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 3/29/05

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 3/29/05

5. Different changes of DNA sequences Listen to the nature Mutation is bad and naturally repaired, thus it could not be responsible for biodiversity. Recombination is good and naturally promoted; it is responsible for diversity inside of species. Transposition is different from mutation and recombination because (1) producing mechanism is different; (2) no mechanism to correct it; (3) existing in nature in a well-controlled manner (10 -5 ). Not repaired but controlled.

6. CHAPTER 10 Homologous recombination at the molecular level Molecular Biology Course

7. All DNA is recombinant DNA. Genetic exchange works constantly to blend and rearrange chromosomes, most obviously during meiosis, when homologous chromosomes pair prior to the first nuclear division. During this pairing, genetic exchange between the chromosomes occurs. This exchange, classically termed crossing over, is one of the results of homologous recombination.

8. OUTLINE 1. Models for Homologous Recombination (two models)** 2. Homologous Recombination Protein Machines (RecBCD pathway)** 3. Homologous Recombination in Eukaryotes (meiosis recombination, proteins) 4. Mating-Type Switching (a gene conversion event) 5. Genetic Consequences of the Mechanism of Homologous Recombination (exchange or conversion)

9. Topic 1: Models for Homologous Recombination 1.Holliday model (Holliday 模型 ) 2.Double-strand break (DSB) repair model ( 双链断裂修复模型 ) CHAPTER 10 Homologous recombination at the molecular level

10.  Alignment ( 结盟 ) of two homologous DNA molecules.  Introduction of breaks in the DNA  Formation of initial short regions of base pairing between the two recombining DNA molecules: strand invasion  Movement of the Holliday junction: branch migration  Cleavage of the Holliday junction: resolution Key steps shared by different models

11. The Holliday model very well illustrates the DNA strand invasion, branch migration, and Holliday junction resolution processes central to homologous recombination. The Holliday model illustrates key steps in homologous recombination Watch the animation for details!

12. 1. Homologous recombination is often initiated by double-stranded breaks (DSB) in DNA, while Holliday model is initiate by the pair of aligned nicks. 2. DSB occurs relatively frequently, but the aligned nicks not. The double-strand break repair model more accurately describes many recombination events

13. DSB breaks Figure 10-3 DSB repair model Processing of the DSB to generate DNA with 3 ’ ss tails Strand invasion of 3 ’ end Second strand invasion and DNA repair synthesis from the 3 ’ ends Branch formation and migration

14. 1. DSBs in DNA arise quite frequently. 2. In bacteria, the major biological role of homologous recombination is to repair DSBs (Ionizing radiation, damage in the DNA template); DSBs also promotes genetic exchange. 3. In eukaryotic cells, homologous recombination is critical for DNA repairing, as well as for the process of chromosomal pairing during meiosis. Double – stranded DNA breaks arise by numerous means and initiate homologous recombination

15. Figure 10-4. Damage in the DNA template can lead to DSB formation during replication ( 复制叉瓦解 )

16. Topic 2: Homologous recombination protein machines---RecBCD pathway 1.RecBCD helicase/nuclease processes broken DNA ends for recombination (  site). 2.RecA protein promotes strand invasion (how?). 3.RuvAB complex promotes branch migration. 4.RuvC resolves the Holliday junction CHAPTER 10 Homologous recombination at the molecular level

17. Watch the animation for details!

18. Topic 3: Homologous recombination in eukaryotes CHAPTER 10 Homologous recombination at the molecular level

19. 1.Critical for DNA repair and the restarting of collapsed ( 瓦解的 ) replication forks. 2.During meiosis, homologous recombination is Required for proper chromosome pairing, thus for maintaining the integrity of the genome. Biological functions of homologous recombination in eukaryotes

20. The duplicated homologous chromosomes must pair. *** Without recombination, chromosome often fails to align properly for the first meiotic division. Figure 10-14 DNA dynamics during meiosis

21. 1.The Spo11 protein introduces DSBs in chromosomal DNA at many locations to initiate meiotic recombination. 2.SPO11 gene is expressed specifically during meiosis, and Spo11-mediated DNA cleavage occurs right around the time when the replicated homologous chromosomes start to pair. Programmed generation of double – stranded DNA breaks occurs during meiosis

22. Figure 10-16 Mechanism of cleavage by Spo11.

23. MRX protein processes the cleaved DNA ends for assembly of the RecA-like strand –exchange proteins Dmc1 is a RecA-like protein that specifically functions in meiotic recombination. Rad51 has a similar function.

24. Figure 10-17 Meiotic recombination pathway

25. Topic 4: mating-type switching CHAPTER 10 Homologous recombination at the molecular level  Mating-type switching is initiated by a site-specific double-strand break  Mating-type switching is a gene conversion event, not associated with crossing over

26. Figure 10-20 Genetic loci encoding mating-type information of yeast S. cerevisiae ( 啤酒酵母 ) HML and HMR loci are called silent cassettes because they are not expressed, which provide a “ store house ” of genetic information used to switch a cell ’ s mating type

27. Intramolocular alignments Rad51-dependent strand invasion Synthesis of two new DNA strands from a information from HMRa Branch migration, new DNA synthesis, and branch resolution

28. Topic 4: Genetic Consequences of the Mechanism of Homologous Recombination (HR) CHAPTER 10 Homologous recombination at the molecular level  HR is generally independent of sequence and therefore the frequency of recombination between any two genes is generally proportional to the distance between those genes. ---The molecular basis of Morgen ’ s chromosome mapping

29. Gene conversion occurs during HR 1.Genes close to the sites of DSB is converted during recombination.

30. Gene conversion occurs during HR 2. Repair of the mismatches in the recombination intermediates.

31. 重点和难点 3/29/05 Topics 1 & 2 are the keys to understand homologous recombination and other topics. Completely understand two animations on your CD CHAPTER 10 Homologous recombination at the molecular level

32. Review your textbook Homework CHAPTER 9 The mutability and repair of DNA