1. Welcome Each of You to My Molecular Biology Class

2. Molecular Biology of the Gene, 5/E --- Watson et al. (2004) Part I: Chemistry and Genetics Part II: Maintenance of the Genome Part III: Expression of the Genome Part IV: Regulation Part V: Methods 3/11/05

3. Part II: Maintenance of the Genome Dedicated to the structure of DNA and the processes that propagate, maintain and alter it from one cell generation to the next

4. Ch 6: The structures of DNA and RNA Ch 7: Chromosomes, chromatins and the nucleosome Ch 8: The replication of DNA Ch 9: The mutability and repair of DNA Ch 10: Homologous recombination at the molecular level Ch 11: Site-specific recombination and transposition of DNA 3/11/05

5. CHAPTER 7: Chromosomes, chromatin, and the nucleosome

6. Consider the structure of DNA within the cell, and the biological relevance of the structure. DNA is associated with proteins in cells, both prokaryotes and eukaryotes, even viruses Each DNA and its associated proteins is called a chromosome

7. Nucleus: 细胞核 ; Nucleolus: 核仁 Nucleoid: 类核 Mitosis: 有丝分裂； Meiosis ：减数分裂 interphase ：分裂间期 Histone: 组蛋白； Nucleosome: 核小体 Chromotasome: 染色小体 Chromosome: 染色体； Chromatin: 染色质； eu-; hetero- Centromere ( 中心粒） Telomere （端粒） Repetitive DNA ( 重复 DNA) Tandem gene cluster （串联基因 簇） Vocabulary

8. The importance of packing of DNA into chromosomes  Chromosome is a compact form of the DNA that readily fits inside the cell  To protect DNA from damage  DNA in a chromosome can be transmitted efficiently to both daughter cells during cell division  Chromosome confers an overall organization to each molecule of DNA, which facilitates gene expression as well as recombination

9. Half of the molecular mass of eukaryotic chromosome is protein  In eukaryotic cells a given region of DNA with its associated proteins is called chromatin  The majority of the associated proteins are small, basic proteins called histones.  Other proteins associated with the chromosome are referred to as non-histone proteins, including numerous DNA binding proteins that regulate the transcription, replication, repair and recombination of DNA. Proteins in chromosome (1)

10.  Nucleosomes: regular association of DNA with histones to form a structure effectively compacting DNA Proteins in chromosome (2)

11. 1.What is the cost (challenge) of compaction of DNA into chromosome? 2.How the challenge could be resolved? 3.What are the advantage of the challenge? CHAPTER 7: Chromosomes, chromatin, and the nucleosome

12. OUTLINE  Chromosome sequence & diversity  Chromosome duplication & segregation  The nucleosome  Higher-order chromatin structure  Regulation of chromatin structure  Nucleosome assembly CHAPTER 7: Chromosomes, chromatin, and the nucleosome

13. Chromosome sequence & diversity CHAPTER 7: Chromosomes, chromatin, and the nucleosome Chromosomes  Shape: circular or linear  Number in an organism is characteristic  Copy: haploid, diploid, polyploid Genomes 3/15/05

14. Difference in the structures of eukaryotic and prokaryotic cells is a key to better understand the molecular processes of genome maintenance and expression, as well as the differences in these processes between eukaryotes and prokaryotes Chromosome sequence & diversity 3/15/05

15. Chromosome sequence & diversity Figure 7-1*

16. Chromosome sequence & diversity  Genome size: the length of DNA associated with one haploid complement of chromosomes  Gene number: the number of genes included in a genome  Gene density: the average number of genes per Mb of genomic DNA Genome & the complexity of the organism See Table 7-2 to find the relationship 3/15/05

17. Table 7-2

18. Chromosome sequence & diversity  Increases in gene size: (1) increase in the sequence of regulatory sequence; (2) presence of introns (splicing)  Increases in the DNA between genes (intergenic sequences): (1) unique; (2) repeated Genes make up only a small proportion of the eukaryotic genome See Figure 7-2, 3, 4, 5; Table 7-3 3/15/05

19. Table 7-3

20. Figure 7-2

21. Figure 7-4*

22. Chromosome duplication & segregation CHAPTER 7: Chromosomes, chromatin, and the nucleosome (1) Critical DNA elements  Origins of replication  Centromeres  Telomeres These elements are not involved in gene expression 3/15/05

23. Sites at which the DNA replication machinery assembles to initiate replication; required fro replication  30-40 kb apart on each eukaryotic chromosome  Only one origin for prokaryotic chromosome Origins of replication Chromosome duplication & segregation

24. Required for the correct segregation of the chromosomes after replication  Direct the formation of kinetochore (an elaborate protein complex) essential for chrom. segregation  One chromosome, one centromere  The size varies (200 bp- >40 kb)  Composed of largely repetitive DNA sequences Centromeres Chromosome duplication & segregation

25. Figure 7-6 Centromeres, origin of replication and telomere are required for eukaryotic chrom. maintenance

26. Cell cycle: a single round of cell division Mitotic cell division: the chrom. Number is maintained during cell division (2) Eukaryotic chromosome duplication & segregation occur in separate phases of the cell cycle Chromosome duplication & segregation

27. Figure 7-10 The eukaryotic mitotic cell cycle

28. Figure 7-11 The events of S phase

29. Figure 7-11 The events of M phase Mitotic spindle

30. M phase: condensed state, completely disentangled from each other G1, S, G2 phases: diffused, significantly less compact. The structure of chrom. changes, e.g. DNA replication requires the nearly complete disassembly and reassembly of the proteins associated with each chromosome (3) Chromosome structure changes as eukaryotic cells divide Chromosome duplication & segregation

31. Chromosome condensation Figure 7-13 Changes in chromatin structure REMEMBER: chromosome is a consistently changing structure (dynamics)

32. Think of the regulatory mechanisms might be involved to CHECK the cell condition (4) The gap phase of the cell cycle allow time to prepare for the next cell cycle stage while also checking that the previous stage is finished correctly. Chromosome duplication & segregation

33. (5) Different levels of chromosome structure can be observed by microscopy Chromosome duplication & segregation

34. Figure 7-13 Forms of chromotin structure seen in EM (electron microscopy)

35. The nucleosome CHAPTER 7: Chromosomes, chromatin, and the nucleosome Nucleosome & histone structures 3/15/05

36. (1) Nucleosomes are the building blocks of chromosomes The nucleosome  The nucleosome is composed of a core of eight histone proteins and the DNA (core DNA, 147 bp) wrapped around them. The DNA between each nucleosome is called a linker DNA. Each eukaryote has a characteristic average linker DNA length (20-60 bp)

37. Figure 7-18 DNA packaged into nucleosome Six-fold DNA compaction

38.  Five abundant histones are H1 (linker histone, 20 kd), H2A, H2B, H3 and H4 (core histones, 11-15 kd).  The core histones share a common structural fold, called histone-fold domain  The core histones each have an N- terminal “tail”, the sites of extensive modifications (2) Histones are small, positively charged (basic) proteins The nucleosome

39. Figure 7-19 The core histones share a common structural fold (1) (2)

40. (3) Many DNA sequence- independent contacts (?) mediate interaction between between the core histones and DNA The nucleosome Figure 7-25

41. (4) The histone N-terminal tails stabilize DNA wrapping around the octamer Figure 7-26 The histone tails emerge from the core of the nucleosome at specific positions, serving as the grooves of a screw to direct the DNA wrapping around the histone core in a left-handed manner.

42. Higher-order chromatin structure CHAPTER 7: Chromosomes, chromatin, and the nucleosome How does it form? 3/15/05

43. (1) Histone H1 binds to the linker DNA between nucleosome, inducing tighter DNA wrapping around the nucleosome Higher-order chromatin structure Figures 7-28, 29

44. (2) Nuclear arrays can form more complex structures: the 30-nm fiber (“zigzag model”) Higher-order chromatin structure Figures 7-30 (40-fold compaction)

45. (3) Further compaction of DNA involves large loops of nucleosomal DNA Higher-order chromatin structure  Additional 10 3 -10 4 -fold compaction is required, but the mechanism is unclear  The nuclear scaffold model is proposed  Additional 10 3 -10 4 -fold compaction is required, but the mechanism is unclear  The nuclear scaffold model is proposed

46. Figures 7-32 The higher- order structure of chromatin. (a) A transmission electron micrograph, (b) A model

47. (3) Histone variants alter nucleosome function Higher-order chromatin structure  Several histone variants are found in enkaryotes  This variants can replace one of the 4 standard histones to form alternate nucleosomes  Several histone variants are found in enkaryotes  This variants can replace one of the 4 standard histones to form alternate nucleosomes

48. Figures 7-33 Alteration of chromatin by incorporation of histone variants CENP-A is associated with the nucleosomes containing centromeric DNA

49. Regulation of chromatin structure CHAPTER 7: Chromosomes, chromatin, and the nucleosome How? 3/15/05

50. The interaction of DNA with the histone octamer is dynamic Regulation of chromatin structure  There are factors acting on the nucleosome to increase or decrease the dynamic nature  The dynamic nature of DNA- binding to the histone core is important for access of DNA by other proteins essential genome expression etc.  There are factors acting on the nucleosome to increase or decrease the dynamic nature  The dynamic nature of DNA- binding to the histone core is important for access of DNA by other proteins essential genome expression etc.

51. Figures 7-34 A model for gaining access to core DNA

52. Nucleosome remodeling complexes facilitate nucleosome movement Regulation of chromatin structure  A large protein complexes facilitate changes in nucleosome location or interaction with the DNA using the energy of ATP hydrolysis.

53. Figures 7-35 Nucleosome movement catalyzed by nucleosome remodeling complexes

54. Modification of the N-terminal tails of the histones alters chromatin accessibility, and specific enzymes are responsible for histone modification Regulation of chromatin structure

55. Figures 7-38 Modification of the histone N-terminal tails alters the function of chromatin

56. Nucleosome assembly CHAPTER 7: Chromosomes, chromatin, and the nucleosome  Nucleosomes are assembled immediately after DNA replication, and the assembly requires histone chaperones 3/15/05

57. Figures 7-41 The inheritance of histones after DNA replication

58. Try to complete all the excises on your study CD Homework