{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T15:02:18Z","timestamp":1790953338182,"version":"4.1.0"},"update-to":[{"DOI":"10.1371\/journal.pbio.3003031","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,2,19]],"date-time":"2025-02-19T00:00:00Z","timestamp":1739923200000}}],"reference-count":87,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2025,2,6]],"date-time":"2025-02-06T00:00:00Z","timestamp":1738800000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"funder":[{"DOI":"10.13039\/100009633","name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","doi-asserted-by":"publisher","award":["F32HD107972"],"award-info":[{"award-number":["F32HD107972"]}],"id":[{"id":"10.13039\/100009633","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000065","name":"National Institute of Neurological Disorders and Stroke","doi-asserted-by":"publisher","award":["R01NS083897"],"award-info":[{"award-number":["R01NS083897"]}],"id":[{"id":"10.13039\/100000065","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000065","name":"National Institute of Neurological Disorders and Stroke","doi-asserted-by":"publisher","award":["R01NS120667"],"award-info":[{"award-number":["R01NS120667"]}],"id":[{"id":"10.13039\/100000065","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000065","name":"National Institute of Neurological Disorders and Stroke","doi-asserted-by":"publisher","award":["R37NS110388"],"award-info":[{"award-number":["R37NS110388"]}],"id":[{"id":"10.13039\/100000065","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000025","name":"National Institute of Mental Health","doi-asserted-by":"publisher","award":["R01MH132089"],"award-info":[{"award-number":["R01MH132089"]}],"id":[{"id":"10.13039\/100000025","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000065","name":"National Institute of Neurological Disorders and Stroke","doi-asserted-by":"publisher","award":["R01NS110388"],"award-info":[{"award-number":["R01NS110388"]}],"id":[{"id":"10.13039\/100000065","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000065","name":"National Institute of Neurological Disorders and Stroke","doi-asserted-by":"publisher","award":["R21NS128374"],"award-info":[{"award-number":["R21NS128374"]}],"id":[{"id":"10.13039\/100000065","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000066","name":"National Institute of Environmental Health Sciences","doi-asserted-by":"publisher","award":["Z01ES102745"],"award-info":[{"award-number":["Z01ES102745"]}],"id":[{"id":"10.13039\/100000066","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosbiology.org"],"crossmark-restriction":false},"short-container-title":["PLoS Biol"],"abstract":"<jats:p>\n                    RNA abundance is controlled by rates of synthesis and degradation. Although mis-regulation of RNA turnover is linked to neurodevelopmental disorders, how it contributes to cortical development is largely unknown. Here, we discover the landscape of RNA stability regulation in the cerebral cortex and demonstrate that intact RNA decay machinery is essential for corticogenesis in vivo. We use SLAM-seq to measure RNA half-lives transcriptome-wide across multiple stages of cortical development. Leveraging these data, we discover\n                    <jats:italic>cis<\/jats:italic>\n                    -acting features associated with RNA stability and probe the relationship between RNA half-life and developmental expression changes. Notably, RNAs that are up-regulated across development tend to be more stable, while down-regulated RNAs are less stable. Using compound mouse genetics, we discover CNOT3, a core component of the CCR4-NOT deadenylase complex linked to neurodevelopmental disease, is essential for cortical development. Conditional knockout of\n                    <jats:italic>Cnot3<\/jats:italic>\n                    in neural progenitors and their progeny in the developing mouse cortex leads to severe microcephaly due to altered cell fate and p53-dependent apoptosis. Finally, we define the molecular targets of CNOT3, revealing it controls expression of poorly expressed, non-optimal mRNAs in the cortex, including cell cycle-related transcripts. Collectively, our findings demonstrate that fine-tuned control of RNA turnover is crucial for brain development.\n                  <\/jats:p>","DOI":"10.1371\/journal.pbio.3003031","type":"journal-article","created":{"date-parts":[[2025,2,6]],"date-time":"2025-02-06T13:57:23Z","timestamp":1738850243000},"page":"e3003031","update-policy":"https:\/\/doi.org\/10.1371\/journal.pbio.corrections_policy","source":"Crossref","is-referenced-by-count":18,"title":["mRNA stability fine-tunes gene expression in the developing cortex to control neurogenesis"],"prefix":"10.1371","volume":"23","author":[{"given":"Lucas D.","family":"Serdar","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacob R.","family":"Egol","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brad","family":"Lackford","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brian D.","family":"Bennett","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guang","family":"Hu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9189-844X","authenticated-orcid":true,"given":"Debra L.","family":"Silver","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2025,2,6]]},"reference":[{"issue":"11","key":"pbio.3003031.ref001","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1038\/nrn3586","article-title":"Molecular logic of neocortical projection neuron specification, development and diversity.","volume":"14","author":"LC Greig","year":"2013","journal-title":"Nat Rev Neurosci."},{"key":"pbio.3003031.ref002","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/bs.ctdb.2020.10.003","article-title":"The regulation of cortical neurogenesis","volume":"142","author":"A Villalba","year":"2021","journal-title":"Curr Top Dev Biol"},{"issue":"13","key":"pbio.3003031.ref003","doi-asserted-by":"crossref","first-page":"2091","DOI":"10.1016\/j.neuron.2024.04.021","article-title":"Making Ramon y Cajal proud: Development of cell identity and diversity in the cerebral cortex","volume":"112","author":"DJ Di Bella","year":"2024","journal-title":"Neuron"},{"issue":"29","key":"pbio.3003031.ref004","doi-asserted-by":"crossref","first-page":"11836","DOI":"10.1073\/pnas.1209647109","article-title":"Transcriptomes of germinal zones of human and mouse fetal neocortex suggest a role of extracellular matrix in progenitor self-renewal","volume":"109","author":"SA Fietz","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"2","key":"pbio.3003031.ref005","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1016\/j.neuron.2014.12.024","article-title":"DeCoN: genome-wide analysis of in vivo transcriptional dynamics during pyramidal neuron fate selection in neocortex","volume":"85","author":"BJ Molyneaux","year":"2015","journal-title":"Neuron"},{"issue":"7868","key":"pbio.3003031.ref006","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1038\/s41586-021-03670-5","article-title":"Molecular logic of cellular diversification in the mouse cerebral cortex","volume":"595","author":"DJ Di Bella","year":"2021","journal-title":"Nature"},{"issue":"6440","key":"pbio.3003031.ref007","doi-asserted-by":"crossref","first-page":"eaav2522","DOI":"10.1126\/science.aav2522","article-title":"Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex","volume":"364","author":"L Telley","year":"2019","journal-title":"Science"},{"issue":"9","key":"pbio.3003031.ref008","doi-asserted-by":"crossref","first-page":"1535","DOI":"10.1242\/dev.069963","article-title":"Transcriptional co-regulation of neuronal migration and laminar identity in the neocortex","volume":"139","author":"KY Kwan","year":"2012","journal-title":"Development"},{"issue":"1","key":"pbio.3003031.ref009","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1002\/wdev.290","article-title":"RNA on the brain: emerging layers of post-transcriptional regulation in cerebral cortex development","volume":"7","author":"AL Lennox","year":"2018","journal-title":"Wiley Interdiscip Rev Dev Biol"},{"issue":"3","key":"pbio.3003031.ref010","doi-asserted-by":"crossref","first-page":"dev188276","DOI":"10.1242\/dev.188276","article-title":"Post-transcriptional regulation by the exosome complex is required for cell survival and forebrain development via repression of P53 signaling","volume":"148","author":"PA Ulmke","year":"2021","journal-title":"Development"},{"issue":"8","key":"pbio.3003031.ref011","doi-asserted-by":"crossref","first-page":"1773","DOI":"10.1038\/mp.2017.173","article-title":"A Upf3b-mutant mouse model with behavioral and neurogenesis defects","volume":"23","author":"L Huang","year":"2018","journal-title":"Mol Psychiatry"},{"issue":"12","key":"pbio.3003031.ref012","doi-asserted-by":"crossref","first-page":"715","DOI":"10.1038\/s41583-018-0079-z","article-title":"Nonsense-mediated RNA decay in the brain: emerging modulator of neural development and disease","volume":"19","author":"SR Jaffrey","year":"2018","journal-title":"Nat Rev Neurosci"},{"issue":"1","key":"pbio.3003031.ref013","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1186\/s13059-021-02530-9","article-title":"NMD abnormalities during brain development in the Fmr1-knockout mouse model of fragile X syndrome","volume":"22","author":"T Kurosaki","year":"2021","journal-title":"Genome Biol"},{"issue":"4","key":"pbio.3003031.ref014","doi-asserted-by":"crossref","first-page":"748","DOI":"10.1016\/j.celrep.2014.01.028","article-title":"Posttranscriptional control of the stem cell and neurogenic programs by the nonsense-mediated RNA decay pathway","volume":"6","author":"CH Lou","year":"2014","journal-title":"Cell Rep"},{"issue":"9","key":"pbio.3003031.ref015","doi-asserted-by":"crossref","first-page":"1127","DOI":"10.1038\/ng2100","article-title":"Mutations in UPF3B, a member of the nonsense-mediated mRNA decay complex, cause syndromic and nonsyndromic mental retardation","volume":"39","author":"PS Tarpey","year":"2007","journal-title":"Nat Genet"},{"issue":"13","key":"pbio.3003031.ref016","doi-asserted-by":"crossref","first-page":"2157","DOI":"10.1016\/j.neuron.2024.04.006","article-title":"Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size","volume":"112","author":"L Lin","year":"2024","journal-title":"Neuron"},{"issue":"5594","key":"pbio.3003031.ref017","doi-asserted-by":"crossref","first-page":"840","DOI":"10.1126\/science.1074560","article-title":"Oscillatory expression of the bHLH factor Hes1 regulated by a negative feedback loop","volume":"298","author":"H Hirata","year":"2002","journal-title":"Science"},{"issue":"1","key":"pbio.3003031.ref018","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1016\/j.celrep.2012.05.017","article-title":"MicroRNA-9 Modulates Hes1 ultradian oscillations by forming a double-negative feedback loop","volume":"2","author":"B Bonev","year":"2012","journal-title":"Cell Rep"},{"issue":"4","key":"pbio.3003031.ref019","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1016\/j.cell.2017.09.003","article-title":"Temporal Control of Mammalian Cortical Neurogenesis by m(6)A Methylation.","volume":"171","author":"KJ Yoon","year":"2017","journal-title":"Cell"},{"issue":"4","key":"pbio.3003031.ref020","doi-asserted-by":"crossref","first-page":"438","DOI":"10.1002\/wrna.1332","article-title":"The Ccr4-Not complex is a key regulator of eukaryotic gene expression","volume":"7","author":"MA Collart","year":"2016","journal-title":"Wiley Interdiscip Rev RNA"},{"issue":"11","key":"pbio.3003031.ref021","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1038\/nsmb.2681","article-title":"Structure and assembly of the NOT module of the human CCR4-NOT complex","volume":"20","author":"A Boland","year":"2013","journal-title":"Nat Struct Mol Biol"},{"issue":"1","key":"pbio.3003031.ref022","doi-asserted-by":"crossref","first-page":"3173","DOI":"10.1038\/s41467-019-11094-z","article-title":"Reconstitution of recombinant human CCR4-NOT reveals molecular insights into regulated deadenylation.","volume":"10","author":"T Raisch","year":"2019","journal-title":"Nat Commun"},{"issue":"8","key":"pbio.3003031.ref023","doi-asserted-by":"crossref","first-page":"1978","DOI":"10.1016\/j.celrep.2016.10.066","article-title":"Reconstitution of Targeted Deadenylation by the Ccr4-Not Complex and the YTH Domain Protein Mmi1","volume":"17","author":"JAW Stowell","year":"2016","journal-title":"Cell Rep"},{"key":"pbio.3003031.ref024","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1016\/j.seizure.2023.03.022","article-title":"A novel pathogenic variant in CNOT3 causing neurodevelopmental delay and epilepsy.","volume":"107","author":"J Lv","year":"2023","journal-title":"Seizure."},{"issue":"11","key":"pbio.3003031.ref025","doi-asserted-by":"crossref","first-page":"1677","DOI":"10.1038\/s41431-019-0413-6","article-title":"De novo variants in CNOT3 cause a variable neurodevelopmental disorder","volume":"27","author":"R Martin","year":"2019","journal-title":"Eur J Hum Genet"},{"issue":"4","key":"pbio.3003031.ref026","doi-asserted-by":"crossref","first-page":"408","DOI":"10.1111\/cge.13819","article-title":"Inherited cases of CNOT3-associated intellectual developmental disorder with speech delay, autism, and dysmorphic facies","volume":"98","author":"R Meyer","year":"2020","journal-title":"Clin Genet"},{"issue":"7","key":"pbio.3003031.ref027","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.3390\/genes12071009","article-title":"Co-Occurring Heterozygous CNOT3 and SMAD6 Truncating Variants: Unusual Presentation and Refinement of the IDDSADF Phenotype.","volume":"12","author":"M Priolo","year":"2021","journal-title":"Genes (Basel)"},{"issue":"2","key":"pbio.3003031.ref028","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1007\/s10048-023-00713-z","article-title":"Clinical features of CNOT3-associated neurodevelopmental disorder in three Chinese patients","volume":"24","author":"P Zhao","year":"2023","journal-title":"Neurogenetics"},{"issue":"1","key":"pbio.3003031.ref029","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1016\/j.ajhg.2020.05.017","article-title":"De Novo Variants in CNOT1, a Central Component of the CCR4-NOT Complex Involved in Gene Expression and RNA and Protein Stability, Cause Neurodevelopmental Delay","volume":"107","author":"L Vissers","year":"2020","journal-title":"Am J Hum Genet"},{"issue":"5","key":"pbio.3003031.ref030","doi-asserted-by":"crossref","first-page":"990","DOI":"10.1016\/j.ajhg.2019.03.017","article-title":"A CCR4-NOT Transcription Complex, Subunit 1, CNOT1, Variant Associated with Holoprosencephaly","volume":"104","author":"P Kruszka","year":"2019","journal-title":"Am J Hum Genet"},{"issue":"516","key":"pbio.3003031.ref031","doi-asserted-by":"crossref","DOI":"10.1126\/scisignal.aan3638","article-title":"The CCR4-NOT deadenylase complex controls Atg7-dependent cell death and heart function","volume":"11","author":"T Yamaguchi","year":"2018","journal-title":"Sci Signal"},{"issue":"1","key":"pbio.3003031.ref032","doi-asserted-by":"crossref","first-page":"1500","DOI":"10.1038\/s41598-017-01628-0","article-title":"Cnot3 enhances human embryonic cardiomyocyte proliferation by promoting cell cycle inhibitor mRNA degradation","volume":"7","author":"B Zhou","year":"2017","journal-title":"Sci Rep"},{"issue":"5","key":"pbio.3003031.ref033","doi-asserted-by":"crossref","first-page":"897","DOI":"10.1016\/j.stemcr.2016.09.007","article-title":"CNOT3-Dependent mRNA Deadenylation Safeguards the Pluripotent State.","volume":"7","author":"X Zheng","year":"2016","journal-title":"Stem Cell Reports"},{"issue":"5","key":"pbio.3003031.ref034","doi-asserted-by":"crossref","first-page":"910","DOI":"10.1002\/stem.1070","article-title":"Cnot1, Cnot2, and Cnot3 maintain mouse and human ESC identity and inhibit extraembryonic differentiation","volume":"30","author":"X Zheng","year":"2012","journal-title":"Stem Cells"},{"key":"pbio.3003031.ref035","article-title":"Cnot3 is required for male germ cell development and spermatogonial stem cell maintenance.","author":"Q Chen","year":"2023","journal-title":"bioRxiv"},{"issue":"12","key":"pbio.3003031.ref036","doi-asserted-by":"crossref","first-page":"1198","DOI":"10.1038\/nmeth.4435","article-title":"Thiol-linked alkylation of RNA to assess expression dynamics","volume":"14","author":"VA Herzog","year":"2017","journal-title":"Nat Methods"},{"issue":"20","key":"pbio.3003031.ref037","doi-asserted-by":"crossref","first-page":"4843","DOI":"10.1242\/dev.129.20.4843","article-title":"Asymmetric Numb distribution is critical for asymmetric cell division of mouse cerebral cortical stem cells and neuroblasts","volume":"129","author":"Q Shen","year":"2002","journal-title":"Development"},{"key":"pbio.3003031.ref038","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/s13064-015-0038-6","article-title":"Dynamic regulation of mRNA decay during neural development","volume":"10","author":"DA Burow","year":"2015","journal-title":"Neural Dev"},{"key":"pbio.3003031.ref039","doi-asserted-by":"crossref","first-page":"458","DOI":"10.1038\/msb.2010.112","article-title":"Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast","volume":"7","author":"C Miller","year":"2011","journal-title":"Mol Syst Biol"},{"issue":"7347","key":"pbio.3003031.ref040","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1038\/nature10098","article-title":"Global quantification of mammalian gene expression control","volume":"473","author":"B Schwanhausser","year":"2011","journal-title":"Nature"},{"issue":"9","key":"pbio.3003031.ref041","doi-asserted-by":"crossref","first-page":"R93","DOI":"10.1186\/gb-2010-11-9-r93","article-title":"Genome-wide analysis of mRNA decay patterns during early Drosophila development","volume":"11","author":"S Thomsen","year":"2010","journal-title":"Genome Biol"},{"issue":"9","key":"pbio.3003031.ref042","doi-asserted-by":"crossref","first-page":"814","DOI":"10.1038\/s41594-020-0465-x","article-title":"Decoding mRNA translatability and stability from the 5\u2019 UTR","volume":"27","author":"L Jia","year":"2020","journal-title":"Nat Struct Mol Biol"},{"issue":"10","key":"pbio.3003031.ref043","doi-asserted-by":"crossref","first-page":"a034728","DOI":"10.1101\/cshperspect.a034728","article-title":"What Are 3\u2019 UTRs Doing?","volume":"11","author":"C. Mayr","year":"2019","journal-title":"Cold Spring Harb Perspect Biol"},{"issue":"4","key":"pbio.3003031.ref044","doi-asserted-by":"crossref","first-page":"e24","DOI":"10.1093\/nar\/gkab1185","article-title":"Analysis of subcellular transcriptomes by RNA proximity labeling with Halo-seq","volume":"50","author":"KL Engel","year":"2022","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"pbio.3003031.ref045","doi-asserted-by":"crossref","first-page":"1670","DOI":"10.1073\/pnas.83.6.1670","article-title":"Identification of a common nucleotide sequence in the 3\u2019-untranslated region of mRNA molecules specifying inflammatory mediators","volume":"83","author":"D Caput","year":"1986","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"19","key":"pbio.3003031.ref046","doi-asserted-by":"crossref","first-page":"2087","DOI":"10.15252\/embj.201694699","article-title":"Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition","volume":"35","author":"AA Bazzini","year":"2016","journal-title":"EMBO J"},{"issue":"7","key":"pbio.3003031.ref047","doi-asserted-by":"crossref","first-page":"1704","DOI":"10.1016\/j.celrep.2018.07.039","article-title":"Attenuated Codon Optimality Contributes to Neural-Specific mRNA Decay in Drosophila","volume":"24","author":"DA Burow","year":"2018","journal-title":"Cell Rep"},{"issue":"2","key":"pbio.3003031.ref048","doi-asserted-by":"crossref","first-page":"e0228730","DOI":"10.1371\/journal.pone.0228730","article-title":"Codon and amino acid content are associated with mRNA stability in mammalian cells.","volume":"15","author":"ME Forrest","year":"2020","journal-title":"PLoS ONE."},{"issue":"12","key":"pbio.3003031.ref049","doi-asserted-by":"crossref","first-page":"1751","DOI":"10.1261\/rna.073239.119","article-title":"Coding regions affect mRNA stability in human cells","volume":"25","author":"A Narula","year":"2019","journal-title":"RNA"},{"issue":"6","key":"pbio.3003031.ref050","doi-asserted-by":"crossref","first-page":"1111","DOI":"10.1016\/j.cell.2015.02.029","article-title":"Codon optimality is a major determinant of mRNA stability","volume":"160","author":"V Presnyak","year":"2015","journal-title":"Cell"},{"key":"pbio.3003031.ref051","doi-asserted-by":"crossref","first-page":"e45396","DOI":"10.7554\/eLife.45396","article-title":"Translation affects mRNA stability in a codon-dependent manner in human cells.","volume":"8","author":"Q Wu","year":"2019","journal-title":"Elife."},{"issue":"3","key":"pbio.3003031.ref052","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1016\/j.tig.2019.12.007","article-title":"Molecular Mechanisms Driving mRNA Degradation by m(6)A Modification.","volume":"36","author":"Y Lee","year":"2020","journal-title":"Trends Genet"},{"issue":"18","key":"pbio.3003031.ref053","doi-asserted-by":"crossref","first-page":"2598","DOI":"10.1093\/bioinformatics\/btu333","article-title":"Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series","volume":"30","author":"MJ Nueda","year":"2014","journal-title":"Bioinformatics"},{"issue":"6488","key":"pbio.3003031.ref054","doi-asserted-by":"crossref","DOI":"10.1126\/science.aay6912","article-title":"The Ccr4-Not complex monitors the translating ribosome for codon optimality","volume":"368","author":"R Buschauer","year":"2020","journal-title":"Science"},{"issue":"15","key":"pbio.3003031.ref055","doi-asserted-by":"crossref","first-page":"6309","DOI":"10.1523\/JNEUROSCI.22-15-06309.2002","article-title":"Cortical excitatory neurons and glia, but not GABAergic neurons, are produced in the Emx1-expressing lineage","volume":"22","author":"JA Gorski","year":"2002","journal-title":"J Neurosci"},{"issue":"12","key":"pbio.3003031.ref056","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1002\/dvg.20256","article-title":"Genetic targeting of principal neurons in neocortex and hippocampus of NEX-Cre mice","volume":"44","author":"S Goebbels","year":"2006","journal-title":"Genesis"},{"key":"pbio.3003031.ref057","first-page":"150","article-title":"The exon junction complex component EIF4A3 is essential for mouse and human cortical progenitor mitosis and neurogenesis","author":"BM Lupan","year":"2023","journal-title":"Development"},{"issue":"9","key":"pbio.3003031.ref058","doi-asserted-by":"crossref","first-page":"e1006282","DOI":"10.1371\/journal.pgen.1006282","article-title":"Haploinsufficiency for Core Exon Junction Complex Components Disrupts Embryonic Neurogenesis and Causes p53-Mediated Microcephaly.","volume":"12","author":"H Mao","year":"2016","journal-title":"PLoS Genet"},{"issue":"3","key":"pbio.3003031.ref059","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1093\/hmg\/ddy350","article-title":"p53 deletion rescues lethal microcephaly in a mouse model with neural stem cell abscission defects","volume":"28","author":"JN Little","year":"2019","journal-title":"Hum Mol Genet"},{"issue":"1","key":"pbio.3003031.ref060","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1016\/j.ydbio.2006.08.035","article-title":"Pax6 controls cerebral cortical cell number by regulating exit from the cell cycle and specifies cortical cell identity by a cell autonomous mechanism","volume":"302","author":"JC Quinn","year":"2007","journal-title":"Dev Biol"},{"issue":"9","key":"pbio.3003031.ref061","doi-asserted-by":"crossref","first-page":"6046","DOI":"10.1523\/JNEUROSCI.15-09-06046.1995","article-title":"The cell cycle of the pseudostratified ventricular epithelium of the embryonic murine cerebral wall","volume":"15","author":"T Takahashi","year":"1995","journal-title":"J Neurosci"},{"issue":"6","key":"pbio.3003031.ref062","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1016\/j.cub.2015.01.041","article-title":"Human-chimpanzee differences in a FZD8 enhancer alter cell-cycle dynamics in the developing neocortex","volume":"25","author":"JL Boyd","year":"2015","journal-title":"Curr Biol"},{"key":"pbio.3003031.ref063","doi-asserted-by":"crossref","first-page":"e78203","DOI":"10.7554\/eLife.78203","article-title":"Aberrant cortical development is driven by impaired cell cycle and translational control in a DDX3X syndrome model.","volume":"11","author":"ML Hoye","year":"2022","journal-title":"Elife."},{"issue":"1","key":"pbio.3003031.ref064","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1016\/j.neuron.2015.12.007","article-title":"Prolonged Mitosis of Neural Progenitors Alters Cell Fate in the Developing Brain","volume":"89","author":"LJ Pilaz","year":"2016","journal-title":"Neuron"},{"issue":"9","key":"pbio.3003031.ref065","doi-asserted-by":"crossref","first-page":"1314","DOI":"10.1038\/s41594-023-01075-8","article-title":"Specific recognition and ubiquitination of translating ribosomes by mammalian CCR4-NOT","volume":"30","author":"E Absmeier","year":"2023","journal-title":"Nat Struct Mol Biol"},{"issue":"2","key":"pbio.3003031.ref066","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1016\/j.devcel.2007.11.014","article-title":"The kinesin-8 motor Kif18A suppresses kinetochore movements to control mitotic chromosome alignment","volume":"14","author":"J Stumpff","year":"2008","journal-title":"Dev Cell"},{"issue":"6","key":"pbio.3003031.ref067","doi-asserted-by":"crossref","first-page":"1503","DOI":"10.1016\/S1097-2765(03)00179-5","article-title":"Identification of transcription factor KLF8 as a downstream target of focal adhesion kinase in its regulation of cyclin D1 and cell cycle progression","volume":"11","author":"J Zhao","year":"2003","journal-title":"Mol Cell"},{"key":"pbio.3003031.ref068","doi-asserted-by":"crossref","first-page":"e10288","DOI":"10.7554\/eLife.10288","article-title":"An extensive program of periodic alternative splicing linked to cell cycle progression","volume":"5","author":"D Dominguez","year":"2016","journal-title":"Elife"},{"issue":"21","key":"pbio.3003031.ref069","doi-asserted-by":"crossref","first-page":"3883","DOI":"10.1242\/dev.005447","article-title":"Divergent roles of ApoER2 and Vldlr in the migration of cortical neurons","volume":"134","author":"I Hack","year":"2007","journal-title":"Development"},{"issue":"6482","key":"pbio.3003031.ref070","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.1126\/science.aax3072","article-title":"Sequencing metabolically labeled transcripts in single cells reveals mRNA turnover strategies","volume":"367","author":"N Battich","year":"2020","journal-title":"Science"},{"issue":"1","key":"pbio.3003031.ref071","doi-asserted-by":"crossref","first-page":"3104","DOI":"10.1038\/s41467-024-47290-9","article-title":"Cell-type-specific mRNA transcription and degradation kinetics in zebrafish embryogenesis from metabolically labeled single-cell RNA-seq.","volume":"15","author":"L Fishman","year":"2024","journal-title":"Nat Commun."},{"issue":"9","key":"pbio.3003031.ref072","doi-asserted-by":"crossref","first-page":"1465","DOI":"10.1084\/jem.20150384","article-title":"CNOT3 contributes to early B cell development by controlling Igh rearrangement and p53 mRNA stability","volume":"212","author":"T Inoue","year":"2015","journal-title":"J Exp Med"},{"key":"pbio.3003031.ref073","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1016\/j.conb.2020.10.001","article-title":"Decoding mixed messages in the developing cortex: translational regulation of neural progenitor fate","volume":"66","author":"ML Hoye","year":"2021","journal-title":"Curr Opin Neurobiol"},{"issue":"14","key":"pbio.3003031.ref074","doi-asserted-by":"crossref","first-page":"2580","DOI":"10.1038\/s41388-018-0603-7","article-title":"CNOT3 targets negative cell cycle regulators in non-small cell lung cancer development","volume":"38","author":"YT Shirai","year":"2019","journal-title":"Oncogene"},{"issue":"2","key":"pbio.3003031.ref075","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1016\/j.bbrc.2012.02.007","article-title":"Involvement of CNOT3 in mitotic progression through inhibition of MAD1 expression","volume":"419","author":"A Takahashi","year":"2012","journal-title":"Biochem Biophys Res Commun"},{"issue":"6","key":"pbio.3003031.ref076","doi-asserted-by":"crossref","first-page":"1089","DOI":"10.1016\/j.molcel.2018.05.033","article-title":"mRNA Deadenylation Is Coupled to Translation Rates by the Differential Activities of Ccr4-Not Nucleases","volume":"70","author":"MW Webster","year":"2018","journal-title":"Mol Cell"},{"issue":"7896","key":"pbio.3003031.ref077","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1038\/s41586-021-04358-6","article-title":"Autism genes converge on asynchronous development of shared neuron classes","volume":"602","author":"B Paulsen","year":"2022","journal-title":"Nature"},{"issue":"5","key":"pbio.3003031.ref078","doi-asserted-by":"crossref","first-page":"997","DOI":"10.1016\/j.cell.2013.10.020","article-title":"Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism","volume":"155","author":"AJ Willsey","year":"2013","journal-title":"Cell"},{"issue":"8","key":"pbio.3003031.ref079","doi-asserted-by":"crossref","first-page":"994","DOI":"10.1101\/gad.14.8.994","article-title":"Induction of medulloblastomas in p53-null mutant mice by somatic inactivation of Rb in the external granular layer cells of the cerebellum","volume":"14","author":"S Marino","year":"2000","journal-title":"Genes Dev"},{"issue":"1","key":"pbio.3003031.ref080","doi-asserted-by":"crossref","first-page":"16878","DOI":"10.1038\/s41598-017-17204-5","article-title":"QuPath: Open source software for digital pathology image analysis.","volume":"7","author":"P Bankhead","year":"2017","journal-title":"Sci Rep"},{"issue":"16","key":"pbio.3003031.ref081","doi-asserted-by":"crossref","first-page":"3439","DOI":"10.1093\/bioinformatics\/bti525","article-title":"BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis","volume":"21","author":"S Durinck","year":"2005","journal-title":"Bioinformatics"},{"issue":"3","key":"pbio.3003031.ref082","doi-asserted-by":"crossref","first-page":"31","DOI":"10.3390\/biotech11030031","article-title":"Bio-Strings: A Relational Database Data-Type for Dealing with Large Biosequences.","volume":"11","author":"S Lifschitz","year":"2022","journal-title":"BioTech (Basel)."},{"issue":"12","key":"pbio.3003031.ref083","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"MI Love","year":"2014","journal-title":"Genome Biol"},{"issue":"2","key":"pbio.3003031.ref084","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1038\/s41587-023-01767-y","article-title":"Dictionary learning for integrative, multimodal and scalable single-cell analysis","volume":"42","author":"Y Hao","year":"2024","journal-title":"Nat Biotechnol"},{"issue":"5\u20136","key":"pbio.3003031.ref085","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1159\/000507113","article-title":"Acute Lengthening of Progenitor Mitosis Influences Progeny Fate during Cortical Development in vivo","volume":"41","author":"A Mitchell-Dick","year":"2019","journal-title":"Dev Neurosci"},{"issue":"1","key":"pbio.3003031.ref086","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"A Dobin","year":"2013","journal-title":"Bioinformatics"},{"issue":"7","key":"pbio.3003031.ref087","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","article-title":"featureCounts: an efficient general purpose program for assigning sequence reads to genomic features","volume":"30","author":"Y Liao","year":"2014","journal-title":"Bioinformatics"}],"updated-by":[{"DOI":"10.1371\/journal.pbio.3003031","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,2,19]],"date-time":"2025-02-19T00:00:00Z","timestamp":1739923200000}}],"container-title":["PLOS Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pbio.3003031","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,19]],"date-time":"2025-02-19T13:37:26Z","timestamp":1739972246000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pbio.3003031"}},"subtitle":[],"editor":[{"given":"Bassem A.","family":"Hassan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,2,6]]},"references-count":87,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2025,2,6]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pbio.3003031","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2024.07.22.604643","asserted-by":"object"}]},"ISSN":["1545-7885"],"issn-type":[{"value":"1545-7885","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,2,6]]}}}