title: Engineering gene networks to emulate Drosophila embryonic pattern formation.
abstract: Pattern formation is essential in the development of higher eukaryotes. For example, in the Drosophila embryo, maternal morphogen gradients establish gap gene expression domain patterning along the anterior-posterior axis, through linkage with an elaborate gene network. To understand the evolution and behaviour of such systems better, it is important to establish the minimal determinants required for patterning. We have therefore engineered artificial transcription-translation networks that generate simple patterns, crudely analogous to the Drosophila gap gene system. The Drosophila syncytium was modelled using DNA-coated paramagnetic beads fixed by magnets in an artificial chamber, forming a gene expression network. Transient expression domain patterns were generated using various levels of network connectivity. Generally, adding more transcription repression interactions increased the "sharpness" of the pattern while reducing overall expression levels. An accompanying computer model for our system allowed us to search for parameter sets compatible with patterning. While it is clear that the Drosophila embryo is far more complex than our simplified model, several features of interest emerge. For example, the model suggests that simple diffusion may be too rapid for Drosophila-scale patterning, implying that sublocalisation, or "trapping," is required. Second, we find that for pattern formation to occur under the conditions of our in vitro reaction-diffusion system, the activator molecules must propagate faster than the inhibitors. Third, adding controlled protease degradation to the system stabilizes pattern formation over time. We have reconstituted transcriptional pattern formation from purified substances, including phage RNA polymerases, ribonucleotides, and an eukaryotic translation extract. We anticipate that the system described here will be generally applicable to the study of any biological network with a spatial component.
authors.affiliation: European Molecular Biology Laboratory, Structures and Biocomputing, Heidelberg, Germany. isalan@embl.de <isalan@embl.de>
authors.forename: Mark
authors.initials: M
authors.lastname: Isalan
authors.forename: Caroline
authors.initials: C
authors.lastname: Lemerle
authors.forename: Luis
authors.initials: L
authors.lastname: Serrano
mesh_terms: D000818:Animals; D019521:Body Patterning / Q000235:genetics*; D004330:Drosophila / Q000196:embryology* / Q000235:genetics*; D004625:Embryo, Nonmammalian / Q000502:physiology*; D005786:Gene Expression Regulation; D005818:Genetic Engineering / Q000379:methods*; D008954:Models, Biological; D009024:Morphogenesis; D014158:Transcription, Genetic
references.citation: Cell. 1994 Sep 9;78(5):855-65
references.pmid: 8087852
references.citation: Nature. 1970 Jan 31;225(5231):420-2
references.pmid: 5411117
references.citation: Science. 2002 Aug 16;297(5584):1183-6
references.pmid: 12183631
references.citation: Proc Natl Acad Sci U S A. 2001 Feb 13;98(4):1437-41
references.pmid: 11171969
references.citation: Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Nov;66(5 Pt 2):056205
references.pmid: 12513584
references.citation: Acta Biotheor. 1996 Nov;44(3-4):249-61
references.pmid: 8953211
references.citation: Proc Natl Acad Sci U S A. 1973 Nov;70(11):3255-9
references.pmid: 4274133
references.citation: Cell. 2000 Dec 8;103(6):981-91
references.pmid: 11136982
references.citation: Cell. 2001 Jun 1;105(5):559-62
references.pmid: 11389824
references.citation: Biotechniques. 1994 Apr;16(4):730-5
references.pmid: 8024796
references.citation: Cell. 1996 Jun 28;85(7):951-61
references.pmid: 8674123
references.citation: EMBO J. 1988 Jun;7(6):1749-56
references.pmid: 2901954
references.citation: Cell. 1995 Jun 16;81(6):967-78
references.pmid: 7540118
references.citation: EMBO J. 1988 Sep;7(9):2881-7
references.pmid: 2846287
references.citation: Genetics. 2004 Aug;167(4):1721-37
references.pmid: 15342511
references.citation: Kybernetik. 1972 Dec;12(1):30-9
references.pmid: 4663624
references.citation: Cell. 2001 Apr 20;105(2):209-19
references.pmid: 11336671
references.citation: Science. 1990 Apr 27;248(4954):495-8
references.pmid: 2158673
references.citation: Nature. 1997 Jun 26;387(6636):913-7
references.pmid: 9202124
references.citation: Cell. 1988 Jul 1;54(1):95-104
references.pmid: 3383245
references.citation: Genes Dev. 1994 Dec 15;8(24):2986-95
references.pmid: 7528157
references.citation: Nature. 1986 Dec 11-17;324(6097):537-45
references.pmid: 2878369
references.citation: Chaos. 1991 Dec;1(4):411-420
references.pmid: 12779937
references.citation: Dev Cell. 2002 Nov;3(5):615-23
references.pmid: 12431369
references.citation: Bioinformatics. 2004 Sep 22;20(14):2212-21
references.pmid: 15059825
references.citation: Dev Cell. 2002 Jun;2(6):785-96
references.pmid: 12062090
references.citation: Bioessays. 2000 Aug;22(8):753-60
references.pmid: 10918306
references.citation: Science. 2002 May 24;296(5572):1466-70
references.pmid: 12029133
references.citation: Nature. 1989 Apr 20;338(6217):629-32
references.pmid: 2704418
references.citation: Phys Rev Lett. 2000 May 1;84(18):4240-3
references.pmid: 10990655
references.citation: Science. 1992 Feb 21;255(5047):986-9
references.pmid: 1546296
references.citation: J Theor Biol. 1969 Oct;25(1):1-47
references.pmid: 4390734
references.citation: Cell. 1991 Nov 29;67(5):955-67
references.pmid: 1720354
references.citation: J Theor Biol. 2001 Jul 21;211(2):115-41
references.pmid: 11419955
references.citation: Proc Natl Acad Sci U S A. 2001 Feb 13;98(4):1432-6
references.pmid: 11171968
references.citation: Nature. 2004 Jul 15;430(6997):368-71
references.pmid: 15254541
references.citation: Nature. 2000 Jan 20;403(6767):335-8
references.pmid: 10659856
references.citation: Curr Biol. 1998 Nov 19;8(23):1277-80
references.pmid: 9822580
references.citation: J Theor Biol. 1998 Mar 7;191(1):103-14
references.pmid: 9593661
references.citation: Development. 1991 Sep;113(1):55-66
references.pmid: 1684934
references.citation: Nature. 1989 Jan 12;337(6203):138-43
references.pmid: 2911348
references.citation: Nature. 1980 Oct 30;287(5785):795-801
references.pmid: 6776413
references.citation: Nature. 1970 Feb 7;225(5232):535-7
references.pmid: 16056595
references.citation: Philos Trans R Soc Lond B Biol Sci. 2015 Apr 19;370(1666):
references.pmid: 25750229
references.citation: Development. 2002 Jun;129(11):2577-89
references.pmid: 12015287
references.citation: Nature. 2002 Nov 14;420(6912):224-30
references.pmid: 12432407
references.citation: Biophys Chem. 2004 Feb 15;107(3):221-7
references.pmid: 14967237
references.citation: Nature. 1990 Aug 9;346(6284):577-80
references.pmid: 2377231
references.citation: Annu Rev Genet. 2000;34:77-137
references.pmid: 11092823
references.citation: Cell. 1988 Jul 1;54(1):83-93
references.pmid: 3383244
references.citation: Nature. 1995 Jun 22;375(6533):654-8
references.pmid: 7791898
references.citation: Dev Biol. 1990 Jul;140(1):57-72
references.pmid: 1972684
references.citation: Phys Rev Lett. 1990 Jun 11;64(24):2953-2956
references.pmid: 10041855
references.citation: Plant Cell. 1993 Oct;5(10):1471-1481
references.pmid: 12271041
references.citation: Dev Cell. 2003 Oct;5(4):635-46
references.pmid: 14536064
references.citation: Cell. 2004 Jan 23;116(2):143-52
references.pmid: 14744427
references.citation: Science. 1972 Feb 11;175(4022):634-6
references.pmid: 17808803
references.citation: Biochemistry. 1992 Aug 25;31(33):7587-94
references.pmid: 1510945
references.citation: Nature. 2003 Apr 10;422(6932):633-7
references.pmid: 12687005
references.citation: Nature. 2000 Jan 20;403(6767):339-42
references.pmid: 10659857
references.citation: Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 2000 Sep;62(3 Pt B):3790-8
references.pmid: 11088896
references.citation: Development. 1990 Oct;110(2):621-8
references.pmid: 2133557
references.citation: Nat Biotechnol. 2001 Jul;19(7):656-60
references.pmid: 11433278
references.citation: Nature. 2000 Jun 1;405(6786):590-3
references.pmid: 10850721
references.citation: Nature. 1996 Feb 22;379(6567):746-9
references.pmid: 8602224
references.citation: Nature. 2001 Oct 25;413(6858):797-803
references.pmid: 11677596
references.citation: Mol Cell Biol. 1998 May;18(5):2892-900
references.pmid: 9566908
references.citation: Science. 1992 Apr 3;256(5053):94-7
references.pmid: 1348871
references.citation: Nature. 1996 Feb 22;379(6567):694-9
references.pmid: 8602214
references.citation: Nature. 1993 Mar 11;362(6416):152-5
references.pmid: 8450886
references.citation: Nature. 2000 Jul 13;406(6792):188-92
references.pmid: 10910359
references.citation: Ann N Y Acad Sci. 1993 Jun 11;684:243-5
references.pmid: 8317843
references.citation: Proc Natl Acad Sci U S A. 2003 Oct 28;100(22):12672-7
references.pmid: 14559971
references.citation: Proc Natl Acad Sci U S A. 1999 Mar 30;96(7):3786-9
references.pmid: 10097115
references.citation: Trends Genet. 1996 Nov;12(11):478-83
references.pmid: 8973159
references.citation: Nat Cell Biol. 2001 Jul;3(7):E151-4
references.pmid: 11433305
references.citation: Nature. 2002 Feb 14;415(6873):798-802
references.pmid: 11845210
references.citation: Cell. 1992 Jan 24;68(2):201-19
references.pmid: 1733499