How do embryos build themselves?

1. How do embryos build themselves?

2. Nested Networks – and other problems In GRN analysis Dave McClay

3. You arrive at differentiation genes and then what?

4. Gene activation GRN Induction Cadherin Cadherin Adhesion Protein- Protein Interaction Signal transduction Cell shape Change - motility Adhesion Adhesion Kinase- phosphatase Cell shape Change - motility

5. Too often, “networks” are actually glossaries. Zaidel-bar lab Singapore, Short, B., JCB 2009

6. Integrin “adhesome” From Zaidel-bar et al Nature Cell biology, 2007

7. Integrin Glossary From Zaidel-bar et al Nature Cell biology, 2007

8. Chromosome maintenance And duplication machinery Merico, et al., 2009 Nature

9. Protein interaction data comparing data from Two species Sharan and Ideker, Nature Biotech. 2006

10. Mammalian sex determination Blanche Capel

11. Actin regulatory network From Springer after Lee, SH,. 2010

12. Gilfillan and Rivera, 2009, Immunol Rev Mast cell activation network

13. Cdc protein kinase and phosphatase network Breitkreutz et al., Science 2011

14. From Burgstaller et al., MBoC 2010

16. Gene activation GRN Induction Cadherin Cadherin Adhesion Protein- Protein Interaction Signal transduction Cell shape Change - motility Adhesion Adhesion Kinase- phosphatase Cell shape Change - motility

17. Justman et al., Science 2009

18. b outside Endo-mes Fig. 2 Mat cb LiCl Endo-Mes Mat Otx c GSK-3 frizzled Micr Mat Otx nb-TCF Maternal & early interactions Wnt8 Ets 4th cleavage SoxB1 Krl Otx Eve Krox b a Interactions in definitive territories LiCl Colored boxes indicate post gastrular domains of expression genes cb c GSK-3 Endoderm Mesoderm Frz to 4th – 6th Cleavage Endo-Mes nb-TCF Wnt8 Rep. of Wnt8 (18 hrs) Otx a Krox Late Wnt8 signal from veg2 Hnf 6 MV2L Mat. N. N Su(H)+ Repressor PMC E(S) ? 7th-9th cleavage Eve Bra GataE FoxA Ub Hmx Delta Pmar1 Delta Lim Zyg. N. UI Eve Gcm GataC FoxB Ets Dri Notch Not Elk Hox11/13b Veg1 endoderm Endomes up to 20-24hours TBr Nrl Cyclophilin, EpHx, Ficolin, Sm37, Sm27, MSP130L Post gastrular terminal or peripheral downstream genes Sm30 Sm50 Kakapo Apo bec OrCT SuTx Pks CAPK Dpt Gelsolin Endo16 Decorin Mes Endo Msp130 FvMo

20. Progression of network states But:

21. Progression of network states Morphogenesis

22. Progression of network states Morphogenesis

23. In the micromeres: In the ectoderm Redox asymmetry ß-catenin P38-P in oral Pmar1 Mic Repressor Nodal in oral Alx1 Gsc BMP Snail Oral Aboral FoxN2/3 Post EMT GRN PMCs move to new site VEGF VegfR FGFR FGF Skeletogenic Network Skeleton production

24. Timing issues: example: duration of a signal

25. ß-catenin Veg 2 ring (16 cells) Large Micromeres (8) Small Micromeres (4) • ß-catenin enters specific • nuclei in a precise • temporal sequence. Cati Logan

26. Nuclear -catenin Signaling is dynamic Transcription Factor expression is dynamic i.e. GRN states are dynamic Wnt 8 Blimp1 Logan et al 1999 Smith et al. 2007

28. Logan et al 1999 Smith et al 2007

30. Croce et al., 2010

31. With Jeni Croce

32. Remove Delta after it signals for 1, 2, or 3 hrs.

33. Network states change so that cells in the Same germ layer, or same territory of a germ Layer assume different GRN states.

34. Problem: Network State Dynamics Hatched blastula Mesenchyme blastula

35. Brachy As cells converge toward the Blastopore they rapidly alter Their GRN state Jeff Gross

36. Gcm HB Bra Gcm MB Bra Gcm MB FoxA Bra FoxA

37. Delta Delta + Gcm FoxA FoxA+Bra Bra

39. Brachyury Fox A Endo NSM BP Expression of Brachyury and FoxA upstream of Hh and invagination is dynamic - Network state running in Endoderm cells rapidly changes as cells converge on Blastopore Jeni Croce

40. Developmental Biology Functional Genomics Molecular Biology Perturbation experiments Systems biology

42. Problems with Networks: It is difficult to reflect dynamics – parameters are missing It is difficult to pair a GRN to events happening in an organism