.1016\/j.celrep.2025.116329_bib85","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/S0092-8674(05)80093-5","article-title":"The Drosophila dorsoventral patterning gene gurken produces a dorsally localized RNA and encodes a TGF alpha-like protein","volume":"75","author":"Neuman-Silberberg","year":"1993","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2025.116329_bib86","doi-asserted-by":"crossref","first-page":"3431","DOI":"10.1242\/dev.065029","article-title":"A late phase of germ plasm accumulation during Drosophila oogenesis requires lost and rumpelstiltskin","volume":"138","author":"Sinsimer","year":"2011","journal-title":"Development"},{"key":"10.1016\/j.celrep.2025.116329_bib87","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1083\/jcb.201009142","article-title":"Loss of the extraproteasomal ubiquitin receptor Rings lost impairs ring canal growth in Drosophila oogenesis","volume":"193","author":"Morawe","year":"2011","journal-title":"J. Cell Biol."},{"key":"10.1016\/j.celrep.2025.116329_bib81","doi-asserted-by":"crossref","first-page":"1983","DOI":"10.1109\/TVCG.2014.2346248","article-title":"UpSet: Visualization of Intersecting Sets","volume":"20","author":"Lex","year":"2014","journal-title":"IEEE Trans. Vis. Comput. Graph."},{"key":"10.1016\/j.celrep.2025.116329_bib88","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1016\/S1097-2765(03)00270-3","article-title":"Pre-mRNA splicing: awash in a sea of proteins","volume":"12","author":"Jurica","year":"2003","journal-title":"Mol. Cell"},{"key":"10.1016\/j.celrep.2025.116329_bib89","doi-asserted-by":"crossref","first-page":"1775","DOI":"10.1126\/science.1074962","article-title":"Essential role for the SMN complex in the specificity of snRNP assembly","volume":"298","author":"Pellizzoni","year":"2002","journal-title":"Science"},{"key":"10.1016\/j.celrep.2025.116329_bib90","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0065606","article-title":"The Sm complex is required for the processing of non-coding RNAs by the exosome","volume":"8","author":"Coy","year":"2013","journal-title":"PLoS One"},{"key":"10.1016\/j.celrep.2025.116329_bib91","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1038\/nrm3742","article-title":"A day in the life of the spliceosome","volume":"15","author":"Matera","year":"2014","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.celrep.2025.116329_bib92","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1038\/nrm1964","article-title":"RNA-quality control by the exosome","volume":"7","author":"Houseley","year":"2006","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.celrep.2025.116329_bib93","doi-asserted-by":"crossref","first-page":"1684","DOI":"10.1093\/nar\/28.8.1684","article-title":"Degradation of ribosomal RNA precursors by the exosome","volume":"28","author":"Allmang","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2025.116329_bib94","doi-asserted-by":"crossref","first-page":"6795","DOI":"10.1093\/nar\/gki982","article-title":"MPP6 is an exosome-associated RNA-binding protein involved in 5.8S rRNA maturation","volume":"33","author":"Schilders","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2025.116329_bib95","doi-asserted-by":"crossref","DOI":"10.1093\/genetics\/iyab179","article-title":"A genetic toolkit for studying transposon control in the Drosophila melanogaster ovary","volume":"220","author":"ElMaghraby","year":"2022","journal-title":"Genetics"},{"key":"10.1016\/j.celrep.2025.116329_bib96","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkaf486","article-title":"RNA-binding protein Ars2 mediates transcriptional silencing of telomeric repeats and transposable elements in the Drosophila germline","volume":"53","author":"Morgunova","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2025.116329_bib97","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1126\/science.1086602","article-title":"The Prp19p-associated complex in spliceosome activation","volume":"302","author":"Chan","year":"2003","journal-title":"Science"},{"key":"10.1016\/j.celrep.2025.116329_bib98","doi-asserted-by":"crossref","first-page":"2421","DOI":"10.1002\/j.1460-2075.1994.tb06527.x","article-title":"Functional association of essential splicing factor(s) with PRP19 in a protein complex","volume":"13","author":"Tarn","year":"1994","journal-title":"EMBO J."},{"key":"10.1016\/j.celrep.2025.116329_bib99","doi-asserted-by":"crossref","first-page":"5455","DOI":"10.1093\/nar\/gky244","article-title":"Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities","volume":"46","author":"Rennie","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2025.116329_bib100","doi-asserted-by":"crossref","first-page":"1622","DOI":"10.1101\/gr.189597.115","article-title":"DIS3 shapes the RNA polymerase II transcriptome in humans by degrading a variety of unwanted transcripts","volume":"25","author":"Szczepi\u0144ska","year":"2015","journal-title":"Genome Res."},{"key":"10.1016\/j.celrep.2025.116329_bib101","doi-asserted-by":"crossref","first-page":"1208","DOI":"10.1038\/s41594-024-01272-z","article-title":"Transcription directionality is licensed by Integrator at active human promoters","volume":"31","author":"Yang","year":"2024","journal-title":"Nat. Struct. Mol. Biol."},{"key":"10.1016\/j.celrep.2025.116329_bib102","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1016\/j.molcel.2013.04.007","article-title":"A transcriptome-wide RNAi screen in the Drosophila ovary reveals factors of the germline piRNA pathway","volume":"50","author":"Czech","year":"2013","journal-title":"Mol. Cell"},{"key":"10.1016\/j.celrep.2025.116329_bib103","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1042\/bj3530417","article-title":"Protein phosphatase 2A: a highly regulated family of serine\/threonine phosphatases implicated in cell growth and signalling","volume":"353","author":"Janssens","year":"2001","journal-title":"Biochem. J."},{"key":"10.1016\/j.celrep.2025.116329_bib104","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1007\/s12013-011-9178-4","article-title":"Order of the proteasomal ATPases and eukaryotic proteasome assembly","volume":"60","author":"Tomko","year":"2011","journal-title":"Cell Biochem. Biophys."},{"key":"10.1016\/j.celrep.2025.116329_bib105","doi-asserted-by":"crossref","first-page":"1977","DOI":"10.1242\/jcs.03008","article-title":"The nuclear ubiquitin-proteasome system","volume":"119","author":"von Mikecz","year":"2006","journal-title":"J. Cell Sci."},{"key":"10.1016\/j.celrep.2025.116329_bib106","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1093\/nar\/gkt892","article-title":"Human snRNA genes use polyadenylation factors to promote efficient transcription termination","volume":"42","author":"O\u2019Reilly","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2025.116329_bib107","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1016\/j.molcel.2018.05.031","article-title":"Targeted Enhancer Activation by a Subunit of the Integrator Complex","volume":"71","author":"Barbieri","year":"2018","journal-title":"Mol. Cell"},{"key":"10.1016\/j.celrep.2025.116329_bib108","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms12331","article-title":"Early programming of the oocyte epigenome temporally controls late prophase I transcription and chromatin remodelling","volume":"7","author":"Navarro-Costa","year":"2016","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2025.116329_bib109","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.05003","article-title":"Systematic imaging reveals features and changing localization of mRNAs in Drosophila development","volume":"4","author":"Jambor","year":"2015","journal-title":"eLife"},{"key":"10.1016\/j.celrep.2025.116329_bib110","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/S1097-2765(00)80173-2","article-title":"The role of oocyte transcription, the 5\u2019UTR, and translation repression and derepression in Drosophila gurken mRNA and protein localization","volume":"3","author":"Saunders","year":"1999","journal-title":"Mol. Cell"},{"key":"10.1016\/j.celrep.2025.116329_bib111","doi-asserted-by":"crossref","first-page":"2148","DOI":"10.1101\/gad.13.16.2148","article-title":"The yeast exosome and human PM-Scl are related complexes of 3\u2019 --> 5\u2019 exonucleases","volume":"13","author":"Allmang","year":"1999","journal-title":"Genes Dev."},{"key":"10.1016\/j.celrep.2025.116329_bib112","doi-asserted-by":"crossref","first-page":"2342","DOI":"10.1038\/emboj.2010.121","article-title":"The human core exosome interacts with differentially localized processive RNases: hDIS3 and hDIS3L","volume":"29","author":"Tomecki","year":"2010","journal-title":"EMBO J."},{"key":"10.1016\/j.celrep.2025.116329_bib113","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1016\/S0092-8674(00)80432-8","article-title":"The exosome: a conserved eukaryotic RNA processing complex containing multiple 3\u2019-->5\u2019 exoribonucleases","volume":"91","author":"Mitchell","year":"1997","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2025.116329_bib114","doi-asserted-by":"crossref","first-page":"1399","DOI":"10.1091\/mbc.e05-08-0805","article-title":"Differential distribution of exosome subunits at the nuclear lamina and in cytoplasmic foci","volume":"17","author":"Graham","year":"2006","journal-title":"Mol. Biol. Cell"},{"key":"10.1016\/j.celrep.2025.116329_bib115","doi-asserted-by":"crossref","first-page":"1367","DOI":"10.1038\/nbt.1511","article-title":"MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification","volume":"26","author":"Cox","year":"2008","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.celrep.2025.116329_bib116","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1038\/nmeth.2019","article-title":"Fiji: an open-source platform for biological-image analysis","volume":"9","author":"Schindelin","year":"2012","journal-title":"Nat. Methods"},{"key":"10.1016\/j.celrep.2025.116329_bib117","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1093\/bioinformatics\/btu647","article-title":"piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing","volume":"31","author":"Han","year":"2015","journal-title":"Bioinformatics"},{"key":"10.1016\/j.celrep.2025.116329_bib118","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"10.1016\/j.celrep.2025.116329_bib119","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"10.1016\/j.celrep.2025.116329_bib138","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1186\/s12864-018-4933-1","article-title":"Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers","volume":"19","author":"Fu","year":"2018","journal-title":"BMC Genom."},{"key":"10.1016\/j.celrep.2025.116329_bib120","article-title":"Completing bacterial genome assemblies with multiplex MinION sequencing","volume":"3","author":"Wick","year":"2017","journal-title":"Microb. Genom."},{"key":"10.1016\/j.celrep.2025.116329_bib121","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"10.1016\/j.celrep.2025.116329_bib122","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"GigaScience"},{"key":"10.1016\/j.celrep.2025.116329_bib124","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/nbt.1754","article-title":"Integrative genomics viewer","volume":"29","author":"Robinson","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.celrep.2025.116329_bib125","doi-asserted-by":"crossref","first-page":"W160","DOI":"10.1093\/nar\/gkw257","article-title":"deepTools2: a next generation web server for deep-sequencing data analysis","volume":"44","author":"Ram\u00edrez","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2025.116329_bib126","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1016\/j.molcel.2010.05.004","article-title":"Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities","volume":"38","author":"Heinz","year":"2010","journal-title":"Mol. Cell"},{"key":"10.1016\/j.celrep.2025.116329_bib127","doi-asserted-by":"crossref","first-page":"E2967","DOI":"10.1073\/pnas.1405500111","article-title":"Optimized CRISPR\/Cas tools for efficient germline and somatic genome engineering in Drosophila","volume":"111","author":"Port","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.celrep.2025.116329_bib128","doi-asserted-by":"crossref","first-page":"3197","DOI":"10.1534\/g3.116.032557","article-title":"Rapid Screening for CRISPR-Directed Editing of the Drosophila Genome Using white Coconversion","volume":"6","author":"Ge","year":"2016","journal-title":"G3 (Bethesda)"},{"key":"10.1016\/j.celrep.2025.116329_bib129","doi-asserted-by":"crossref","first-page":"1794","DOI":"10.1021\/pr101065j","article-title":"Andromeda: a peptide search engine integrated into the MaxQuant environment","volume":"10","author":"Cox","year":"2011","journal-title":"J. Proteome Res."},{"key":"10.1016\/j.celrep.2025.116329_bib130","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1016\/j.cell.2009.04.027","article-title":"Collapse of Germline piRNAs in the Absence of Argonaute3 Reveals Somatic piRNAs in Flies","volume":"137","author":"Li","year":"2009","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2025.116329_bib131","article-title":"Automatic stage identification of Drosophila egg chamber based on DAPI images","volume":"6","author":"Jia","year":"2016","journal-title":"Sci. Rep."},{"key":"10.1016\/j.celrep.2025.116329_bib132","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1186\/1758-907X-3-9","article-title":"Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection","volume":"3","author":"Zhang","year":"2012","journal-title":"Silence"},{"key":"10.1016\/j.celrep.2025.116329_bib133","doi-asserted-by":"crossref","first-page":"731","DOI":"10.1038\/nmeth1005-731","article-title":"The External RNA Controls Consortium: a progress report","volume":"2","author":"Baker","year":"2005","journal-title":"Nat. Methods"},{"key":"10.1016\/j.celrep.2025.116329_bib134","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1186\/1471-2164-6-150","article-title":"Proposed methods for testing and selecting the ERCC external RNA controls","volume":"6","year":"2005","journal-title":"BMC Genom."},{"key":"10.1016\/j.celrep.2025.116329_bib135","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1038\/nmeth.2483","article-title":"Comparative analysis of RNA sequencing methods for degraded or low-input samples","volume":"10","author":"Adiconis","year":"2013","journal-title":"Nat. Methods"},{"key":"10.1016\/j.celrep.2025.116329_bib136","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0042882","article-title":"Selective depletion of rRNA enables whole transcriptome profiling of archival fixed tissue","volume":"7","author":"Morlan","year":"2012","journal-title":"PLoS One"},{"key":"10.1016\/j.celrep.2025.116329_bib137","doi-asserted-by":"crossref","first-page":"2502","DOI":"10.1101\/gad.178962.111","article-title":"Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila","volume":"25","author":"Khodor","year":"2011","journal-title":"Genes Dev."},{"key":"10.1016\/j.celrep.2025.116329_bib123","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"10.1016\/j.celrep.2025.116329_bib139","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1038\/s42003-022-03224-z","article-title":"Co-transcriptional splicing efficiency is a gene-specific feature that can be regulated by TGF\u03b2","volume":"5","author":"S\u00e1nchez-Escabias","year":"2022","journal-title":"Commun. Biol."},{"key":"10.1016\/j.celrep.2025.116329_bib140","unstructured":"Ogle, D.H., Doll, J.C., Wheeler, A.P., and Dinno, A. (2025). FSA: Simple Fisheries Stock Assessment Methods. https:\/\/fishr-core-team.github.io\/FSA\/."},{"key":"10.1016\/j.celrep.2025.116329_bib141","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1016\/j.molcel.2018.10.038","article-title":"Maelstrom Represses Canonical Polymerase II Transcription within Bi-directional piRNA Clusters in Drosophila melanogaster","volume":"73","author":"Chang","year":"2019","journal-title":"Mol. Cell"}],"container-title":["Cell Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2211124725011003?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2211124725011003?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T12:49:59Z","timestamp":1790599799000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2211124725011003"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,10]]},"references-count":141,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2025,10]]}},"alternative-id":["S2211124725011003"],"URL":"https:\/\/doi.org\/10.1016\/j.celrep.2025.116329","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2025.03.05.641556","asserted-by":"object"}]},"ISSN":["2211-1247"],"issn-type":[{"value":"2211-1247","type":"print"}],"subject":[],"published":{"date-parts":[[2025,10]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Defining the roles of the Integrator, NEXT, and nuclear exosome complexes in Drosophila oogenesis","name":"articletitle","label":"Article Title"},{"value":"Cell Reports","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.celrep.2025.116329","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Authors. Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"116329"}}