The cell cycle coordinates core functions such as replication and cell division. However, cell-cycle-regulated transcription in the control of non-core functions, such as cell identity maintenance through specific transcription factors (TFs) and signalling pathways remains unclear. Here, we provide a resource consisting of mapped transcriptomes in unsynchronized HeLa and U2OS cancer cells sorted for cell cycle phase by Fucci reporter expression. We developed a novel algorithm for data analysis that enables efficient visualization and data comparisons and identified cell cycle synchronization of Notch signalling and TFs associated with development. Furthermore, the cell cycle synchronizes with the circadian clock, providing a possible link between developmental transcriptional networks and the cell cycle. In conclusion we find that cell cycle synchronized transcriptional patterns are temporally compartmentalized and more complex than previously anticipated, involving genes, which control cell identity and development.

Central European Institute of Technology Masaryk University Brno Czech Republic

Department of Cytokinetics Institute of Biophysics CAS v v i Královopolská 135 Brno Czech Republic

Department of Experimental Biology Faculty of Science Masaryk University Brno Czech Republic

Department of Medical Biochemistry and Biophysics Karolinska Institutet Stockholm Sweden

Department of Physiology and Pharmacology Karolinska Institutet Stockholm Sweden

International Clinical Research Center Center for Biomolecular and Cellular Engineering St Anne's University Hospital in Brno Brno Czech Republic

Science for Life Laboratory Division of Translational Medicine and Chemical Biology Department of Medical Biochemistry and Biophysics Karolinska Institutet Stockholm Sweden

Science for Life Laboratory KTH Royal Institute of Technology Stockholm Sweden

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Bertoli C, Skotheim JM, de Bruin RA. Control of cell cycle transcription during G1 and S phases. Nat Rev Mol Cell Biol. 2013;14(8):518–28. doi: 10.1038/nrm3629 ; PubMed Central PMCID: PMCPMC4569015. PubMed DOI PMC

Matsui T, Nieto-Estevez V, Kyrychenko S, Schneider JW, Hsieh J. RB controls growth, survival, and neuronal migration in human cerebral organoids. Development. 2017. doi: 10.1242/dev.143636 . PubMed DOI PMC

Naser R, Vandenbosch R, Omais S, Hayek D, Jaafar C, Al Lafi S, et al. Role of the Retinoblastoma protein, Rb, during adult neurogenesis in the olfactory bulb. Sci Rep. 2016;6:20230 doi: 10.1038/srep20230 ; PubMed Central PMCID: PMCPMC4742828. PubMed DOI PMC

Sadasivam S, DeCaprio JA. The DREAM complex: master coordinator of cell cycle-dependent gene expression. Nat Rev Cancer. 2013;13(8):585–95. doi: 10.1038/nrc3556 ; PubMed Central PMCID: PMCPMC3986830. PubMed DOI PMC

Pauklin S, Vallier L. The cell-cycle state of stem cells determines cell fate propensity. Cell. 2013;155(1):135–47. doi: 10.1016/j.cell.2013.08.031 ; PubMed Central PMCID: PMCPMC3898746. PubMed DOI PMC

Imayoshi I, Isomura A, Harima Y, Kawaguchi K, Kori H, Miyachi H, et al. Oscillatory control of factors determining multipotency and fate in mouse neural progenitors. Science. 2013;342(6163):1203–8. doi: 10.1126/science.1242366 . PubMed DOI

Shimojo H, Ohtsuka T, Kageyama R. Oscillations in notch signaling regulate maintenance of neural progenitors. Neuron. 2008;58(1):52–64. doi: 10.1016/j.neuron.2008.02.014 . PubMed DOI

Davidson G, Shen J, Huang YL, Su Y, Karaulanov E, Bartscherer K, et al. Cell cycle control of wnt receptor activation. Dev Cell. 2009;17(6):788–99. doi: 10.1016/j.devcel.2009.11.006 . PubMed DOI

Olmeda D, Castel S, Vilaro S, Cano A. Beta-catenin regulation during the cell cycle: implications in G2/M and apoptosis. Mol Biol Cell. 2003;14(7):2844–60. doi: 10.1091/mbc.E03-01-0865 ; PubMed Central PMCID: PMCPMC165681. PubMed DOI PMC

Joshi KK, Berge M, Radhakrishnan SK, Viollier PH, Chien P. An Adaptor Hierarchy Regulates Proteolysis during a Bacterial Cell Cycle. Cell. 2015;163(2):419–31. doi: 10.1016/j.cell.2015.09.030 ; PubMed Central PMCID: PMCPMC4600535. PubMed DOI PMC

Palmisano A, Zamborszky J, Oguz C, Csikasz-Nagy A. Molecular Network Dynamics of Cell Cycle Control: Periodicity of Start and Finish. Methods Mol Biol. 2017;1524:331–49. doi: 10.1007/978-1-4939-6603-5_21 . PubMed DOI

White MA, Riles L, Cohen BA. A systematic screen for transcriptional regulators of the yeast cell cycle. Genetics. 2009;181(2):435–46. doi: 10.1534/genetics.108.098145 ; PubMed Central PMCID: PMCPMC2644938. PubMed DOI PMC

Lu Y, Cross FR. Periodic cyclin-Cdk activity entrains an autonomous Cdc14 release oscillator. Cell. 2010;141(2):268–79. doi: 10.1016/j.cell.2010.03.021 ; PubMed Central PMCID: PMCPMC4549071. PubMed DOI PMC

Bieler J, Cannavo R, Gustafson K, Gobet C, Gatfield D, Naef F. Robust synchronization of coupled circadian and cell cycle oscillators in single mammalian cells. Mol Syst Biol. 2014;10:739 doi: 10.15252/msb.20145218 ; PubMed Central PMCID: PMCPMC4299496. PubMed DOI PMC

Hoffmann J, Symul L, Shostak A, Fischer T, Naef F, Brunner M. Non-circadian expression masking clock-driven weak transcription rhythms in U2OS cells. PLoS One. 2014;9(7):e102238 doi: 10.1371/journal.pone.0102238 ; PubMed Central PMCID: PMCPMC4090172. PubMed DOI PMC

Matsuo T, Yamaguchi S, Mitsui S, Emi A, Shimoda F, Okamura H. Control mechanism of the circadian clock for timing of cell division in vivo. Science. 2003;302(5643):255–9. doi: 10.1126/science.1086271 . PubMed DOI

Karpowicz P, Zhang Y, Hogenesch JB, Emery P, Perrimon N. The circadian clock gates the intestinal stem cell regenerative state. Cell Rep. 2013;3(4):996–1004. doi: 10.1016/j.celrep.2013.03.016 ; PubMed Central PMCID: PMCPMC3982394. PubMed DOI PMC

Dominguez D, Tsai YH, Gomez N, Jha DK, Davis I, Wang Z. A high-resolution transcriptome map of cell cycle reveals novel connections between periodic genes and cancer. Cell Res. 2016;26(8):946–62. doi: 10.1038/cr.2016.84 ; PubMed Central PMCID: PMCPMC4973334. PubMed DOI PMC

Whitfield ML, Sherlock G, Saldanha AJ, Murray JI, Ball CA, Alexander KE, et al. Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol Biol Cell. 2002;13(6):1977–2000. doi: 10.1091/mbc.02-02-0030. ; PubMed Central PMCID: PMCPMC117619. PubMed DOI PMC

Sakaue-Sawano A, Kurokawa H, Morimura T, Hanyu A, Hama H, Osawa H, et al. Visualizing spatiotemporal dynamics of multicellular cell-cycle progression. Cell. 2008;132(3):487–98. doi: 10.1016/j.cell.2007.12.033 . PubMed DOI

Mort RL, Ford MJ, Sakaue-Sawano A, Lindstrom NO, Casadio A, Douglas AT, et al. Fucci2a: a bicistronic cell cycle reporter that allows Cre mediated tissue specific expression in mice. Cell Cycle. 2014;13(17):2681–96. doi: 10.4161/15384101.2015.945381 ; PubMed Central PMCID: PMCPMC4613862. PubMed DOI PMC

Daynac M, Morizur L, Kortulewski T, Gauthier LR, Ruat M, Mouthon MA, et al. Cell Sorting of Neural Stem and Progenitor Cells from the Adult Mouse Subventricular Zone and Live-imaging of their Cell Cycle Dynamics. J Vis Exp. 2015;(103). doi: 10.3791/53247 ; PubMed Central PMCID: PMCPMC4692602. PubMed DOI PMC

Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139–40. doi: 10.1093/bioinformatics/btp616 ; PubMed Central PMCID: PMCPMC2796818. PubMed DOI PMC

Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, et al. STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 2015;43(Database issue): D447–52. doi: 10.1093/nar/gku1003 ; PubMed Central PMCID: PMCPMC4383874. PubMed DOI PMC

Hayami S, Yoshimatsu M, Veerakumarasivam A, Unoki M, Iwai Y, Tsunoda T, et al. Overexpression of the JmjC histone demethylase KDM5B in human carcinogenesis: involvement in the proliferation of cancer cells through the E2F/RB pathway. Mol Cancer. 2010;9:59 doi: 10.1186/1476-4598-9-59 ; PubMed Central PMCID: PMCPMC2848192. PubMed DOI PMC

DeGregori J, Kowalik T, Nevins JR. Cellular targets for activation by the E2F1 transcription factor include DNA synthesis- and G1/S-regulatory genes. Mol Cell Biol. 1995;15(8):4215–24. ; PubMed Central PMCID: PMCPMC230660. PubMed PMC

Chong JL, Wenzel PL, Saenz-Robles MT, Nair V, Ferrey A, Hagan JP, et al. E2f1-3 switch from activators in progenitor cells to repressors in differentiating cells. Nature. 2009;462(7275):930–4. doi: 10.1038/nature08677 ; PubMed Central PMCID: PMCPMC2806193. PubMed DOI PMC

Penzo-Mendez AI. Critical roles for SoxC transcription factors in development and cancer. Int J Biochem Cell Biol. 2010;42(3):425–8. doi: 10.1016/j.biocel.2009.07.018 ; PubMed Central PMCID: PMCPMC2862366. PubMed DOI PMC

Shi S, Cao X, Gu M, You B, Shan Y, You Y. Upregulated Expression of SOX4 Is Associated with Tumor Growth and Metastasis in Nasopharyngeal Carcinoma. Dis Markers. 2015;2015:658141 doi: 10.1155/2015/658141 ; PubMed Central PMCID: PMCPMC4633550. PubMed DOI PMC

Zhao L, Arsenault M, Ng ET, Longmuss E, Chau TC, Hartwig S, et al. SOX4 regulates gonad morphogenesis and promotes male germ cell differentiation in mice. Dev Biol. 2017. doi: 10.1016/j.ydbio.2017.01.013 . PubMed DOI

Liu Y, Cui L, Huang J, Ji EH, Chen W, Messadi D, et al. SOX4 Promotes Progression in OLP-Associated Squamous Cell Carcinoma. J Cancer. 2016;7(11):1534–40. doi: 10.7150/jca.15689 ; PubMed Central PMCID: PMCPMC4964137. PubMed DOI PMC

Pal K, Mukhopadhyay S. Primary cilium and sonic hedgehog signaling during neural tube patterning: role of GPCRs and second messengers. Dev Neurobiol. 2015;75(4):337–48. doi: 10.1002/dneu.22193 . PubMed DOI

Shi X, Wang Q, Gu J, Xuan Z, Wu JI. SMARCA4/Brg1 coordinates genetic and epigenetic networks underlying Shh-type medulloblastoma development. Oncogene. 2016;35(44):5746–58. doi: 10.1038/onc.2016.108 . PubMed DOI

Qinyu L, Long C, Zhen-dong D, Min-min S, Wei-ze W, Wei-ping Y, et al. FOXO6 promotes gastric cancer cell tumorigenicity via upregulation of C-myc. FEBS Lett. 2013;587(14):2105–11. doi: 10.1016/j.febslet.2013.05.027 . PubMed DOI

Han M, Xu W, Cheng P, Jin H, Wang X. Histone demethylase lysine demethylase 5B in development and cancer. Oncotarget. 2017;8(5):8980–91. doi: 10.18632/oncotarget.13858 . PubMed DOI PMC

Hohenauer T, Moore AW. The Prdm family: expanding roles in stem cells and development. Development. 2012;139(13):2267–82. doi: 10.1242/dev.070110 . PubMed DOI

Jones HW Jr., McKusick VA, Harper PS, Wuu KD. George Otto Gey. (1899–1970). The HeLa cell and a reappraisal of its origin. Obstet Gynecol. 1971;38(6):945–9. . PubMed

Ponten J, Saksela E. Two established in vitro cell lines from human mesenchymal tumours. Int J Cancer. 1967;2(5):434–47. . PubMed

Zhang X, Friedman A, Heaney S, Purcell P, Maas RL. Meis homeoproteins directly regulate Pax6 during vertebrate lens morphogenesis. Genes Dev. 2002;16(16):2097–107. doi: 10.1101/gad.1007602 ; PubMed Central PMCID: PMCPMC186446. PubMed DOI PMC

Briscoe J, Pierani A, Jessell TM, Ericson J. A homeodomain protein code specifies progenitor cell identity and neuronal fate in the ventral neural tube. Cell. 2000;101(4):435–45. . PubMed

Shahi MH, Afzal M, Sinha S, Eberhart CG, Rey JA, Fan X, et al. Regulation of sonic hedgehog-GLI1 downstream target genes PTCH1, Cyclin D2, Plakoglobin, PAX6 and NKX2.2 and their epigenetic status in medulloblastoma and astrocytoma. BMC Cancer. 2010;10:614 doi: 10.1186/1471-2407-10-614 ; PubMed Central PMCID: PMCPMC2989332. PubMed DOI PMC

Garside VC, Cullum R, Alder O, Lu DY, Vander Werff R, Bilenky M, et al. SOX9 modulates the expression of key transcription factors required for heart valve development. Development. 2015;142(24):4340–50. doi: 10.1242/dev.125252 . PubMed DOI

Brent AE, Braun T, Tabin CJ. Genetic analysis of interactions between the somitic muscle, cartilage and tendon cell lineages during mouse development. Development. 2005;132(3):515–28. doi: 10.1242/dev.01605 . PubMed DOI

Thakurela S, Tiwari N, Schick S, Garding A, Ivanek R, Berninger B, et al. Mapping gene regulatory circuitry of Pax6 during neurogenesis. Cell Discov. 2016;2:15045 doi: 10.1038/celldisc.2015.45 ; PubMed Central PMCID: PMCPMC4860964. PubMed DOI PMC

Luo H, Jin K, Xie Z, Qiu F, Li S, Zou M, et al. Forkhead box N4 (Foxn4) activates Dll4-Notch signaling to suppress photoreceptor cell fates of early retinal progenitors. Proc Natl Acad Sci U S A. 2012;109(9):E553–62. doi: 10.1073/pnas.1115767109 ; PubMed Central PMCID: PMCPMC3295323. PubMed DOI PMC

Dequeant ML, Pourquie O. Segmental patterning of the vertebrate embryonic axis. Nat Rev Genet. 2008;9(5):370–82. doi: 10.1038/nrg2320 . PubMed DOI

Carrieri FA, Dale JK. Turn It Down a Notch. Front Cell Dev Biol. 2016;4:151 doi: 10.3389/fcell.2016.00151 ; PubMed Central PMCID: PMCPMC5241280. PubMed DOI PMC

Soza-Ried C, Ozturk E, Ish-Horowicz D, Lewis J. Pulses of Notch activation synchronise oscillating somite cells and entrain the zebrafish segmentation clock. Development. 2014;141(8):1780–8. doi: 10.1242/dev.102111 . PubMed DOI

Williams DR, Shifley ET, Braunreiter KM, Cole SE. Disruption of somitogenesis by a novel dominant allele of Lfng suggests important roles for protein processing and secretion. Development. 2016;143(5):822–30. doi: 10.1242/dev.128538 . PubMed DOI

Resende TP, Ferreira M, Teillet MA, Tavares AT, Andrade RP, Palmeirim I. Sonic hedgehog in temporal control of somite formation. Proc Natl Acad Sci U S A. 2010;107(29):12907–12. doi: 10.1073/pnas.1000979107 ; PubMed Central PMCID: PMCPMC2919945. PubMed DOI PMC

Janich P, Pascual G, Merlos-Suarez A, Batlle E, Ripperger J, Albrecht U, et al. The circadian molecular clock creates epidermal stem cell heterogeneity. Nature. 2011;480(7376):209–14. doi: 10.1038/nature10649 . PubMed DOI

Jensen LD, Cao Z, Nakamura M, Yang Y, Brautigam L, Andersson P, et al. Opposing effects of circadian clock genes bmal1 and period2 in regulation of VEGF-dependent angiogenesis in developing zebrafish. Cell Rep. 2012;2(2):231–41. doi: 10.1016/j.celrep.2012.07.005 . PubMed DOI

Morgan R. Pax6 is a direct, positively regulated target of the circadian gene Clock. Dev Dyn. 2004;230(4):643–50. doi: 10.1002/dvdy.20097 . PubMed DOI

Wang Y, Solt LA, Kojetin DJ, Burris TP. Regulation of p53 stability and apoptosis by a ROR agonist. PLoS One. 2012;7(4):e34921 doi: 10.1371/journal.pone.0034921 ; PubMed Central PMCID: PMCPMC3324542. PubMed DOI PMC

Yoshitane H, Ozaki H, Terajima H, Du NH, Suzuki Y, Fujimori T, et al. CLOCK-controlled polyphonic regulation of circadian rhythms through canonical and noncanonical E-boxes. Mol Cell Biol. 2014;34(10):1776–87. doi: 10.1128/MCB.01465-13 ; PubMed Central PMCID: PMCPMC4019033. PubMed DOI PMC

Schick S, Becker K, Thakurela S, Fournier D, Hampel MH, Legewie S, et al. Identifying Novel Transcriptional Regulators with Circadian Expression. Mol Cell Biol. 2015;36(4):545–58. doi: 10.1128/MCB.00701-15 ; PubMed Central PMCID: PMCPMC4751687. PubMed DOI PMC

Ben-Porath I, Thomson MW, Carey VJ, Ge R, Bell GW, Regev A, et al. An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors. Nat Genet. 2008;40(5):499–507. doi: 10.1038/ng.127 ; PubMed Central PMCID: PMCPMC2912221. PubMed DOI PMC

Huang S. On the intrinsic inevitability of cancer: from foetal to fatal attraction. Semin Cancer Biol. 2011;21(3):183–99. doi: 10.1016/j.semcancer.2011.05.003 . PubMed DOI

Naxerova K, Bult CJ, Peaston A, Fancher K, Knowles BB, Kasif S, et al. Analysis of gene expression in a developmental context emphasizes distinct biological leitmotifs in human cancers. Genome Biol. 2008;9(7):R108 doi: 10.1186/gb-2008-9-7-r108 ; PubMed Central PMCID: PMCPMC2530866. PubMed DOI PMC

Muratovska A, Zhou C, He S, Goodyer P, Eccles MR. Paired-Box genes are frequently expressed in cancer and often required for cancer cell survival. Oncogene. 2003;22(39):7989–97. doi: 10.1038/sj.onc.1206766 . PubMed DOI

Hsieh YW, Yang XJ. Dynamic Pax6 expression during the neurogenic cell cycle influences proliferation and cell fate choices of retinal progenitors. Neural Dev. 2009;4:32 doi: 10.1186/1749-8104-4-32 ; PubMed Central PMCID: PMCPMC2741438. PubMed DOI PMC

Andersson ER, Sandberg R, Lendahl U. Notch signaling: simplicity in design, versatility in function. Development. 2011;138(17):3593–612. doi: 10.1242/dev.063610 . PubMed DOI

Meinhardt H. Models for patterning primary embryonic body axes: The role of space and time. Semin Cell Dev Biol. 2015;42:103–17. doi: 10.1016/j.semcdb.2015.06.005 . PubMed DOI

Hubaud A, Pourquie O. Signalling dynamics in vertebrate segmentation. Nat Rev Mol Cell Biol. 2014;15(11):709–21. doi: 10.1038/nrm3891 . PubMed DOI

Bessho Y, Hirata H, Masamizu Y, Kageyama R. Periodic repression by the bHLH factor Hes7 is an essential mechanism for the somite segmentation clock. Genes Dev. 2003;17(12):1451–6. doi: 10.1101/gad.1092303 ; PubMed Central PMCID: PMCPMC196074. PubMed DOI PMC

Briscoe J, Small S. Morphogen rules: design principles of gradient-mediated embryo patterning. Development. 2015;142(23):3996–4009. doi: 10.1242/dev.129452 ; PubMed Central PMCID: PMCPMC4712844. PubMed DOI PMC

Perrimon N, Pitsouli C, Shilo BZ. Signaling mechanisms controlling cell fate and embryonic patterning. Cold Spring Harb Perspect Biol. 2012;4(8):a005975 doi: 10.1101/cshperspect.a005975 ; PubMed Central PMCID: PMCPMC3405863. PubMed DOI PMC

Islam S, Zeisel A, Joost S, La Manno G, Zajac P, Kasper M, et al. Quantitative single-cell RNA-seq with unique molecular identifiers. Nat Methods. 2014;11(2):163–6. doi: 10.1038/nmeth.2772 . PubMed DOI

Carpenter AE, Jones TR, Lamprecht MR, Clarke C, Kang IH, Friman O, et al. CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol. 2006;7(10):R100 doi: 10.1186/gb-2006-7-10-r100 ; PubMed Central PMCID: PMCPMC1794559. PubMed DOI PMC

R Development Core Team. R: A Language and Environment for Statistical Computing. Vienna, Austria: the R Foundation for Statistical Computing; 2011. Available from: http://www.R-project.org/.

Wickham H. ggplot2: Elegant Graphics for Data Analysis. New York, USA: Springer-Verlag; 2009.

Wickham H, Francois R. dplyr: A Grammar of Data Manipulation. R package version 0.5.0.2016. Available from: https://CRAN.R-project.org/package=dplyr.

Gerritsen H. mapplots: Data Visualisation on Maps. R package version 1.5. 2014. Available from: https://CRAN.R-project.org/package=mapplots.

Engels B. XNomial: Exact Goodness-of-Fit Test for Multinomial Data with Fixed Probabilities. R package version 1.0.4.2015. Available from: https://CRAN.R-project.org/package=XNomial.

Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4(1):44–57. doi: 10.1038/nprot.2008.211 . PubMed DOI