Accomplish the gene regulation of prokaryotes, we comeback to the eukaryotes.

1. Accomplish the gene regulation of prokaryotes, we comeback to the eukaryotes. You well exclaim with it’s complication and accuration.

2. Chapter 17 Gene Regulation in Eukaryotes

3. Similarity And Difference of regulation between eukaryotes and prokaryote

4. Similarity : Principles are the same: signals, activators and repressors, recruitment and allostery, cooperative binding Expression of a gene can be regulated at the similar steps, and the initiation of transcription is the most pervasively regulated step. Difference: Pre-mRNA splicing adds an important step for regulation. The eukaryotic transcriptional machinery is more elaborate than its bacterial counterpart. Nucleosomes and their modifiers influence access to genes. Many eukaryotic genes have more regulatory binding sites and are controlled by more regulatory proteins than are bacterial genes.

5. Topic 1 Conserved Mechanisms of Transcriptional Regulation from Yeast to Mammals

6. The basic features of gene regulation are the same in all eukaryotes, because of the similarity in their transcription and nucleosome structure. • The typical eukaryotic activators works in a manner similar to the simplest bacterial case. • Repressors work in a variety of ways

7. Domain swap experiment Moving domains among proteins, proving that domains can be dissected into separate parts of the proteins. Many similar experiments shows that DNA binding domains and activating regions areseparable.

8. DNA-binding domains and activating regions are separable: • Activator produces a protein bound to the DNA normally but did not activate transcription. • Fusion of the C-terminal region of the activator to the DNA binding domain of a bacterial repressor, LexA activates the transcription of the reporter gene. Domain swap experiment

9. 1-2 Eukaryotic regulators use a range of DNA binding domains, but DNA recognition involves the same principles as found in bacteria • Homeodomain proteins • Zinc containing DNA-binding domain • Leucine zipper motif • Helix-Loop-Helix proteins

10. Both of these proteins use hydrophobic amino acid residues for dimerization.

11. Bactrial regulatory proteins • Most use the helix-turn-helix motif to bind DNA target • Most bind as dimers to DNA sequence: each monomer inserts an a helix into the major groove. • Eukaryotic regulatory proteins • Recognize the DNA using the similar principles, with some variations in detail. • Some form heterodimers to recognize DNA, extending the range of DNA-binding specificity.

12. Homeodomain proteins: The homeodomain is a class of helix-turn-helix DNA-binding domain and recognizes DNA in essentially the same way as those bacterial proteins Figure 17-5

13. Zinc containing DNA-binding domains finger domain:Zinc finger proteins (TFIIIA) and Zinc cluster domain (Gal4) Figure 17-6

14. Leucine Zipper Motif:The Motif combines dimerization and DNA-binding surfaces within a single structural unit. Figure 17-7

15. Helix-Loop-Helix motif: Because the region of the a-helix that binds DNA contains baisc amino acids residues, Leucine zipper and HLH proteins are often called basic zipper and basic HLH proteins. Figure 17-8

16. 1-3 Activating regions are not well-defined structures • The activating regions are grouped on the basis of amino acids content • Acidic activation domains • Glutamine-rich domains • Proline-rich domains

17. Ⅱ Recruitment of Protein Complexes to Genes by Eukaryotic Activation

18. 2-1 Interacting with parts of the transcription machinery. • Some activators not only recruit parts of the transcriptional machinery, they also induce allosteric changes in them

19. The eukaryotic transcriptional machinery contains polymerase and numerous proteins being organized to several complexes, such as the Mediator and the TFⅡD complex. Activators interact with one or more of these complexes and recruit them to the gene. Figure 17-9

20. At most genes, the transcription machinery is not prebound, and appear at the promoter only upon activation. Thus, no allosteric activation of the prebound polymerase has been evident in eukaryotic regulation

21. 2-2 Activators also recruit nucleosome modifiers that help the transcription machinery bind at the promoter • Modifiers direct recruitment of the transcriptional machinery • Modifiers help activate a gene inaccessibly packed within chromatin

22. Two types of Nucleosome modifiers : • Those add chemical groups to the tails of histones, such as histone acetyl transferases(HATs) • Those remodel the nucleosomes, such as the ATP-dependent activity of SWI/SNF

23. Two basic models for how these modification help activate a gene : • Remodeling and certain modification can uncover DNA-binding sites that would otherwise remain inaccessible within the nucleosome. • By adding acetyl groups, it creates specific binding sites on nucleosomes for proteins bearing so-called bromodomains.

24. Fig 17-11 Local alterations in chromatin directed by activators

25. 2-3 Action at a distance: loops and insulators Many enkaryotic activators－particularly in highereukaryotes－work from a distance. • Some proteins help, for example Chip protein in Drosophila. • The compacted chromosome structure help. DNA is wrapped in nucleosomes in eukaryotes.So sites separated by many base pairs may not be as far apart in the cell as thought.

26. Specific elements called insulators control the actions of activators, preventing the activating the non-specific genes

27. Insulators block activation by enhancers Figure 17-12

28. Transcriptional Silencing Silencing is a specializes form of repression that can spread along chromatin, switching off multiple genes without the need for each to bear binding sites for specific repressor. Insulator elements can block this spreading, so insulators protect genes from both indiscriminate activation and repression.

29. E.P: A gene inserted at random into the mammalian genome is often “silenced” because it becomes incorporated into a particularly dense form of chromatin called heterochromatin .But if insulators are placed up-and downstream of that gene they protect it from silencing.

30. 2-4 Appropriate regulation of some groups of genes requires locus control region (LCR). Figure 17-13

31. A group of regulatory elements collectively called the locus control region (LCR), is found 30-50 kb upstream of the cluster of globin genes. It’s made up of multiple-sequence elements : something like enhancers, insulators or promoters. It binds regulatory proteins that cause the chromatin structure to “open up”, allowing access to the array of regulators.

32. Another group of mouse genes whose expression is regulated in a temporarily and spatially ordered sequence are called HoxD genes. They are controlled by an element called the GCR (global control region) in a manner very like that of LCR.

33. Ⅲ Signal Integration and Combinatorial Control

34. 3-1 Activators work together synergistically to integrate signals

35. In eukaryotic cells, numerous signals are often required to switch a gene on. So at many genes multiple activators must work together. They do these by working synergistically: two activators working together is greater than the sum of each of them working alone. Three strategies of synergy : • Two activators recruit a single complex • Activators help each other binding cooperativity • One activator recruit something that helps the second activator bind

36. a.“Classical” cooperative binding b. Both proteins interacting with a third protein d. Binding a protein unwinds the DNA from nucleosome a little, revealing the binding site for another protein c. A protein recruits a remodeller to reveal a binding site for another protein Figure 17-14

37. 3-2 Signal integration: the HO gene is controlled by two regulators; one recruits nucleosome modifiers and the other recruits mediator

38. The HO gene is involved in the budding of yeast. It has two activators : SWI5 and SBF. alter the nucleosome Figure 17-15

39. SBF cannot bind its sites unaided; their disposition within chromatin prohibits it. SWI5 can bind to its sites unaided but cannot, from that distance, activate the HO gene. SWI5 can, however, recruit nucleosome modifiers. These act on nucleosomes over the SBF sites

40. 3-3 Signal integration: Cooperative binding of activators at the human b-interferon gene.

41. The human β-interferon gene is activated in cells upon viral infection. Infection triggers three activators : NFκB, IRF, and Jun/ATF. They bind cooperatively to sites within an enhancer, form a structure called enhanceosome. Figure 17-16

42. 3-4 Combinatory control lies at the hear of the complexity and diversity of eukaryotes

43. There is extensive combinatorial control in eukaryotes. Four signals Figure 17-17 Three signals In complex multicellular organisms, combinatorial control involves many more regulators and genes than shown above, and repressors as well as activators can be involved.

44. 3-5 Combinatory control of the mating-type genes from S. cerevisiae

45. The yeast S.cerevisiae exists in three forms: two haploid cells of different mating types－ a and a －and the diploid formed when an aand an a cell mate and fuse.Cells of the two mating types differ because they express different sets of genes : aspecific genes and a specific genes.

46. a cell make the regulatory protein a1,acell make the protein a1 and a2. A fourth regulator protein Mcm1 is also involved in regulatory the mating-type specific genes and is present in both cell types.

47. Control of cell-type specific genes in yeast Figure 17-18

48. Ⅳ Transcriptional Repressors

49. In eukaryotes, repressorsdon’t work by binding to sites that overlap the promoter and thus block binding of polymerase, but most common work by recruiting nucleosome modifiers.

50. Ways in which eukaryotic repressor Work a and b Figure 17-19