1. Copyright (c) by W. H. Freeman and Company 10.3 Eukaryotic gene control: purposes and general principles  Unlike bacterial cells and most single cell eukaryotes, cells in multicelular organisms have relatively few genes that are reversibly regulated by environmental conditions  However, gene control in multicellular organisms is important for development and differentiation, and is generally not reversible

2. Copyright (c) by W. H. Freeman and Company 10.3 Many genes in higher eukaryotes are regulated by controlling their transcription Figure 10-22 The nascent chain (run-on) assay allows measurement of the rate of transcription of a given gene

3. Copyright (c) by W. H. Freeman and Company 10.3 Differential synthesis of 12 mRNAs encoding liver-specific genes Figure 10-23

4. Copyright (c) by W. H. Freeman and Company 10.3 Regulatory elements in eukaryotic DNA often are many kilobases from start sites  The basic principles that control transcription in bacteria also apply to eukaryotic organisms: transcription is initiated at a specific base pair and is controlled by the binding of trans- acting proteins (transcription factors) to cis-acting regulatory DNA sequences  However, eukaryotic cis-acting elements are often much further from the promoter they regulate, and transcription from a single promoter may be regulated by binding of multiple transcription factors to alternative control elements  Transcription control sequences can be identified by analysis of a 5-deletion series

5. Copyright (c) by W. H. Freeman and Company 10.3 Construction and analysis of a 5-deletion series Figure 10-24

6. Copyright (c) by W. H. Freeman and Company 10.3 Analysis of labeled nascent transcripts allows mapping of the transcription-initiation site Figure 10-28

7. Copyright (c) by W. H. Freeman and Company 10.3 RNA polymerase II initiates transcription at DNA sequences corresponding to the 5 cap of mRNAs Figure 10-29 “Runs off”

8. Copyright (c) by W. H. Freeman and Company 10.4 The TATA box is a highly conserved promoter in eukaryotic DNA Figure 10-30 Alternative promoters in eukaryotes include initiators and CpG islands 5’-YYA +1 N-T/A-YYY-3’ (Y=C/T)

9. Copyright (c) by W. H. Freeman and Company 10.4 Identification of transcription-control elements with linker mutants Figure 10-31

10. Copyright (c) by W. H. Freeman and Company 10.4 Promoter-proximal elements help regulate eukaryotic genes Figure 10-32

11. Copyright (c) by W. H. Freeman and Company 10.4 Transcription by RNA polymerase II often is stimulated by distant enhancer sites Figure 10-33 Identification of the SV40 enhancer region

12. Copyright (c) by W. H. Freeman and Company 10.4 Most eukaryotic genes are regulated by multiple transcription control mechanisms Figure 10-34

13. Copyright (c) by W. H. Freeman and Company 10.5 Transcription factors may be identified by biochemical techniques Figure 10-35

14. Copyright (c) by W. H. Freeman and Company 10.5 In vivo assay for transcription factor activity Figure 10-37

15. Copyright (c) by W. H. Freeman and Company 10.5 A series of Gal4 deletion mutants demonstrated that transcription factors are composed of separable DNA-binding and activation domains Figure 10-38

16. Copyright (c) by W. H. Freeman and Company 10.5 Transcriptional activators are modular proteins composed of distinct functional domains Figure 10-39

17. Copyright (c) by W. H. Freeman and Company 10.5 DNA-binding domains can be classified into numerous structural types  Homeodomain proteins  Zinc-finger proteins  Winged-helix (forkhead) proteins  Leucine-zipper proteins  Helix-loop-helix proteins

18. Copyright (c) by W. H. Freeman and Company 10.5 Homeodomain from Engrailed protein interacting with its specific DNA recognition site Figure 10-40

19. Copyright (c) by W. H. Freeman and Company 10.5 Interactions of C 2 H 2 and C 4 zinc-finger domains with DNA Figure 10-41

20. Copyright (c) by W. H. Freeman and Company 10.5 Interaction between a C 6 zinc-finger protein (Gal4) and DNA Figure 10-42

21. Copyright (c) by W. H. Freeman and Company 10.5 Interaction of a homodimeric leucine-zipper protein and DNA Figure 10-43 dimerização assegurada pela interacção dos a.a. Hidrofóbicos (ex:leucina) espaçados regularmente

22. Copyright (c) by W. H. Freeman and Company 10.5 Interaction of a helix-loop-helix in a homodimeric protein and DNA Figure 10-44

23. Copyright (c) by W. H. Freeman and Company 10.5 Heterodimeric transcriptional factors increase gene-control options Figure 10-45

24. Copyright (c) by W. H. Freeman and Company 10.5 Activation domains exhibit considerable structural diversity Figure 10-47 Figure 10-46

25. Copyright (c) by W. H. Freeman and Company 10.5 Multiprotein complexes form on enhancers Figure 10-48

26. Copyright (c) by W. H. Freeman and Company 10.5 Many repressors are the functional converse of activators  Eukaryotic transcription is regulated by repressors as well as activators  Repressor-binding sites can be identified and repressors purified by the same techniques used for activators  Many eukaryotic repressors have two domains: a DNA- binding domain and a repressor domain

27. Copyright (c) by W. H. Freeman and Company 10.6 RNA polymerase II transcription- initiation complex  Initiation by Pol II requires general transcription factors, which position Pol II at initiation sites and are required for transcription of most genes transcribed by this polymerase  General transcription factors are multimeric and highly conserved  Proteins comprising the Pol II transcription-initiation complex assemble in a specific order in vitro but most of the proteins may combine to form a holoenzyme complex in vivo

28. Copyright (c) by W. H. Freeman and Company 10.6 Stepwise assembly of Pol II transcription-initiation complex in vitro Figure 10-50

29. Copyright (c) by W. H. Freeman and Company 10.6 The conserved C-terminal domain of TBP binds to TATA-box DNA Figure 10-51 TBP is a subunit of TFIID

30. Copyright (c) by W. H. Freeman and Company 10.6 Structural model of the complex of promoter DNA, TBP, TFIIB, and Pol II Figure 10-53

31. Copyright (c) by W. H. Freeman and Company 10.7 Activators stimulate the highly cooperative assembly of initiation complexes Figure 10-60 Binding sites for activators that control transcription of the mouse TTR gene

32. Copyright (c) by W. H. Freeman and Company 10.7 Model for cooperative assembly of an activated transcription-initiation complex in the TTR promoter Figure 10-61

33. Copyright (c) by W. H. Freeman and Company 10.7 Repressors interfere directly with transcription initiation in several ways Figure 10-62

34. Copyright (c) by W. H. Freeman and Company 10.7 Lipid-soluble hormones control the activities of nuclear receptors Figure 10-63

35. Copyright (c) by W. H. Freeman and Company 10.7 Domain structure of nuclear receptors Figure 10-64

36. Copyright (c) by W. H. Freeman and Company 10.7 Response elements are DNA sites that bind several major nuclear receptors Figure 10-65

37. Copyright (c) by W. H. Freeman and Company 10.7 Model of hormone-dependent gene activation by the glucocorticoid receptor Figure 10-67

38. Copyright (c) by W. H. Freeman and Company 10.7 Polypeptide hormones signal phosphorylation of some transcription factors Figure 10-68 Model of IFN  -mediated gene activation by phosphorylation and dimerization of Stat1 

39. Copyright (c) by W. H. Freeman and Company 10.8 Transcription initiation by Pol I and Pol III is analogous to that by Pol II Figure 10-69

40. Copyright (c) by W. H. Freeman and Company 10.8 Other transcription systems  T7 and related bacteriophages express monomeric, largely unregulated RNA polymerases  Mitochondrial DNA is transcribed by RNA polymerases with similarities to bacteriophage and bacterial enzymes  Transcription of chloroplast DNA resembles bacterial transcription  Transcription by archaeans is closer to eukaryotic than to bacterial transcription