Synthetic Developmental Biology: Understanding Through Reconstitution

Literature Cited

1. Andrae J, Gallini R, Betsholtz C 2008. Role of platelet-derived growth factors in physiology and medicine. Genes Dev 22:101276–312
   [Google Scholar]
2. Aydin B, Mazzoni EO. 2019. Cell reprogramming: the many roads to success. Annu. Rev. Cell Dev. Biol. 35:433–52
   [Google Scholar]
3. Benne R, Hershey JW. 1978. Mechanism of action of protein synthesis initiation factors from rabbit reticulocytes. J. Biol. Chem. 253:93078–87
   [Google Scholar]
4. Blau HM, Chiu C-P, Webster C 1983. Cytoplasmic activation of human nuclear genes in stable heterocaryons. Cell 32:41171–80
   [Google Scholar]
5. Briggs JA, Li VC, Lee S, Woolf CJ, Klein A, Kirschner MW 2017. Mouse embryonic stem cells can differentiate via multiple paths to the same state. eLife 6:e26945
   [Google Scholar]
6. Briscoe J, Small S. 2015. Morphogen rules: design principles of gradient-mediated embryo patterning. Development 142:233996–4009
   [Google Scholar]
7. Chang JB, Ferrell JE Jr 2013. Mitotic trigger waves and the spatial coordination of the Xenopus cell cycle. Nature 500:7464603–7
   [Google Scholar]
8. Cheng X, Ferrell JE Jr 2018. Apoptosis propagates through the cytoplasm as trigger waves. Science 361:6402607–12
   [Google Scholar]
9. Chitu V, Stanley ER. 2006. Colony-stimulating factor 1 in immunity and inflammation. Curr. Opin. Immunol. 18:139–48
   [Google Scholar]
10. Crocker J, Tsai A, Stern DL 2017. A fully synthetic transcriptional platform for a multicellular eukaryote. Cell Rep 18:1287–96
    [Google Scholar]
11. Davidson D. 1983. The mechanism of feather pattern development in the chick. 1. The time of determination of feather position. J. Embryol. Exp. Morphol. 74:245–59
    [Google Scholar]
12. Davies J. 2017. Using synthetic biology to explore principles of development. Development 144:71146–58
    [Google Scholar]
13. Davis RL, Weintraub H, Lassar AB 1987. Expression of a single transfected cDNA converts fibroblasts to myoblasts. Cell 51:6987–1000
    [Google Scholar]
14. Deneke VE, Melbinger A, Vergassola M, Di Talia S 2016. Waves of Cdk1 activity in S phase synchronize the cell cycle in Drosophila embryos. Dev. Cell 38:4399–412
    [Google Scholar]
15. Dequéant M-L, Pourquié O. 2008. Segmental patterning of the vertebrate embryonic axis. Nat. Rev. Genet. 9:5370–82
    [Google Scholar]
16. Ebrahimkhani MR, Ebisuya M. 2019. Synthetic developmental biology: build and control multicellular systems. Curr. Opin. Chem. Biol. 52:9–15
    [Google Scholar]
17. Elowitz MB, Lim WA. 2010. Build life to understand it. Nature 468:7326889–90
    [Google Scholar]
18. Fakhouri WD, Ay A, Sayal R, Dresch J, Dayringer E, Arnosti DN 2010. Deciphering a transcriptional regulatory code: modeling short‐range repression in the Drosophila embryo. Mol. Syst. Biol. 6:1341
    [Google Scholar]
19. Fletcher DA. 2016. Bottom-up biology: harnessing engineering to understand nature. Dev. Cell 38:6587–89
    [Google Scholar]
20. Grunwald GB. 1991. The conceptual and experimental foundations of vertebrate embryonic cell adhesion research. Dev. Biol. 7:129–58
    [Google Scholar]
21. Gurdon JB, Elsdale TR, Fischberg M 1958. Sexually mature individuals of Xenopus laevis from the transplantation of single somatic nuclei. Nature 182:462764–65
    [Google Scholar]
22. Hart Y, Reich-Zeliger S, Antebi YE, Zaretsky I, Mayo AE et al. 2014. Paradoxical signaling by a secreted molecule leads to homeostasis of cell levels. Cell 158:51022–32
    [Google Scholar]
23. Howard J, Grill SW, Bois JS 2011. Turing's next steps: the mechanochemical basis of morphogenesis. Nat. Rev. Mol. Cell Biol. 12:6392–98
    [Google Scholar]
24. Hubaud A, Regev I, Mahadevan L, Pourquié O 2017. Excitable dynamics and Yap-dependent mechanical cues drive the segmentation clock. Cell 171:3668–82.e11
    [Google Scholar]
25. Huch M, Knoblich JA, Lutolf MP, Martinez-Arias A 2017. The hope and the hype of organoid research. Development 144:6938–41
    [Google Scholar]
26. Hughes AJ, Miyazaki H, Coyle MC, Zhang J, Laurie MT et al. 2018. Engineered tissue folding by mechanical compaction of the mesenchyme. Dev. Cell 44:2165–78.e6
    [Google Scholar]
27. Jiang TX, Jung HS, Widelitz RB, Chuong CM 1999. Self-organization of periodic patterns by dissociated feather mesenchymal cells and the regulation of size, number and spacing of primordia. Development 126:224997–5009
    [Google Scholar]
28. Johnson HE, Toettcher JE. 2019. Signaling dynamics control cell fate in the early Drosophila embryo. Dev. Cell 48:3361–70.e3
    [Google Scholar]
29. Keller R, Danilchik M. 1988. Regional expression, pattern and timing of convergence and extension during gastrulation of Xenopus laevis. . Development 103:1193–209
    [Google Scholar]
30. Kirillova AO, Kraus YA, Markov AV 2018. Dissociation–reaggregation experiments in cnidarians as a model system for the study of the regulative capacity of metazoan development. Biol. Bull. Rev. 8:1–11
    [Google Scholar]
31. Kmita M, Duboule D. 2003. Organizing axes in time and space: 25 years of colinear tinkering. Science 301:5631331–33
    [Google Scholar]
32. Krieg M, Arboleda-Estudillo Y, Puech PH, Käfer J, Graner F et al. 2008. Tensile forces govern germ-layer organization in zebrafish. Nat. Cell Biol. 10:4429–36
    [Google Scholar]
33. Lassar AB, Paterson BM, Weintraub H 1986. Transfection of a DNA locus that mediates the conversion of 10T12 fibroblasts to myoblasts. Cell 47:5649–56
    [Google Scholar]
34. Lauschke VM, Tsiairis CD, François P, Aulehla A 2013. Scaling of embryonic patterning based on phase-gradient encoding. Nature 493:7430101–5
    [Google Scholar]
35. LeBon L, Lee TV, Sprinzak D, Jafar-Nejad H, Elowitz MB 2014. Fringe proteins modulate Notch-ligand cis and trans interactions to specify signaling states. eLife 3:e02950
    [Google Scholar]
36. Li P, Markson JS, Wang S, Chen S, Vachharajani V, Elowitz MB 2018. Morphogen gradient reconstitution reveals Hedgehog pathway design principles. Science 360:6388543–48
    [Google Scholar]
37. Lienert F, Lohmueller JJ, Garg A, Silver PA 2014. Synthetic biology in mammalian cells: next generation research tools and therapeutics. Nat. Rev. Mol. Cell Biol. 15:295–107
    [Google Scholar]
38. Mammoto T, Ingber DE. 2010. Mechanical control of tissue and organ development. Development 137:91407–20
    [Google Scholar]
39. Mathur M, Xiang JS, Smolke CD 2017. Mammalian synthetic biology for studying the cell. J. Cell Biol. 216:173–82
    [Google Scholar]
40. Matsuda M, Koga M, Woltjen K, Nishida E, Ebisuya M 2015. Synthetic lateral inhibition governs cell-type bifurcation with robust ratios. Nat. Commun. 6:6195
    [Google Scholar]
41. McKenna A, Gagnon JA. 2019. Recording development with single cell dynamic lineage tracing. Development 146:12dev169730
    [Google Scholar]
42. Moloney DJ, Panin VM, Johnston SH, Chen J, Shao L et al. 2000. Fringe is a glycosyltransferase that modifies Notch. Nature 406:6794369–75
    [Google Scholar]
43. Morris SA, Daley GQ. 2013. A blueprint for engineering cell fate: current technologies to reprogram cell identity. Cell Res 23:133–48
    [Google Scholar]
44. Müller P, Rogers KW, Jordan BM, Lee JS, Robson D et al. 2012. Differential diffusivity of Nodal and Lefty underlies a reaction-diffusion patterning system. Science 336:6082721–24
    [Google Scholar]
45. Müller P, Rogers KW, Yu SR, Brand M, Schier AF 2013. Morphogen transport. Development 140:81621–38
    [Google Scholar]
46. Mumm JS, Kopan R. 2000. Notch signaling: from the outside. Dev. Biol. 228:2151–65
    [Google Scholar]
47. Nieuwkoop PD. 1969. The formation of the mesoderm in urodelean amphibians. I. Induction by the endoderm. Wilhelm Roux Arch. Entwickl. Mech. Org. 162:4341–73
    [Google Scholar]
48. Ramos AI, Barolo S. 2013. Low-affinity transcription factor binding sites shape morphogen responses and enhancer evolution. Philos. Trans. R. Soc. B 368:163220130018
    [Google Scholar]
49. Rogers KW, Lord ND, Gagnon JA, Pauli A, Zimmerman S et al. 2017. Nodal patterning without Lefty inhibitory feedback is functional but fragile. eLife 6:e28785
    [Google Scholar]
50. Rogers KW, Schier AF. 2011. Morphogen gradients: from generation to interpretation. Annu. Rev. Cell Dev. Biol. 27:377–407
    [Google Scholar]
51. Rossi G, Manfrin A, Lutolf MP 2018. Progress and potential in organoid research. Nat. Rev. Genet. 19:11671–87
    [Google Scholar]
52. Salazar-Ciudad I. 2003. Mechanisms of pattern formation in development and evolution. Development 130:102027–37
    [Google Scholar]
53. Santorelli M, Lam C, Morsut L 2019. Synthetic development: building mammalian multicellular structures with artificial genetic programs. Curr. Opin. Biotechnol. 59:130–40
    [Google Scholar]
54. Sayre MH, Tschochner H, Kornberg RD 1992. Reconstitution of transcription with five purified initiation factors and RNA polymerase II from Saccharomyces cerevisiae. J. Biol. Chem 267:3223376–82
    [Google Scholar]
55. Sekine R, Shibata T, Ebisuya M 2018. Synthetic mammalian pattern formation driven by differential diffusivity of Nodal and Lefty. Nat. Commun. 9:5456
    [Google Scholar]
56. Sha W, Moore J, Chen K, Lassaletta AD, Yi C-S et al. 2003. Hysteresis drives cell-cycle transitions in Xenopus laevis egg extracts. PNAS 100:3975–80
    [Google Scholar]
57. Shahbazi MN, Siggia ED, Zernicka-Goetz M 2019. Self-organization of stem cells into embryos: a window on early mammalian development. Science 364:6444948–51
    [Google Scholar]
58. Shyer AE, Rodrigues AR, Schroeder GG, Kassianidou E, Kumar S, Harland RM 2017. Emergent cellular self-organization and mechanosensation initiate follicle pattern in the avian skin. Science 357:6353811–15
    [Google Scholar]
59. Siggia ED, Warmflash A. 2018. Modeling mammalian gastrulation with embryonic stem cells. Curr. Top. Dev. Biol. 129:1–23
    [Google Scholar]
60. Simunovic M, Brivanlou AH. 2017. Embryoids, organoids and gastruloids: new approaches to understanding embryogenesis. Development 144:6976–85
    [Google Scholar]
61. Sjöqvist M, Andersson ER. 2017. Do as I say, Not(ch) as I do: lateral control of cell fate. Dev. Biol. 447:158–70
    [Google Scholar]
62. Smith JC. 1989. Mesoderm induction and mesoderm-inducing factors in early amphibian development. Development 105:4665–77
    [Google Scholar]
63. Spemann H, Mangold H. 1924. Über Induktion von Embryonalanlagen durch Implantation artfremder Organisatoren. Arch. Mikrosk. Anat. Entwickl. 100:599–638
    [Google Scholar]
64. Sprinzak D, Lakhanpal A, LeBon L, Garcia-Ojalvo J, Elowitz MB 2011. Mutual inactivation of Notch receptors and ligands facilitates developmental patterning. PLOS Comput. Biol. 7:6e1002069
    [Google Scholar]
65. Sprinzak D, Lakhanpal A, LeBon L, Santat LA, Fontes ME et al. 2010. Cis-interactions between Notch and Delta generate mutually exclusive signalling states. Nature 465:729486–90
    [Google Scholar]
66. Steinberg MS. 1963. Reconstruction of tissues by dissociated cells. Science 141:3579401–8
    [Google Scholar]
67. Steinberg MS, Takeichi M. 1994. Experimental specification of cell sorting, tissue spreading, and specific spatial patterning by quantitative differences in cadherin expression. PNAS 91:1206–9
    [Google Scholar]
68. Stumpf HF. 1966. Mechanism by which cells estimate their location within the body. Nature 212:5060430–31
    [Google Scholar]
69. Takahashi K, Tanabe K, Ohnuki M, Narita M, Ichisaka T et al. 2007. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131:5861–72
    [Google Scholar]
70. Takahashi K, Yamanaka S. 2006. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126:4663–76
    [Google Scholar]
71. Technau U, Holstein TW. 1992. Cell sorting during the regeneration of Hydra from reaggregated cells. Dev. Biol. 151:1117–27
    [Google Scholar]
72. Toda S, Blauch LR, Tang SKY, Morsut L, Lim WA 2018. Programming self-organizing multicellular structures with synthetic cell–cell signaling. Science 361:6398156–62
    [Google Scholar]
73. Toda S, Brunger JM, Lim WA 2019. Synthetic development: learning to program multicellular self-organization. Curr. Opin. Syst. Biol. 14:41–49
    [Google Scholar]
74. Townes PL, Holtfreter J. 1955. Directed movements and selective adhesion of embryonic amphibian cells. J. Exp. Zool. 128:153–120
    [Google Scholar]
75. Tsai TY-C, Sikora M, Xia P, Colak-Champollion T, Knaut H et al. 2019. An adhesion code ensures robust pattern formation during tissue morphogenesis. bioRxiv 803635. https://doi.org/10.1101/803635
    [Crossref]
76. Tsiairis CD, Aulehla A. 2016. Self-organization of embryonic genetic oscillators into spatiotemporal wave patterns. Cell 164:4656–67
    [Google Scholar]
77. Turing A. 1952. The chemical basis of morphogenesis. Philos. Trans. R. Soc. B 237:64137–72
    [Google Scholar]
78. Velasco S, Ibrahim MM, Kakumanu A, Garipler G, Aydin B et al. 2017. A multi-step transcriptional and chromatin state cascade underlies motor neuron programming from embryonic stem cells. Cell Stem Cell 20:2205–17.e8
    [Google Scholar]
79. Vergassola M, Deneke VE, Di Talia S 2018. Mitotic waves in the early embryogenesis of Drosophila: bistability traded for speed. PNAS 115:10E2165–74
    [Google Scholar]
80. Vierbuchen T, Ostermeier A, Pang ZP, Kokubu Y, Südhof TC, Wernig M 2010. Direct conversion of fibro-blasts to functional neurons by defined factors. Nature 463:72841035–41
    [Google Scholar]
81. Vincent BJ, Estrada J, DePace AH 2016. The appeasement of Doug: a synthetic approach to enhancer biology. Integr. Biol. 8:4475–84
    [Google Scholar]
82. Warmflash A, Sorre B, Etoc F, Siggia ED, Brivanlou AH 2014. A method to recapitulate early embryonic spatial patterning in human embryonic stem cells. Nat. Methods 11:8847–54
    [Google Scholar]
83. Wichterle H, Lieberam I, Porter JA, Jessell TM 2002. Directed differentiation of embryonic stem cells into motor neurons. Cell 110:3385–97
    [Google Scholar]
84. Widelitz RB, Jiang TX, Chen CW, Stott NS, Jung HS, Chuong CM 1999. Wnt-7a in feather morphogenesis: involvement of anterior–posterior asymmetry and proximal–distal elongation demonstrated with an in vitro reconstitution model. Development 126:122577–87
    [Google Scholar]
85. Wieschaus E, Nüsslein-Volhard C. 2016. The Heidelberg screen for pattern mutants of Drosophila: a personal account. Annu. Rev. Cell Dev. Biol. 32:1–46
    [Google Scholar]
86. Wolpert L. 1969. Positional information and the spatial pattern of cellular differentiation. J. Theor. Biol. 25:11–47
    [Google Scholar]
87. Xiong F, Tentner AR, Huang P, Gelas A, Mosaliganti KR et al. 2013. Specified neural progenitors sort to form sharp domains after noisy Shh signaling. Cell 153:3550–61
    [Google Scholar]
88. Yeeles JTP, Janska A, Early A, Diffley JFX 2017. How the eukaryotic replisome achieves rapid and efficient DNA replication. Mol. Cell 65:1105–16
    [Google Scholar]
89. Yoshioka-Kobayashi K, Matsumiya M, Niino Y, Isomura A, Kori H et al. 2020. Coupling delay controls synchronized oscillation in the segmentation clock. Nature 580:7801119–23
    [Google Scholar]
90. Zheng Y, Xue X, Shao Y, Wang S, Esfahani SN et al. 2019. Controlled modelling of human epiblast and amnion development using stem cells. Nature 573:7774421–25
    [Google Scholar]
91. Zhou X, Franklin RA, Adler M, Jacox JB, Bailis W et al. 2018. Circuit design features of a stable two-cell system. Cell 172:4744–57.e17
    [Google Scholar]