Chapter 21

1. Chapter 21 Regulation of Transcription

2. 21.1 Introduction21.2 Response elements identify genes under common regulation21.3 There are many types of DNA-binding domains21.4 A zinc finger motif is a DNA-binding domain21.5 Steroid receptors are transcription factors21.6 Steroid receptors have zinc fingers21.7 Binding to the response element is activated by ligand-binding21.8 Steroid receptors recognize response elements by a combinatorial code21.9 Homeodomains bind related targets in DNA21.10 Helix-loop-helix proteins interact by combinatorial association21.11 Leucine zippers are involved in dimer formation21.12 Transcription initiation requires changes in chromatin structure21.13 Chromatin remodeling is an active process21.14 Activation of transcription requires changes in nucleosome organization at the promoter21.15 Histone acetylation and deacetylation control chromatin activity21.16 Polycomb and trithorax are antagonistic repressors and activators21.17 An LCR may control a domain21.18 Insulators block enhancer actions21.19 Insulators can vary in strength21.20 A domain has several types of elements21.21 Gene expression is associated with demethylation 21.22 CpG islands are regulatory targets

3. 21.1 Introduction Activation of gene structureInitiation of transcriptionProcessing the transcriptTransport to cytoplasmTranslation of mRNA

4. 21.2 Response elements identify genes under common regulation Table 21.1 Incucible transcription factors bind to response elements that identify groups of promoters or enhancers subject to coordinate control.

5. 21.2 Response elements identify genes under common regulation Figure 21.1 The regulatory region of a human metallothionein gene contains regulator elements in both its promoter and enhancer. The promoter has elements for metal induction; an enhancer has an element for response to glucocorticoid. Promoter elements are shown above the map, and proteins that bind them are indicated below.

6. 21.3 There are many types of DNA-binding domains Figure 21.2 The activity of a regulatory transcription factor may be controlled by synthesis of protein, covalent modification of protein, ligand binding, or binding of inhibitors that sequester the protein or affect its ability to bind to DNA.

7. 21.3 There are many types of DNA-binding domains Figure 28.19 Oncogenes that code for transcription factors have mutations that inactivate transcription (v-erbA and possibly v-rel) or that activate transcription (v-jun and v-fos).

8. 21.4 A zinc finger motif is a DNA-binding domain Figure 21.3 Transcription factor SP1 has a series of three zinc fingers, each with a characteristic pattern of cysteine and histidine residues that constitute the zinc-binding site.

9. 21.4 A zinc finger motif is a DNA-binding domain Figure 21.4 Zinc fingers may form a-helices that insert into the major groove, associated with b-sheets on the other side.

10. 21.4 A zinc finger motif is a DNA-binding domain Figure 21.5 The first finger of a steroid receptor controls specificity of DNA-binding (positions shown in red); the second finger controls specificity of dimerization (positions shown in blue). The expanded view of the first finger shows that discrimination between GRE and ERE target sequences rests on two amino acids at the base.

11. Receptor is a transmembrane protein, located in the plasma membrane, that binds a ligand in a domain on the extracellular side, and as a result has a change in activity of the cytoplasmic domain. (The same term is sometimes used also for the steroid receptors, which are transcription factors that are activated by binding ligands that are steroids or other small molecules.) 21.5 Steroid receptors have several independent domains

12. 21.5 Steroid receptors have several independent domains Figure 21.6 Several types of hydrophobic small molecules activate transcription factors. Corticoids and steroid sex hormones are synthesized from cholesterol, vitamin D is a steroid, thyroid hormones are synthesized from tyrosine, and retinoic acid is synthesized from isoprene (in fish liver).

13. 21.5 Steroid receptors have several independent domains Figure 21.7 Glucocorticoids regulate gene transcription by causing their receptor to bind to an enhancer whose action is needed for promoter function.

14. 21.5 Steroid receptors have several independent domains Figure 21.8 Receptors for many steroid and thyroid hormones have a similar organization, with an individual N-terminal region, conserved DNA-binding region, and a C-terminal hormone-binding region.

15. 21.5 Steroid receptors have several independent domains Figure 21.8 Receptors for many steroid and thyroid hormones have a similar organization, with an individual N-terminal region, conserved DNA-binding region, and a C-terminal hormone-binding region.

16. 21.5 Steroid receptors have several independent domains Figure 21.5 The first finger of a steroid receptor controls specificity of DNA-binding (positions shown in red); the second finger controls specificity of dimerization (positions shown in blue). The expanded view of the first finger shows that discrimination between GRE and ERE target sequences rests on two amino acids at the base.

17. 21.5 Steroid receptors have several independent domains Figure 21.19 Coactivators may have HAT activities that acetylate the tails of nucleosomal histones.

18. 21.5 Steroid receptors have several independent domains Figure 21.20 A repressor complex contains three components: a DNA binding subunit, a corepressor, and a histone deacetylase.

19. 21.5 Steroid receptors have several independent domains Figure 21.9 TR and RAR bind the SMRT corepressor in the absence of ligand. The promoter is not expressed. When SMRT is displaced by binding of ligand, the receptor binds a coactivator complex. This leads to activation of transcription by the basal apparatus.

20. 21.6 Homeodomains bind related targets in DNA Figure 21.10 The homeodomain may be the sole DNA-binding motif in a transcriptional regulator or may be combined with other motifs. It represents a discrete (60 residue) part of the protein.

21. 21.6 Homeodomains bind related targets in DNA Figure 21.11 The homeodomain of the Antennapedia gene represents the major group of genes containing homeoboxes in Drosophila; engrailed (en) represents another type of homeotic gene; and the mammalian factor Oct-2 represents a distantly related group of transcription factors. The homeodomain is conventionally numbered from 1 to 60. It starts with the N-terminal arm, and the three helical regions occupy residues 10-22,28-38, and 42-58.

22. 21.6 Homeodomains bind related targets in DNA Figure 21.12 Helix 3 of the homeodomain binds in the major groove of DNA, with helices 1 and 2 lying outside the double helix. Helix 3 contacts both the phosphate backbone and specific bases. The N-terminal arm lies in the minor groove, and makes additional contacts.

23. 21.6 Homeodomains bind related targets in DNA Figure 29.8 The posterior pathway has two branches, responsible for abdominal development and germ cell formation.

24. 21.7 Helix-loop-helix proteins interact by combinatorial association Figure 21.13 All HLH proteins have regions corresponding to helix 1 and helix 2, separated by a loop of 10-24 residues. Basic HLH proteins have a region with conserved positive charges immediately adjacent to helix 1.

25. 21.7 Helix-loop-helix proteins interact by combinatorial association Figure 21.14 An HLH dimer in which both subunits are of the bHLH type can bind DNA, but a dimer in which one subunit lacks the basic region cannot bind DNA.

26. 21.8 Leucine zippers are involved in dimer formation Figure 21.15 The basic regions of the bZIP motif are held together by the dimerization at the adjacent zipper region when the hydrophobic faces of two leucine zippers interact in parallel orientation.

27. 21.8 Leucine zippers are involved in dimer formation Figure 20.19 An enhancer contains several structural motifs. The histogram plots the effect of all mutations that reduce enhancer function to <75% of wild type. Binding sites for proteins are indicated below the histogram.

28. Chromatin remodeling describes the energy-dependent displacement or reorganization of nucleosomes that occurs in conjunction with activation of genes for transcription. 21.9 Chromatin remodeling is an active process

29. 21.9 Chromatin remodeling is an active process Figure 21.16 The pre-emptive model for transcription of chromatin proposes that if nucleosomes form at a promoter, transcription factors (and RNA polymerase) cannot bind. If transcription factors (and RNA polymerase) bind to the promoter to establish a stable complex for initiation, histones are excluded.

30. 21.9 Chromatin remodeling is an active process Figure 21.17 The dynamic model for transcription of chromatin relies upon factors that can use energy provided by hydrolysis of ATP to displace nucleosomes from specific DNA sequences.

31. 21.9 Chromatin remodeling is an active process Figure 21.18 Hormone receptor and NF1 cannot bind simultaneously to the MMTV promoter in the form of linear DNA, but can bind when the DNA is presented on a nucleosomal surface.

32. 21.9 Chromatin remodeling is an active process Figure 21.18 Hormone receptor and NF1 cannot bind simultaneously to the MMTV promoter in the form of linear DNA, but can bind when the DNA is presented on a nucleosomal surface.

33. 21.10 Histone acetylation and deacetylation control chromatin activity HAT (histone acetyltransferase) enzymes modify histones by addition of acetyl groups; some transcriptional coactivators have HAT activity.HDAC (histone deacetyltransferase) enzymes remove acetyl groups from histones; they may be associated with repressors of transcription.

34. 21.10 Histone acetylation and deacetylation control chromatin activity Figure 20.26 An upstream transcription factor may bind a coactivator that contacts the basal apparatus.

35. 21.10 Histone acetylation and deacetylation control chromatin activity Figure 21.19 Coactivators may have HAT activities that acetylate the tails of nucleosomal histones.

36. 21.10 Histone acetylation and deacetylation control chromatin activity Figure 21.20 A repressor complex contains three components: a DNA binding subunit, a corepressor, and a histone deacetylase.

37. 21.11 Polycomb and trithorax are antagonistic repressors and activators Figure 21.21 Pc-G proteins do not initiate repression, but are responsible for maintaining it.

38. 21.11 Polycomb and trithorax are antagonistic repressors and activators Figure 19.45 Extension of heterochromatin inactivates genes. The probability that a gene will be inactivated depends on its distance from the heterochromatin region.

39. 21.12 Long range regulation and insulation of domains Domain of a chromosome may refer either to a discrete structural entity defined as a region within which supercoiling is independent of other domains; or to an extensive region including an expressed gene that has heightened sensitivity to degradation by the enzyme DNAase I.MAR (matrix attachment site; also known as SAR for scaffold attachment site) is a region of DNA that attaches to the nuclear matrix.

40. 21.12 Long range regulation and insulation of domains Figure 4.1 Each of the a-like and b-like globin gene families is organized into a single cluster that includes functional genes and pseudogenes (y).

41. 21.12 Long range regulation and insulation of domains Figure 4.1 Each of the a-like and b-like globin gene families is organized into a single cluster that includes functional genes and pseudogenes (y).

42. 21.12 Long range regulation and insulation of domains Figure 21.22 A globin domain is marked by hypersensitive sites at either end. The group of sites at the 5￠side constitutes the LCR and is essential for the function of all genes in the cluster.

43. 21.12 Long range regulation and insulation of domains Figure 19.42 Sensitivity to DNAase I can be measured by determining the rate of disappearance of the material hybridizing with a particular probe.

44. 21.12 Long range regulation and insulation of domains Figure 21.23 Specialized chromatin structures that include hypersensitive sites mark the ends of a domain in the D. melanogaster genome and insulate genes between them from the effects of surrounding sequences.

45. 21.12 Long range regulation and insulation of domains Figure 21.24 A protein that binds to the insulator scs￠is localized at interbands in Drosophila polytene chromosomes. Red staining identifies the DNA (the bands) on both the upper and lower samples; green staining identifies BEAF32 (often at interbands) on the upper sample. Yellow shows coincidence of the two labels. Some of the more prominent stained interbands are marked by white lines. Photograph kindly provided by Uli Laemmli.

46. 21.12 Long range regulation and insulation of domains Figure 21.25 The insulator of the gypsy transposon blocks the action of an enhancer when it is placed between the enhancer and the promoter.

47. 21.12 Long range regulation and insulation of domains Figure 29.32 The homeotic genes of the ANT-C complex confer identity on the most anterior segments of the fly. The genes vary in size, and are interspersed with other genes. The antp gene is very large and has alternative forms of expression.

48. 21.12 Long range regulation and insulation of domains Figure 21.26 Fab-7 is a boundary element that is necessary for the independence of regulatory elements iab-6 and iab-7.

49. 21.12 Long range regulation and insulation of domains Figure 21.27 Domains may possess three types of sites: insulators to prevent effects from spreading between domains; MARs to attach the domain to the nuclear matrix; and LCRs that are required for initiation of transcription.

50. 21.13 Gene expression is associated with demethylation Figure 21.28 The restriction enzyme MspI cleaves all CCGG sequences whether or not they are methylated at the second C, but HpaII cleaves only nonmethylated CCGG tetramers.