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BPTF functions within nucleosome and remodeling factor (NURF), a complex comprising sucrose non-fermenting like (SNF2L), an Imitation SWItching (ISWI) chromatin remodeling protein encoded by the SWI\/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 (SMARCA1) gene. Surprisingly, ablation of Smarca1 resulted in mice with enlarged brains, a direct contrast to the phenotype of NEDDFL patients. To model the NEDDFL syndrome, we generated forebrain-specific Bptf knockout (Bptf conditional Knockout (cKO)) mice. The Bptf cKO mice were born in normal Mendelian ratios, survived to adulthood but were smaller in size with severe cortical hypoplasia. Prolonged progenitor cell cycle length and a high incidence of cell death reduced the neuronal output. Cortical lamination was also disrupted with reduced proportions of deep layer neurons, and neuronal maturation defects that impaired the acquisition of distinct cell fates (e.g. COUP-TF-interacting protein 2 (Ctip2)+ neurons). RNAseq and pathway analysis identified altered expression of fate-determining transcription factors and the biological pathways involved in neural development, apoptotic signaling and amino acid biosynthesis. Dysregulated genes were enriched for MYC Proto-Oncogene, BHLH Transcription Factor (Myc)-binding sites, a known BPTF transcriptional cofactor. We propose the Bptf cKO mouse as a valuable model for further study of the NEDDFL syndrome.<\/jats:p>","DOI":"10.1093\/hmg\/ddac119","type":"journal-article","created":{"date-parts":[[2022,5,23]],"date-time":"2022-05-23T14:16:35Z","timestamp":1653315395000},"page":"3405-3421","source":"Crossref","is-referenced-by-count":11,"title":["Generation of a mouse model of the neurodevelopmental disorder with dysmorphic facies and distal limb anomalies syndrome"],"prefix":"10.1093","volume":"31","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3721-0488","authenticated-orcid":false,"given":"Gerardo","family":"Zapata","sequence":"first","affiliation":[{"name":"Regenerative Medicine Program , Ottawa Hospital Research Institute, Ottawa, Ontario K1H 8L6 , Canada"},{"name":"Departments of Biochemistry , Microbiology and Immunology, University of Ottawa, Ottawa, Ontario K1H8M5 , Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keqin","family":"Yan","sequence":"additional","affiliation":[{"name":"Regenerative Medicine Program , Ottawa Hospital Research Institute, Ottawa, Ontario K1H 8L6 , Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9227-2016","authenticated-orcid":false,"given":"David J","family":"Picketts","sequence":"additional","affiliation":[{"name":"Regenerative Medicine Program , Ottawa Hospital Research Institute, Ottawa, Ontario K1H 8L6 , Canada"},{"name":"Departments of Biochemistry , Microbiology and Immunology, University of Ottawa, Ottawa, Ontario K1H8M5 , Canada"},{"name":"Departments of Biochemistry , Microbiology and Immunology, Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario K1H8M5 , Canada"},{"name":"Department of Medicine , University of Ottawa, Ottawa, Ontario K1H8M5 , Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,5,23]]},"reference":[{"key":"2022101308120314400_ref1","doi-asserted-by":"crossref","first-page":"105055","DOI":"10.1016\/j.neuint.2021.105055","article-title":"Chromatin remodelling complexes in cerebral cortex development and neurodevelopmental disorders","volume":"147","author":"D'Souza","year":"2021","journal-title":"Neurochem. 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Commun."},{"key":"2022101308120314400_ref25","doi-asserted-by":"crossref","first-page":"3795","DOI":"10.1172\/JCI81979","article-title":"ZIC2-dependent OCT4 activation drives self-renewal of human liver cancer stem cells","volume":"125","author":"Zhu","year":"2015","journal-title":"J. Clin. Invest."},{"key":"2022101308120314400_ref26","doi-asserted-by":"crossref","first-page":"e1000241","DOI":"10.1371\/journal.pgen.1000241","article-title":"Essential role of chromatin remodeling protein Bptf in early mouse embryos and embryonic stem cells","volume":"4","author":"Landry","year":"2008","journal-title":"PLoS Genet."},{"key":"2022101308120314400_ref27","doi-asserted-by":"crossref","first-page":"6819","DOI":"10.1128\/MCB.01058-08","article-title":"Transcriptional regulator BPTF\/FAC1 is essential for trophoblast differentiation during early mouse development","volume":"28","author":"Goller","year":"2008","journal-title":"Mol. Cell. Biol."},{"key":"2022101308120314400_ref28","doi-asserted-by":"crossref","first-page":"4181","DOI":"10.1038\/ncomms5181","article-title":"Snf2h-mediated chromatin organization and histone H1 dynamics govern cerebellar morphogenesis and neural maturation","volume":"5","author":"Alvarez-Saavedra","year":"2014","journal-title":"Nat. Commun."},{"key":"2022101308120314400_ref29","doi-asserted-by":"crossref","first-page":"258","DOI":"10.1172\/JCI200522329","article-title":"The chromatin-remodeling protein ATRX is critical for neuronal survival during corticogenesis","volume":"115","author":"Berube","year":"2005","journal-title":"J. Clin. Invest."},{"key":"2022101308120314400_ref30","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":"Gorski","year":"2002","journal-title":"J. Neurosci."},{"key":"2022101308120314400_ref31","doi-asserted-by":"crossref","first-page":"33878","DOI":"10.18632\/oncotarget.5302","article-title":"BPTF promotes tumor growth and predicts poor prognosis in lung adenocarcinomas","volume":"6","author":"Dai","year":"2015","journal-title":"Oncotarget"},{"key":"2022101308120314400_ref32","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1186\/s12974-019-1530-4","article-title":"C3aR signaling and gliosis in response to neurodevelopmental damage in the cerebellum","volume":"16","author":"Young","year":"2019","journal-title":"J. Neuroinflammation"},{"key":"2022101308120314400_ref33","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1016\/j.conb.2008.05.006","article-title":"The determination of projection neuron identity in the developing cerebral cortex","volume":"18","author":"Leone","year":"2008","journal-title":"Curr. Opin. Neurobiol."},{"key":"2022101308120314400_ref34","doi-asserted-by":"crossref","first-page":"274","DOI":"10.3389\/fnins.2015.00274","article-title":"Switching modes in corticogenesis: mechanisms of neuronal subtype transitions and integration in the cerebral cortex","volume":"9","author":"Toma","year":"2015","journal-title":"Front. Neurosci."},{"key":"2022101308120314400_ref35","doi-asserted-by":"crossref","first-page":"e4934","DOI":"10.1073\/pnas.1701495114","article-title":"Neurog2 and Ascl1 together regulate a postmitotic derepression circuit to govern laminar fate specification in the murine neocortex","volume":"114","author":"Dennis","year":"2017","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"2022101308120314400_ref36","doi-asserted-by":"crossref","first-page":"243","DOI":"10.3389\/fnmol.2019.00243","article-title":"Snf2h drives chromatin remodeling to prime upper layer cortical neuron development","volume":"12","author":"Alvarez-Saavedra","year":"2019","journal-title":"Front. Mol. Neurosci."},{"key":"2022101308120314400_ref37","doi-asserted-by":"crossref","first-page":"e2220","DOI":"10.1038\/cddis.2016.121","article-title":"Stalled replication forks within heterochromatin require ATRX for protection","volume":"7","author":"Huh","year":"2016","journal-title":"Cell Death Dis."},{"key":"2022101308120314400_ref38","doi-asserted-by":"crossref","first-page":"11382","DOI":"10.1073\/pnas.0804918105","article-title":"The Fezf2-Ctip2 genetic pathway regulates the fate choice of subcortical projection neurons in the developing cerebral cortex","volume":"105","author":"Chen","year":"2008","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"2022101308120314400_ref39","doi-asserted-by":"crossref","first-page":"16021","DOI":"10.1073\/pnas.0806791105","article-title":"SOX5 postmitotically regulates migration, postmigratory differentiation, and projections of subplate and deep-layer neocortical neurons","volume":"105","author":"Kwan","year":"2008","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"2022101308120314400_ref40","doi-asserted-by":"crossref","first-page":"19071","DOI":"10.1073\/pnas.1216793109","article-title":"A network of genetic repression and derepression specifies projection fates in the developing neocortex","volume":"109","author":"Srinivasan","year":"2012","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"2022101308120314400_ref41","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1523\/JNEUROSCI.4131-10.2011","article-title":"Tbr1 and Fezf2 regulate alternate corticofugal neuronal identities during neocortical development","volume":"31","author":"McKenna","year":"2011","journal-title":"J. Neurosci."},{"key":"2022101308120314400_ref42","doi-asserted-by":"crossref","first-page":"364","DOI":"10.1016\/j.neuron.2007.12.012","article-title":"Satb2 regulates callosal projection neuron identity in the developing cerebral cortex","volume":"57","author":"Alcamo","year":"2008","journal-title":"Neuron"},{"key":"2022101308120314400_ref43","doi-asserted-by":"crossref","first-page":"e1152346","DOI":"10.1080\/23723556.2016.1152346","article-title":"c-MYC partners with BPTF in human cancer","volume":"3","author":"Richart","year":"2016","journal-title":"Mol. Cell. Oncol."},{"key":"2022101308120314400_ref44","first-page":"987","volume":"G3 (Bethesda)","author":"Kwon","year":"2012","journal-title":"oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets"},{"key":"2022101308120314400_ref45","doi-asserted-by":"crossref","first-page":"226","DOI":"10.3389\/fnins.2018.00226","article-title":"ATP-dependent chromatin remodeling during cortical neurogenesis","volume":"12","author":"Sokpor","year":"2018","journal-title":"Front. Neurosci."},{"key":"2022101308120314400_ref46","doi-asserted-by":"crossref","first-page":"256","DOI":"10.1016\/j.devcel.2013.04.005","article-title":"Chromatin regulation by BAF170 controls cerebral cortical size and thickness","volume":"25","author":"Tuoc","year":"2013","journal-title":"Dev. Cell"},{"key":"2022101308120314400_ref47","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1016\/j.devcel.2015.11.005","article-title":"A dynamic unfolded protein response contributes to the control of cortical neurogenesis","volume":"35","author":"Laguesse","year":"2015","journal-title":"Dev. Cell"},{"key":"2022101308120314400_ref48","doi-asserted-by":"crossref","first-page":"4011","DOI":"10.1002\/jcp.29297","article-title":"c-Myc controls the fate of neural progenitor cells during cerebral cortex development","volume":"235","author":"Wang","year":"2020","journal-title":"J. Cell. Physiol."},{"key":"2022101308120314400_ref49","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1523\/JNEUROSCI.0899-12.2013","article-title":"Neuronal basic helix-loop-helix proteins Neurod2\/6 regulate cortical commissure formation before midline interactions","volume":"33","author":"Bormuth","year":"2013","journal-title":"J. Neurosci."},{"key":"2022101308120314400_ref50","doi-asserted-by":"crossref","first-page":"dev157719","DOI":"10.1242\/dev.157719","article-title":"A non-canonical role for the proneural gene Neurog1 as a negative regulator of neocortical neurogenesis","volume":"145","author":"Han","year":"2018","journal-title":"Development"},{"key":"2022101308120314400_ref51","doi-asserted-by":"crossref","first-page":"662774","DOI":"10.3389\/fnmol.2021.662774","article-title":"The role of neurod genes in brain development, function, and disease","volume":"14","author":"Tutukova","year":"2021","journal-title":"Front. Mol. Neurosci."},{"key":"2022101308120314400_ref52","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1002\/jnr.22182","article-title":"NeuroD6 genomic signature bridging neuronal differentiation to survival via the molecular chaperone network","volume":"88","author":"Uittenbogaard","year":"2010","journal-title":"J. Neurosci. Res."},{"key":"2022101308120314400_ref53","doi-asserted-by":"crossref","first-page":"109269","DOI":"10.1016\/j.celrep.2021.109269","article-title":"Transcriptional repression by FEZF2 restricts alternative identities of cortical projection neurons","volume":"35","author":"Tsyporin","year":"2021","journal-title":"Cell Rep."},{"key":"2022101308120314400_ref54","doi-asserted-by":"crossref","first-page":"3546","DOI":"10.1073\/pnas.1108718109","article-title":"Protooncogene Ski cooperates with the chromatin-remodeling factor Satb2 in specifying callosal neurons","volume":"109","author":"Baranek","year":"2012","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"2022101308120314400_ref55","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1093\/hmg\/ddab081","article-title":"Transgenic mice with an R342X mutation in Phf6 display clinical features of Borjeson-Forssman-Lehmann Syndrome","volume":"30","author":"Ahmed","year":"2021","journal-title":"Hum. Mol. Genet."},{"key":"2022101308120314400_ref56","doi-asserted-by":"crossref","first-page":"1338","DOI":"10.12688\/f1000research.15931.1","article-title":"FastQ screen: a tool for multi-genome mapping and quality control","volume":"7","author":"Wingett","year":"2018","journal-title":"F1000Res"},{"key":"2022101308120314400_ref57","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"2022101308120314400_ref58","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.3317","article-title":"HISAT: a fast spliced aligner with low memory requirements","volume":"12","author":"Kim","year":"2015","journal-title":"Nat. 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