1. William S. Klug Michael R. Cummings Charlotte A
William S. Klug Michael R. Cummings Charlotte A. Spencer Concepts of Genetics Eighth Edition Chapter 17 Regulation of Gene Expression in Eukaryotes
Copyright © 2006 Pearson Prentice Hall, Inc.

2. Eukaryotic Gene Regulation Differs from Regulation in Prokaryotes
• Much more genetic info
• Chromatin structure
• Many chromosomes
• Transcription separated from translation
• Transcripts are processed, have longer half-lives
• Translational control used
• Higher eukaryotes are multicellular

3. Figure 17-1 Copyright © 2006 Pearson Prentice Hall, Inc.
Figure 17-1 Various levels of regulation that are possible during the expression of the genetic material.
Figure Copyright © 2006 Pearson Prentice Hall, Inc.

4. Chromosome Organization in the Nucleus Influences Gene Expression

5. Figure 17-2a Copyright © 2006 Pearson Prentice Hall, Inc.
Figure 17-2a (a) In the nucleus, each chromosome occupies a discrete territory, and is separated from other chromosomes by an interchromosomal domain, where mRNA transcription and processing is thought to occur. (b) FISH probes hybridized to human chromsome 7. At left is hybridization to metaphase chromosomes. In the nucleus (right) the probes reveal the location of the territories occupied by chromosome 7.
Figure 17-2a Copyright © 2006 Pearson Prentice Hall, Inc.

6. Transcription Initiation Is a Major Form of Gene Regulation

7. Cis regulatory sequences
Figure 17-3 Expression of eukaryotic genes is controlled by regulatory elements directly adjacent to the gene, such as promoters, and by sequences that can be far from the transcriptional unit, such as enhancers and silencers.
Figure Copyright © 2006 Pearson Prentice Hall, Inc.

8. Transcription Initiation Is a Major Form of Gene Regulation
Promoters Have a Modular Organization

9. Figure 17-4 Copyright © 2006 Pearson Prentice Hall, Inc.
Figure 17-4 Summary of the effects of point mutations in the promoter region on transcription of the -globin gene. Each line represents the level of transcription produced by a single nucleotide mutation (relative to wild type) in a separate experiment. Dots represent nucleotides in which no mutation was obtained. Note that mutations within the specific elements of the promoter have the greatest effect on the level of transcription.
-110
-70 to -80
-25 to-30
Figure Copyright © 2006 Pearson Prentice Hall, Inc.

10. Figure 17-5 Copyright © 2006 Pearson Prentice Hall, Inc.
Figure 17-5 Organization of the promoter regions in several genes expressed in eukaryotic cells, illustrating the variable nature, number, and arrangement of controlling elements.
Figure Copyright © 2006 Pearson Prentice Hall, Inc.

11. Transcription Initiation Is a Major Form of Gene Regulation
Enhancers Control the Rate of Transcription
In yeast, upstream activator sequence (UAS)

12. Figure 17-6 Copyright © 2006 Pearson Prentice Hall, Inc.
Figure 17-6 DNA sequence for the SV40 enhancer. Boxed sequences are those required for maximum enhancer effect. The brackets below the sequence name the various sequence motifs within this region. The two domains of the enhancer (A and B) are indicated.
Figure Copyright © 2006 Pearson Prentice Hall, Inc.

13. Transcription in Eukaryotes Requires Several Steps
Transcription Requires Chromatin Remodeling

14. Figure 17-7 Copyright © 2006 Pearson Prentice Hall, Inc.
Figure 17-7 Nucleosomes can inhibit multiple steps required for gene transcription. The binding of enhancer transcription factors requires accessing nucleosomal DNA and may result in displacement of the nucleosome. Similarly, the formation of the basal transcription complex at the TATA box, other upstream elements (USEs) and the core promoter site is also suppressed by nucleosomes. Finally, RNA polymerase II is slowed by the presence of nucleosomes.
Figure Copyright © 2006 Pearson Prentice Hall, Inc.

15. Figure 17-8 Copyright © 2006 Pearson Prentice Hall, Inc.
Figure 17-8 The SWI/SNF nucleosome remodeling complexes can be directed to specific DNA sites in several ways. (a) Transcription factors, including those with leucine zipper domains can target binding. (b) Histone components of nucleosomes modified by acetylation can serve as SWI/SNF targets. (c) Methlyated DNA regions can also be target sites for nucleosome remodeling complexes.
Figure Copyright © 2006 Pearson Prentice Hall, Inc.

16. Figure 17-9a Copyright © 2006 Pearson Prentice Hall, Inc.
Figure 17-9a Three mechanisms that might be used to alter nucleosome structure by the ATP hydrolysis-dependent remodeling complex SWI/SNF. (a) DNA–histone contacts may be loosened. (b) The path of the DNA around an unaltered nucleosome core particle may be altered. (c) The conformation of the nucleosome core particle may be altered.
Figure 17-9a Copyright © 2006 Pearson Prentice Hall, Inc.

17. Figure 17-9b Copyright © 2006 Pearson Prentice Hall, Inc.
Figure 17-9b Three mechanisms that might be used to alter nucleosome structure by the ATP hydrolysis-dependent remodeling complex SWI/SNF. (a) DNA–histone contacts may be loosened. (b) The path of the DNA around an unaltered nucleosome core particle may be altered. (c) The conformation of the nucleosome core particle may be altered.
Figure 17-9b Copyright © 2006 Pearson Prentice Hall, Inc.

18. Figure 17-9c Copyright © 2006 Pearson Prentice Hall, Inc.
Figure 17-9c Three mechanisms that might be used to alter nucleosome structure by the ATP hydrolysis-dependent remodeling complex SWI/SNF. (a) DNA–histone contacts may be loosened. (b) The path of the DNA around an unaltered nucleosome core particle may be altered. (c) The conformation of the nucleosome core particle may be altered.
Figure 17-9c Copyright © 2006 Pearson Prentice Hall, Inc.

19. Histone Modification Is Part of Chromatin Remodeling

20. Figure 17-10 Copyright © 2006 Pearson Prentice Hall, Inc.
Figure Proposed model of the action of HAT and HD complexes. Transcription factors recruit the complex to the gene, which either adds or removes acetyl groups, aiding in either opening or closing the chromatin structure.
Figure Copyright © 2006 Pearson Prentice Hall, Inc.

21. Reduction of positive charge on histone protein weakens
interactions between histone and DNA

22. Assembly of the Basal Transcription Complex Occurs at the Promoter
RNA Polymerases and Transcription
Formation of the Transcription Initiation Complex

23. Figure 17-11 Copyright © 2006 Pearson Prentice Hall, Inc.
Figure The assembly of transcription factors required for the initiation of transcription by RNA polymerase II.
Figure Copyright © 2006 Pearson Prentice Hall, Inc.

24. Figure 17-12 Copyright © 2006 Pearson Prentice Hall, Inc.
Figure Molecular complex formed between the TATA-box binding protein (green) and the 8-bp TATA-box nucleotide sequence (red) and its phosphodiester backbone (yellow).
Figure Copyright © 2006 Pearson Prentice Hall, Inc.

25. Activators Bind to Enhancers and Change the Rate of Transcription Initiation

26. Figure 17-13 Copyright © 2006 Pearson Prentice Hall, Inc.
Figure Formation of DNA loops allows factors that bind to enhancers at a distance from the promoter to interact with regulatory proteins in the transcription complex and to maximize transcription.
Figure Copyright © 2006 Pearson Prentice Hall, Inc.

28. Figure 17-14 Copyright © 2006 Pearson Prentice Hall, Inc.
Figure A helix–turn–helix or homeodomain in which (a) three planes of the -helix of the protein are established, and (b) these domains bind in the grooves of the DNA molecule.
Figure Copyright © 2006 Pearson Prentice Hall, Inc.

29. Figure 17-15 Copyright © 2006 Pearson Prentice Hall, Inc.
Figure (a) A zinc finger in which cysteine and histidine residues bind to a atom. (b) This loops the amino acid chain out into a fingerlike configuration.
Figure Copyright © 2006 Pearson Prentice Hall, Inc.

30. Figure 17-16 Copyright © 2006 Pearson Prentice Hall, Inc.
Figure (a) A leucine zipper is the result of dimers from leucine residue at every other turn of the -helix in facing stretches of two polypeptide chains. (b) When the -helical regions form a leucine zipper, the regions beyond the zipper form a Y-shaped region that grips the DNA in a scissorlike configuration.
Figure Copyright © 2006 Pearson Prentice Hall, Inc.

31. DNA Methylation and Regulation of Gene Expression

32. Figure 17-19a Copyright © 2006 Pearson Prentice Hall, Inc.
Figure 17-19a The restriction enzymes HpaII and MspI recognize and cut at CCGG sequences. (a) If the second cytosine is methylated (indicated by an asterisk), HpaII will not cut. (b) The enzyme MspI cuts at all CCGG sites, whether or not the second cytosine is methylated. Thus, the state of methylation of a given gene in a given tissue can be determined by cutting DNA extracted from that tissue with HpaII and MspI.
Figure 17-19a Copyright © 2006 Pearson Prentice Hall, Inc.

33. Figure 17-19b Copyright © 2006 Pearson Prentice Hall, Inc.
Figure 17-19b The restriction enzymes HpaII and MspI recognize and cut at CCGG sequences. (a) If the second cytosine is methylated (indicated by an asterisk), HpaII will not cut. (b) The enzyme MspI cuts at all CCGG sites, whether or not the second cytosine is methylated. Thus, the state of methylation of a given gene in a given tissue can be determined by cutting DNA extracted from that tissue with HpaII and MspI.
Figure 17-19b Copyright © 2006 Pearson Prentice Hall, Inc.

34. Figure 17-20 Copyright © 2006 Pearson Prentice Hall, Inc.
Figure The base 5-azacytosine, which has a nitrogen at the 5 position and can be incorporated into DNA in place of deoxycytidine during DNA synthesis. The base 5-azacytosine cannot be methylated, causing undermethylation of the CpG dinucleotide wherever it has been incorporated.
Figure Copyright © 2006 Pearson Prentice Hall, Inc.

35. Das and Singal (2004) J. Clin. Oncol.

36. Posttranscriptional Regulation of Gene Expression
Alternative Splicing Pathways for mRNA

37. Figure 17-21 Copyright © 2006 Pearson Prentice Hall, Inc.
Figure Patterns of alternative splicing in a eukaryotic mRNA. Exons are represented by cylinders. The normal splicing pattern is shown above the exons; alternative patterns of splicing are shown below the exons. Note that alternative splicing can add exons and a new poly (A) site. Alternative splice sites are often used in multiple combinations, resulting in many different mRNAs from a single transcript.
Figure Copyright © 2006 Pearson Prentice Hall, Inc.

38. Alternative Splicing and Cell Function

39. Figure 17-22 Copyright © 2006 Pearson Prentice Hall, Inc.
Figure Alternative splicing in the human SLO gene. (a) The cochlea of the inner ear, which contains a basilar membrane carrying hair cells. (b) A cross-sectional view of the basilar membrane, showing the single row of inner cells, and three rows of outer cells. (c) The basilar membrane laid out to show the arrangement of hair cells and the frequency gradient of sound received by hairs along the membrane. (d) Exon–intron organization of the SLO gene. Normal splicing events are shown above the exons; alternative sites are shown below the exons. Constitutive exons are silver, alternative exons are purple, and the STREX exon is magenta. (e) The presence or absence of the STREX exon affects the function of the calcium-sensitive potassium channel found in the plasma membrane of the inner hair cells.
Figure Copyright © 2006 Pearson Prentice Hall, Inc.

40. Figure 17-22d Copyright © 2006 Pearson Prentice Hall, Inc.
Figure 17-22d Alternative splicing in the human SLO gene. (a) The cochlea of the inner ear, which contains a basilar membrane carrying hair cells. (b) A cross-sectional view of the basilar membrane, showing the single row of inner cells, and three rows of outer cells. (c) The basilar membrane laid out to show the arrangement of hair cells and the frequency gradient of sound received by hairs along the membrane. (d) Exon–intron organization of the SLO gene. Normal splicing events are shown above the exons; alternative sites are shown below the exons. Constitutive exons are silver, alternative exons are purple, and the STREX exon is magenta. (e) The presence or absence of the STREX exon affects the function of the calcium-sensitive potassium channel found in the plasma membrane of the inner hair cells.
Figure 17-22d Copyright © 2006 Pearson Prentice Hall, Inc.

41. Figure 17-22e Copyright © 2006 Pearson Prentice Hall, Inc.
Figure 17-22e Alternative splicing in the human SLO gene. (a) The cochlea of the inner ear, which contains a basilar membrane carrying hair cells. (b) A cross-sectional view of the basilar membrane, showing the single row of inner cells, and three rows of outer cells. (c) The basilar membrane laid out to show the arrangement of hair cells and the frequency gradient of sound received by hairs along the membrane. (d) Exon–intron organization of the SLO gene. Normal splicing events are shown above the exons; alternative sites are shown below the exons. Constitutive exons are silver, alternative exons are purple, and the STREX exon is magenta. (e) The presence or absence of the STREX exon affects the function of the calcium-sensitive potassium channel found in the plasma membrane of the inner hair cells.
Figure 17-22e Copyright © 2006 Pearson Prentice Hall, Inc.

42. Alternative Splicing Amplifies the Number of Proteins Produced by a Genome

43. Figure 17-23 Copyright © 2006 Pearson Prentice Hall, Inc.
Dscam gene from Drosophila
Figure (Top) Organization of the Dscam gene in Drosophila melanogaster and the transcribed pre-mRNA. Each mRNA will contain one of the 12 possible exons for exon 4 (red), one of the 48 possible exons for exon 6 (blue), one of 33 for exon 9 (green), and one of 2 for exon 17 (yellow). If all possible combinations of these exons are used, the Dscam gene can encode 38,016 different versions of the DSCAM protein.
12 x 48 x 33 x 2 = 38,016
Figure Copyright © 2006 Pearson Prentice Hall, Inc.

44. RNA Silencing of Gene Expression

45. Figure 17-24 Copyright © 2006 Pearson Prentice Hall, Inc.
Figure (a) The action of Dicer and RISC (RNA-induced silencing complex). Dicer binds to double-stranded RNA molecules and cleaves them into nucleotide molecules called small interfering RNAs (siRNAs). These bind to a multiprotein RISC complex and are unwound to form single-stranded molecules that target mRNAs with complementary sequences, marking them for degradation. (b) Binding of the catalytic domains of Dicer monomers to RNA. Domains marked with an asterisk are inactive. Cutting by the active domains produces fragments nucleotides long.
Figure Copyright © 2006 Pearson Prentice Hall, Inc.

46. Figure 17-25 Copyright © 2006 Pearson Prentice Hall, Inc.
Figure Mechanisms of gene regulation by RNA gene silencing. In the cytoplasm, two systems operate to silence genes. (Middle) In siRNA mediated silencing, a precursor RNA molecule is processed by Dicer, a protein with RNAse activity to form an antisense single stranded RNA that combines with a protein complex with endonuclease activity. siRNA/RISC (RNA-induced silencing complex) binds to mRNAs with complementary sequences, and cuts the mRNA into fragments that are degraded. This process is called RNAi in animal cells, and posttranslational gene silencing (PTGS) in plants. (Right) A partially double-stranded precursor is processed by Dicer to yield microRNA (miRNA) that binds to complementary -untranslated regions (UTRs) of mRNA, inhibiting translation. In plants, miRNAs cause arrest of translation. (Left) Small RNAs, processed by Dicer, play a role in RNA-directed DNA methylation (RdDM). These RNAs combine with DNA methyl transferases (DMTases) to methylate cytosine residues in promoter regions (purple circles), silencing genes.
Figure Copyright © 2006 Pearson Prentice Hall, Inc.

47. Alternative Splicing and mRNA Stability Can Regulate Gene Expression
Sex Determination in Drosophila: A Model for Regulation of Alternative Splicing

48. Figure 17-26 Copyright © 2006 Pearson Prentice Hall, Inc.
Figure Hierarchy of gene regulation for sex determination in Drosophila. In females, the X:A ratio activates transcription of the Sxl gene. The product of this gene binds to premRNA of the tra gene and directs its splicing in a female-specific fashion. The female-specific TRA protein, in combination with the TRA-2 protein, directs female-specific splicing of dsx pre-mRNA, resulting in a female-specific protein (DSX-F). This protein, in combination with the IX protein, suppresses the pathway of male sexual development and activates the female pathway. In males, the X:A ratio does not activate Sxl. The result is a male-specific processing of tra pre-mRNA, resulting in no functional TRA protein, which in turn leads to male-specific processing of dsx transcripts, which results in a male-specific (DSX-M) protein that activates the pathway for male sexual development.
Figure Copyright © 2006 Pearson Prentice Hall, Inc.

49. Controlling mRNA Stability

50. Figure 17-27 Copyright © 2006 Pearson Prentice Hall, Inc.
Figure Model of posttranslational regulation of tubulin synthesis.
Figure Copyright © 2006 Pearson Prentice Hall, Inc.