Morgan, D. O. The Cell Cycle: Principles of Control (New Science Press, 2007).
Orr-Weaver, T. L. When bigger is better: the role of polyploidy in organogenesis. Trends Genet. 31, 307–315 (2015).
Choksi, S. P., Lauter, G., Swoboda, P. & Roy, S. Switching on cilia: transcriptional networks regulating ciliogenesis. Development 141, 1427–1441 (2014).
Spassky, N. & Meunier, A. The development and functions of multiciliated epithelia. Nat. Rev. Mol. Cell Biol. 18, 423–436 (2017).
Al Jord, A. et al. Calibrated mitotic oscillator drives motile ciliogenesis. Science 358, 803–806 (2017).
Vladar, E. K. et al. Cyclin-dependent kinase control of motile ciliogenesis. eLife 7, e36375 (2018).
Walentek, P. Signaling control of mucociliary epithelia: stem cells, cell fates, and the plasticity of cell identity in development and disease. Cells Tissues Organs 211, 736–753 (2022).
Mahjoub, M. R., Nanjundappa, R. & Harvey, M. N. Development of a multiciliated cell. Curr. Opin. Cell Biol. 77, 102105 (2022).
Tan, F. E. et al. Myb promotes centriole amplification and later steps of the multiciliogenesis program. Development 140, 4277–4286 (2013).
Vladar, E. K. & Stearns, T. Molecular characterization of centriole assembly in ciliated epithelial cells. J. Cell Biol. 178, 31–42 (2007).
Byrnes, L. E., Deleon, R., Reiter, J. F. & Choksi, S. P. Opposing transcription factors MYCL and HEY1 mediate the Notch-dependent airway stem cell fate decision. Preprint at bioRxiv https://doi.org/10.1101/2022.10.05.511009 (2022).
Vladar, E. K. & Brody, S. L. in Methods in Enzymology Vol. 525 (ed. Marshall, W. F.) 285–309 (Academic Press, 2013).
Pan, J.-H. et al. Myb permits multilineage airway epithelial cell differentiation. Stem Cells 32, 3245–3256 (2014).
Lewis, M. & Stracker, T. H. Transcriptional regulation of multiciliated cell differentiation. Semin. Cell Dev. Biol. 110, 51–60 (2021).
Gomes Pereira, S., Dias Louro, M. A. & Bettencourt-Dias, M. Biophysical and quantitative principles of centrosome biogenesis and structure. Annu. Rev. Cell Dev. Biol. 37, 43–63 (2021).
Zhao, H. et al. The Cep63 paralogue Deup1 enables massive de novo centriole biogenesis for vertebrate multiciliogenesis. Nat. Cell Biol. 15, 1434–1444 (2013).
Klos Dehring, D. A. et al. Deuterosome-mediated centriole biogenesis. Dev. Cell 27, 103–112 (2013).
Breslow, D. K. & Holland, A. J. Mechanism and regulation of centriole and cilium biogenesis. Annu. Rev. Biochem. 88, 691–724 (2019).
Gönczy, P. Centrosomes and cancer: revisiting a long-standing relationship. Nat. Rev. Cancer 15, 639–652 (2015).
García, S. R. et al. Novel dynamics of human mucociliary differentiation revealed by single-cell RNA sequencing of nasal epithelial cultures. Development 146, dev177428 (2019).
Ma, L., Quigley, I., Omran, H. & Kintner, C. Multicilin drives centriole biogenesis via E2f proteins. Genes Dev. 28, 1461–1471 (2014).
Kim, S., Ma, L., Shokhirev, M. N., Quigley, I. & Kintner, C. Multicilin and activated E2f4 induce multiciliated cell differentiation in primary fibroblasts. Sci. Rep. 8, 12369 (2018).
Plasschaert, L. W. et al. A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte. Nature 560, 377–381 (2018).
Montoro, D. T. et al. A revised airway epithelial hierarchy includes CFTR-expressing ionocytes. Nature 560, 319–324 (2018).
Zheng, S. C. et al. Universal prediction of cell-cycle position using transfer learning. Genome Biol. 23, 41 (2022).
Grant, G. D., Kedziora, K. M., Limas, J. C., Cook, J. G. & Purvis, J. E. Accurate delineation of cell cycle phase transitions in living cells with PIP-FUCCI. Cell Cycle 17, 2496–2516 (2018).
Choksi, S. P., Babu, D., Lau, D., Yu, X. & Roy, S. Systematic discovery of novel ciliary genes through functional genomics in the zebrafish. Development 141, 3410–3419 (2014).
Rubin, S. M., Sage, J. & Skotheim, J. M. Integrating old and new paradigms of G1/S control. Mol. Cell 80, 183–192 (2020).
Matsushime, H., Roussel, M. F., Ashmun, R. A. & Sherr, C. J. Colony-stimulating factor 1 regulates novel cyclins during the G1 phase of the cell cycle. Cell 65, 701–713 (1991).
Xiong, Y., Connolly, T., Futcher, B. & Beach, D. Human D-type cyclin. Cell 65, 691–699 (1991).
Fassl, A., Geng, Y. & Sicinski, P. CDK4 and CDK6 kinases: from basic science to cancer therapy. Science 375, eabc1495 (2022).
Basant, A. & Glotzer, M. Spatiotemporal regulation of RhoA during cytokinesis. Curr. Biol. 28, R570–R580 (2018).
Funk, M. C. et al. Cyclin O (Ccno) functions during deuterosome-mediated centriole amplification of multiciliated cells. EMBO J. 34, 1078–1089 (2015).
Westendorp, B. et al. E2F7 represses a network of oscillating cell cycle genes to control S-phase progression. Nucleic Acids Res. 40, 3511–3523 (2012).
Li, J. et al. Synergistic function of E2F7 and E2F8 is essential for cell survival and embryonic development. Dev. Cell 14, 62–75 (2008).
Skene, P. J. & Henikoff, S. An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. eLife 6, e21856 (2017).
Fischer, M., Grossmann, P., Padi, M. & DeCaprio, J. A. Integration of TP53, DREAM, MMB-FOXM1 and RB-E2F target gene analyses identifies cell cycle gene regulatory networks. Nucleic Acids Res. 44, 6070–6086 (2016).
Kumar, V. et al. The regulatory roles of motile cilia in CSF circulation and hydrocephalus. Fluids Barriers CNS 18, 31 (2021).
Spektor, A., Tsang, W. Y., Khoo, D. & Dynlacht, B. D. Cep97 and CP110 suppress a cilia assembly program. Cell 130, 678–690 (2007).
Graser, S. et al. Cep164, a novel centriole appendage protein required for primary cilium formation. J. Cell Biol. 179, 321–330 (2007).
Kim, S., Chien, Y.-H., Ryan, A. & Kintner, C. Emi2 enables centriole amplification during multiciliated cell differentiation. Sci. Adv. 8, eabm7538 (2022).
Revinski, D. R. et al. CDC20B is required for deuterosome-mediated centriole production in multiciliated cells. Nat. Commun. 9, 4668 (2018).
Chen, H.-Z. et al. Canonical and atypical E2Fs regulate the mammalian endocycle. Nat. Cell Biol. 14, 1192–1202 (2012).
Lammens, T., Li, J., Leone, G. & De Veylder, L. Atypical E2Fs: new players in the E2F transcription factor family. Trends Cell Biol. 19, 111–118 (2009).
Peterson, N. G. & Fox, D. T. Communal living: the role of polyploidy and syncytia in tissue biology. Chromosome Res. 29, 245–260 (2021).
Edgar, B. A., Zielke, N. & Gutierrez, C. Endocycles: a recurrent evolutionary innovation for post-mitotic cell growth. Nat. Rev. Mol. Cell Biol. 15, 197–210 (2014).
You, Y. & Brody, S. L. Culture and differentiation of mouse tracheal epithelial cells. Methods Mol. Biol. 945, 123–143 (2013).
Wolock, S. L., Lopez, R. & Klein, A. M. Scrublet: computational identification of cell doublets in single-cell transcriptomic data. Cell Syst. 8, 281–291.e9 (2019).
McGinnis, C. S., Murrow, L. M. & Gartner, Z. J. DoubletFinder: doublet detection in single-cell RNA sequencing data using artificial nearest neighbors. Cell Syst. 8, 329–337.e4 (2019).
Young, M. D. & Behjati, S. SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data. Gigascience 9, giaa151 (2020).
Stuart, T. et al. Comprehensive integration of single-cell data. Cell 177, 1888–1902.e21 (2019).
Cao, J. et al. The single-cell transcriptional landscape of mammalian organogenesis. Nature 566, 496–502 (2019).
Phipson, B. et al. propeller: testing for differences in cell type proportions in single cell data. Bioinformatics 38, 4720–4726 (2022).
Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2010).
Kowalczyk, M. S. et al. Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells. Genome Res. 25, 1860–1872 (2015).
Andreatta, M. & Carmona, S. J. UCell: robust and scalable single-cell gene signature scoring. Comput. Struct. Biotechnol. J. 19, 3796–3798 (2021).
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
Wickham, H., Navarro, D. & Pedersen, T. L. ggplot2: Elegant Graphics for Data Analysis 3rd edn https://ggplot2-book.org/ (Springer, 2024).
Horani, A., Nath, A., Wasserman, M. G., Huang, T. & Brody, S. L. Rho-associated protein kinase inhibition enhances airway epithelial basal-cell proliferation and lentivirus transduction. Am. J. Respir. Cell Mol. Biol. 49, 341–347 (2013).
Meers, M. P., Bryson, T. D., Henikoff, J. G. & Henikoff, S. Improved CUT&RUN chromatin profiling tools. eLife 8, e46314 (2019).
Janssens, D. & Henikoff, S. CUT&RUN: targeted in situ genome-wide profiling with high efficiency for low cell numbers. protocols.io https://doi.org/10.17504/protocols.io.zcpf2vn (2019).
Liu, N. Library prep for CUT&RUN with NEBNext® UltraTM II DNA Library Prep Kit for Illumina® (E7645). protocols.io https://doi.org/10.17504/protocols.io.bagaibse (2021).
Zhu, Q., Liu, N., Orkin, S. H. & Yuan, G.-C. CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis. Genome Biol. 20, 192 (2019).
Zheng, Y., Ahmad, K. & Henikoff, S. CUT&Tag data processing and analysis tutorial. protocols.io https://doi.org/10.17504/protocols.io.bjk2kkye (2020).
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Zhang, Y. et al. Model-based analysis of ChIP–seq (MACS). Genome Biol. 9, R137 (2008).
Yu, G., Wang, L.-G. & He, Q.-Y. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics 31, 2382–2383 (2015).
Livak, K. J. & Schmittgen, T. D. Analysis of relative gene expression data using real-time quantitative PCR and the (2({}^{-{Delta Delta }_{{rm{T}}}})) method. Methods 25, 402–408 (2001).
Mou, H. et al. Dual SMAD signaling inhibition enables long-term expansion of diverse epithelial basal cells. Cell Stem Cell 19, 217–231 (2016).
lb15. multiciliation_cycle: v1.1.3. Zenodo https://doi.org/10.5281/zenodo.10896100 (2024).
lb15. autoCutandRun: v1.1.1. Zenodo https://doi.org/10.5281/zenodo.10896066 (2024).
lb15. autoSeurat: v1.1.2. Zenodo https://doi.org/10.5281/zenodo.10896071 (2024).
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