1. 4061 Molecular and Cellular Principles of Animal Development

2. 4061 Molecular and Cellular Principles of Animal Development Classic approaches to embryonic development Molecular approach- genes take centre stage ‘genetic programs underlying development’ ‘Programs executed by molecular networks of proteins operating within and between cells’ ‘In order to understand development we need to understand the underlying genetic circuitry’ ‘Moving from an organism-based approach towards molecular mechanisms’

3. Primary Question How can a complex animal emerge from a single egg? Fourth century BC Aristotle dissected chicken’s eggs Principle of ‘epigenesis’- development a process of growth in size combined with increasing complexity and organization Descriptive Embryology Development of microscope in seventeenth century Experimental Embryology Wilhelm Roux- ‘empirical approach Manipulate frog embryo and observe consequences ‘embryonic induction ’

4. Developmental Genetics (70’s) Drosophila melanogaster – transmission of genetic traits Genetics meets Molecular Biology Clone the developmental genes Developmental Biology Fusion of Molecular Biology, genetics and morphology

5. Impact on Society In vitro fertilization (IVF) ‘Teratology’ effect of environmental agents (chemicals, viruses, radiation) on embryos Chromosomal basis of some human birth defects (amniocentesis) Future Functional genomics - therapeutic targets - combinatorial chemistry Tissue repair - Stem cells - ex vivo tissue engineering - organogenesis Genetic engineering - ‘cloning’!!!

6. Readings from Gilbert 10 th edition Chapter 1 p5-29 Comprehending Development- intro read for general interest (same pages in 9 th edition) Chapter 2 Differential Gene Expression p31-65 (p35- 67 in 9 th Edition)

7. The essence of embryonic development: A regulated expansion in cell numbers, co- ordinated in space and time with an increase in cell diversity

8. Primary Question How can a complex animal emerge from a single egg? Questions of Differentiation Questions of morphogenesis Questions of growth Questions of regeneration Questions of evolution Questions of environmental adaptation

9. SC/BIOL 4061,SC/BCHM 4061 Molecular and Cellular Principles of Animal Development Winter term, 2016 OUTLINE Course Director: John McDermott PhD Office : 427b Life Sciences Building Office tel extension: 30344 Email address: jmcderm@yorku.cajmcderm@yorku.ca Web site: www.yorku.ca/jmcderm/ Scheduled Office hours: TBA (email for an appointment or to request an alternate time to meet) Topic outline 1) Introduction to Molecular Analysis of Development - Descriptive embryology -Genetics and molecular biology 2) Programs and Regulatory Elements in DNA 3) Transcriptional Circuits- epigenetic regulation of gene expression- differential gene expression 4) Gastrulation and early development- axis specification and formation 5) Features of Major Model Organisms- Mouse, Chick, Drosophila 6) Techniques for the study of Mouse Development: gene targeting/editing technology 7) Receptors, Ligands 8) Cell-cell communication, Signaling Networks, Induction and Competence 9) Molecular Co-ordination of Cell Division and Differentiation ( Myogenesis) 10) Focus on Paraxial Mesoderm, Somitogenesis and Patterning

10. 11) Cell Death in Development 12) Lineage Generation - Embryonic and Adult Stem cell properties and lineage commitment 13) Cell Type Specification, Induction of pluripotency in stem cells (iPS) and cell fate programming 14) Patterning in 1 and 2 Dimensions 15) Molecular and cellular basis of 3D Patterning- Heart development 16) Postembryonic development: Regeneration and Aging 17) Developmental mechanisms of evolutionary conservation and change Evaluation 1 Test (prior to Reading week -date: Tues 9 th Feb) 30% 1 Essay (HARD COPY due date 24 th March by 5pm ) 30% (In some cases students may be able to do a class presentation in lieu of the essay assignment on permission of the instructor) 1 Test (Final in exam period date -TBA) 40% Course Text: (10 th edition available in York bookstore) Developmental Biology Companion web site: www.devbio.comwww.devbio.com Scott F.Gilbert Sinauer Associates, Inc ISBN 0-87893-384-6

11. ZYGOTE CLEAVAGE GASTRULATION ectoderm mesoderm endoderm

12. 4061

13. Comparative embryology snake tortoisechicken dolphin monkey Ernst Haeckel (4 edn 1903)

15. The development of animal model systems. Nematode C.elegans

16. The development of animal model systems Fruit fly Drosophila melanogaster A P V D

17. The development of animal model systems, cont’d Frog Xenopus laevis

18. The development of animal model systems, cont’d Zebrafish

19. The development of animal model systems, cont’d Chick

20. The development of animal model systems, cont’d Mouse

21. Types of evidence Correlative- weakest Loss of function Gain of function

22. A few classical terms concerning cell migration during gastrulation

23. Programs and regulatory elements in DNA and RNA Gilbert, Chapter 2 p35-67 Differential Gene Transcription

24. DNA content and number of genes 21,733 17,000 21,000 24,189

25. Phylogenetic analysis DNA content and number of genes, cont’d

26. Fundamental principles of development at the cellular level: a)Cell proliferation b)Continuous but regulated increase in cell diversity

28. General pattern of regulatory sequences

29. Model for assembly of the RNA polymerase II initiation complex on a TATA-containing promoter

31. mRNA GENE TF Gene A (on)Gene D (on)Gene C (off)Gene B (on) mRNA Protein AProtein BProtein D 5`5` 3`3`

32. Homeodomain Engrailed Zinc Finger ZIF 268 Zinc Finger Gluc. Receptor Regulation of Transcription Factors Ribbon

33. Leucine Zipper GCN 4 GCN 4:DNA HLH-leucine zipper MAX

34. Modular design of eukaryotic transcription factors DNA b.d.Act.d N C Transcription factor xCANNTG DNA b.d. N unrelated protein C DNA b.d. N tgacgtca unrelated proteinAct.d C

35. Control of CREB activity by cAMP CREB P OFFON Ser 133 Nucleus C C R + C R cAMP C R C PKA holoenzyme PKA catalytic subunit

36. Regulation of NFkB activity p65 p50 I p65 I P P p50 Nucleus

37. Fig 2.8 Fusion of reporter genes to the enhancer region 13.5d Myf 5 LacZ reporter expressed in eye, facial limb muscles and segmented myotome GFP fused to a lens crystallin promoter in Xenopus tropicalis

38. Epigenetic control of gene expression

39. Nucleosome and chromatin structure

40. 5.10 TAF II 250, a TAF that binds TBP, can function as a histone acetyltransferase

41. Figure 2.3 Nucleosome and chromatin structure (Part 3)

42. DNA RNA Protein modification functional protein interacting with other proteins Cell Signalling What regulates the transcription factors ?

43. Overview of RNA processing in eukaryotes using β-globin genes

44. Alternative Splicing E1E3E2I1I2 E1 E2E3 E2E1 E3 E1 gene RNA 1 mRNA 1 mRNA 2 RNA 2

45. Alternative Splicing E1E3E2I1I2 E1 E2E3 E2E1 E3 E1 gene RNA 1 mRNA 1 mRNA 2 RNA 2