1. Biochemistry Sixth Edition Chapter 31 The Control of Gene Expression Part II: Eukaryotes (cis vs. trans) Copyright © 2007 by W. H. Freeman and Company Berg Tymoczko Stryer

2. Transcriptional regulation: prokaryotes vs. eukaryotes Greater complexity of genomes E coliyeast human One1646 4.6 Mb0.2-2.2 Mb50-250 Mb 2000 proteins600025,000 Chromosome Size Eukaryotes: * Different cell types * No operons * nuleosome/chromatin structure

10. RNA polymerase II promoter: 3 common elements Mutagenesis exp’ts, footprinting, and sequence comparisons 1 2 3 Initiator element (-3 ~ +5) Downstream core promoter element (+28 ~ +32)

13. Combinatorial control !!

15. DNA: proteins  ionic interaction

18. * Sequence-specific * Promoter-proximal or enhancer sites (conserved recognition seq.) * motifs? Initiates txn by interacting with RNA pol II & co. Prevents DNA binding Homo-dimer or hetero-dimer

19. Activation domains recruit: * Proteins that promote transcription (co-factors) * RNA pol. II * ex. intermediary proteins (ex. mediator)

20. 25-30 subunits

23. Activation domains: * Less conserved than DNA-binding (acidic, hydrophobic, Q-rich, P-rich) 1.Redundant 2.Modular 3.Act synergistically

24. Homo-dimer or hetero-dimer

25. Prevents (or regulate) DNA binding

28. Steroid hormone system of gene expression *cholesterol derived *hydrophobic molecules *membrane permeable *bind to nuclear receptors & progesterone

30. Steroid hormone system of gene expression Nuclear hormone receptors: *large protein family (>50 in human) *binds signaling molecule (or “ligand”) *binds specific DNA sites with consensus sequence -> gene expression *modular domains

32. Ligand binding induces conformational change However, DNA binding is not altered

33. Coactivator recruitment by estrogen receptor Coactivator modifies chromatin structure

34. Steroid-hormone receptors are drug targets Agonists: molecules that bind receptor and trigger signaling pathway Anabolic steroids

35. Antagonists: molecules that bind receptor and do not trigger signaling pathway -> competitive inhibitors SERMs: selective estrogen receptor modulators -> treatment of breast cancer

36. Binding but no conformation changes: *blocking coactivator recruitment *inhibiting gene expression

38. Enhancers: * No promoter activity * Increase txn * Long range  Binding sites for cell type-specific regulatory proteins  Regulation through chromatin structure (not directly on pol.)

39. Enhancer of muscle-specific enzyme  non-muscle gene

40.  -galactosidase activity can be monitored by X-Gal Application: reporter assay TA cloning