1.
Ozbudak, E. M., Thattai, M., Kurtser, I., Grossman, A. D. & van Oudenaarden, A. Regulation of noise in the expression of a single gene. Nat. Genet. 31, 69–73 (2002).
2.
Elowitz, M. B., Levine, A. J., Siggia, E. D. & Swain, P. S. Stochastic gene expression in a single cell. Science 297, 1183–1186 (2002).
3.
Adachi, N. & Lieber, M. R. Bidirectional gene organization: a common architectural feature of the human genome. Cell 109, 807–809 (2002).
4.
Yang, L. & Yu, J. A comparative analysis of divergently-paired genes (DPGs) among Drosophila and vertebrate genomes. BMC Evol. Biol. 9, 55 (2009).
5.
Arnone, J. T., Robbins-Pianka, A., Arace, J. R., Kass-Gergi, S. & McAlear, M. A. The adjacent positioning of co-regulated gene pairs is widely conserved across eukaryotes. BMC Genomics 13, 546 (2012).
6.
Yan, C., Wu, S., Pocetti, C. & Bai, L. Regulation of cell-to-cell variability in divergent gene expression. Nat. Commun. 7, 11099 (2016).
7.
Hubaud, A. & Pourquié, O. Signalling dynamics in vertebrate segmentation. Nat. Rev. Mol. Cell Biol. 15, 709–721 (2014).
8.
Lewis, J. Autoinhibition with transcriptional delay: a simple mechanism for the zebrafish somitogenesis oscillator. Curr. Biol. 13, 1398–1408 (2003).
9.
Giudicelli, F., Ozbudak, E. M., Wright, G. J. & Lewis, J. Setting the tempo in development: an investigation of the zebrafish somite clock mechanism. PLoS Biol. 5, e150 (2007).
10.
Harima, Y., Takashima, Y., Ueda, Y., Ohtsuka, T. & Kageyama, R. Accelerating the tempo of the segmentation clock by reducing the number of introns in the Hes7 gene. Cell Rep. 3, 1–7 (2013).
11.
Ay, A., Knierer, S., Sperlea, A., Holland, J. & Özbudak, E. M. Short-lived Her proteins drive robust synchronized oscillations in the zebrafish segmentation clock. Development 140, 3244–3253 (2013).
12.
Schröter, C. et al. Topology and dynamics of the zebrafish segmentation clock core circuit. PLoS Biol. 10, e1001364 (2012).
13.
Hanisch, A. et al. The elongation rate of RNA polymerase II in zebrafish and its significance in the somite segmentation clock. Development 140, 444–453 (2013).
14.
Keskin, S. et al. Noise in the vertebrate segmentation clock is boosted by time delays but tamed by Notch signaling. Cell Rep. 23, 2175–2185 (2018).
15.
Choorapoikayil, S., Willems, B., Ströhle, P. & Gajewski, M. Analysis of her1 and her7 mutants reveals a spatio temporal separation of the somite clock module. PLoS ONE 7, e39073 (2012).
16.
Henry, C. A. et al. Two linked hairy/Enhancer of split-related zebrafish genes, her1 and her7, function together to refine alternating somite boundaries. Development 129, 3693–3704 (2002).
17.
Lleras Forero, L. et al. Segmentation of the zebrafish axial skeleton relies on notochord sheath cells and not on the segmentation clock. eLife 7, e33843 (2018).
18.
Becskei, A., Kaufmann, B. B. & van Oudenaarden, A. Contributions of low molecule number and chromosomal positioning to stochastic gene expression. Nat. Genet. 37, 937–944 (2005).
19.
Raj, A., Peskin, C. S., Tranchina, D., Vargas, D. Y. & Tyagi, S. Stochastic mRNA synthesis in mammalian cells. PLoS Biol. 4, e309 (2006).
20.
Fukaya, T., Lim, B. & Levine, M. Enhancer control of transcriptional bursting. Cell 166, 358–368 (2016).
21.
Schröter, C. et al. Dynamics of zebrafish somitogenesis. Dev. Dyn. 237, 545–553 (2008).
22.
Kawamura, A. et al. Zebrafish hairy/enhancer of split protein links FGF signaling to cyclic gene expression in the periodic segmentation of somites. Genes Dev. 19, 1156–1161 (2005).
23.
Novák, B. & Tyson, J. J. Design principles of biochemical oscillators. Nat. Rev. Mol. Cell Biol. 9, 981–991 (2008).
24.
Trofka, A. et al. The Her7 node modulates the network topology of the zebrafish segmentation clock via sequestration of the Hes6 hub. Development 139, 940–947 (2012).
25.
Delaune, E. A., François, P., Shih, N. P. & Amacher, S. L. Single-cell-resolution imaging of the impact of Notch signaling and mitosis on segmentation clock dynamics. Dev. Cell 23, 995–1005 (2012).
26.
Moreno-Mateos, M. A. et al. CRISPRscan: designing highly efficient sgRNAs for CRISPR–Cas9 targeting in vivo. Nat. Methods 12, 982–988 (2015).
27.
Jao, L. E., Wente, S. R. & Chen, W. Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system. Proc. Natl Acad. Sci. USA 110, 13904–13909 (2013).
28.
Cooper, M. S. et al. Visualizing morphogenesis in transgenic zebrafish embryos using BODIPY TR methyl ester dye as a vital counterstain for GFP. Dev. Dyn. 232, 359–368 (2005).
29.
Sarkans, U. et al. The BioStudies database-one stop shop for all data supporting a life sciences study. Nucleic Acids Res. 46 (D1), D1266–D1270 (2018).
30.
Riedel-Kruse, I. H., Müller, C. & Oates, A. C. Synchrony dynamics during initiation, failure, and rescue of the segmentation clock. Science 317, 1911–1915 (2007).
31.
Gomez, C. et al. Control of segment number in vertebrate embryos. Nature 454, 335–339 (2008).
32.
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).
33.
Soroldoni, D. et al. Genetic oscillations. A Doppler effect in embryonic pattern formation. Science 345, 222–225 (2014).
34.
Anderson, D. F. A modified next reaction method for simulating chemical systems with time dependent propensities and delays. J. Chem. Phys. 127, 214107 (2007).
35.
Cohen, J. Statistical Power Analysis for the Behavioral Sciences (L. Erlbaum Associates, 1988).
36.
Faul, F., Erdfelder, E., Lang, A. G. & Buchner, A. G*Power 3: a flexible statistical power analysis program for the social, behavioral, and biomedical sciences. Behav. Res. Methods 39, 175–191 (2007).