BMCB625:Materials

Biochemistry Dep’t and course “quick” Links:

“This week’s tasks” Course web-page BMCB625

BMB Seminar Series

"Universal Slide Template" BMCB625:Discussion_Univ_template

Protein Crystallography Tutorial

Amazing page of links for all of your structural biology needs

Class Focus, Spring 2007

1. Organization Meeting and Rules of Engagement
2. Biochemistry and Structure of Replicating Machines at the Protein-DNA Interface
3. Molecular Mechanisms of Genomic Information Expansion
4. A Revealing Structure of the Exon Junction Complex

Week 1: Introduction and Scheduling

Presentation Zen

1. Slide Zen
2. Delivery Zen
3. Feel free to add links that help you

Evaluation Forms

• Evaluation Form MC
• Evaluation Form Presenter 1(Intro)
• Evaluation Form Presenter 2

Week 2: Rewrite the textbooks on DNA Replication

Papers

1. Lopes M, Foiani M, and Sogo JM. Multiple mechanisms control chromosome integrity after replication fork uncoupling and restart at irreparable UV lesions. Mol Cell. 2006 Jan 6;21(1):15-27. DOI:10.1016/j.molcel.2005.11.015 |
2. Heller RC and Marians KJ. Replication fork reactivation downstream of a blocked nascent leading strand. Nature. 2006 Feb 2;439(7076):557-62. DOI:10.1038/nature04329 |

Bonus Materials

3. Lehmann AR and Fuchs RP. Gaps and forks in DNA replication: Rediscovering old models. DNA Repair (Amst). 2006 Dec 9;5(12):1495-8. DOI:10.1016/j.dnarep.2006.07.002 |
4. Bell SD. Molecular biology: prime-time progress. Nature. 2006 Feb 2;439(7076):542-3. DOI:10.1038/439542a |
5. Rupp WD and Howard-Flanders P. Discontinuities in the DNA synthesized in an excision-defective strain of Escherichia coli following ultraviolet irradiation. 1968. DNA Repair (Amst). 2005 May 2;4(5):620-33.

6. Review: Replisome assembly and the direct restart of stalled replication forks.

   Heller RC, & Marians KJ. Nat Rev Mol Cell Biol. 2006 Dec;7(12):932-43. Epub 2006 Nov 8.

   [1]

7. Gamper H, Lehman N, Piette J, and Hearst JE. Purification of circular DNA using benzoylated naphthoylated DEAE-cellulose. DNA. 1985 Apr;4(2):157-64. DOI:10.1089/dna.1985.4.157 |
8. Liberi G, Maffioletti G, Lucca C, Chiolo I, Baryshnikova A, Cotta-Ramusino C, Lopes M, Pellicioli A, Haber JE, and Foiani M. Rad51-dependent DNA structures accumulate at damaged replication forks in sgs1 mutants defective in the yeast ortholog of BLM RecQ helicase. Genes Dev. 2005 Feb 1;19(3):339-50. DOI:10.1101/gad.322605 |
9. Viguera E, Rodríguez A, Hernández P, Krimer DB, Trellez O, and Schvartzman JB. A computer model for the analysis of DNA replication intermediates by two-dimensional agarose gel electrophoresis. Gene. 1998 Sep 14;217(1-2):41-9. DOI:10.1016/s0378-1119(98)00375-8 |
10. Dijkwel PA, Vaughn JP, and Hamlin JL. Mapping of replication initiation sites in mammalian genomes by two-dimensional gel analysis: stabilization and enrichment of replication intermediates by isolation on the nuclear matrix. Mol Cell Biol. 1991 Aug;11(8):3850-9. DOI:10.1128/mcb.11.8.3850-3859.1991 |
11. Brewer BJ and Fangman WL. The localization of replication origins on ARS plasmids in S. cerevisiae. Cell. 1987 Nov 6;51(3):463-71. DOI:10.1016/0092-8674(87)90642-8 |

BND Cellulose Protocol [1]

Using Caffeine to Elute Replication Intermediates with Single Stranded Regions [2]

Lecture Slides

DNA Replication Slides (pdf)‎

Chris and Mahta's Slides (ppt)

Supplemental Slides (ppt)‎

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BMCB625:DNA Replication

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Week 3: Go, Ichi, Nii, and San;New Components of DNA Replication

Papers

12. Moyer SE, Lewis PW, and Botchan MR. Isolation of the Cdc45/Mcm2-7/GINS (CMG) complex, a candidate for the eukaryotic DNA replication fork helicase. Proc Natl Acad Sci U S A. 2006 Jul 5;103(27):10236-10241. DOI:10.1073/pnas.0602400103 |

Bonus Materials

13. Takayama Y, Kamimura Y, Okawa M, Muramatsu S, Sugino A, and Araki H. GINS, a novel multiprotein complex required for chromosomal DNA replication in budding yeast. Genes Dev. 2003 May 1;17(9):1153-65. DOI:10.1101/gad.1065903 |
14. Kubota Y, Takase Y, Komori Y, Hashimoto Y, Arata T, Kamimura Y, Araki H, and Takisawa H. A novel ring-like complex of Xenopus proteins essential for the initiation of DNA replication. Genes Dev. 2003 May 1;17(9):1141-52. DOI:10.1101/gad.1070003 |
15. Forsburg SL. Eukaryotic MCM proteins: beyond replication initiation. Microbiol Mol Biol Rev. 2004 Mar;68(1):109-31. DOI:10.1128/MMBR.68.1.109-131.2004 |
16. Laskey RA and Madine MA. A rotary pumping model for helicase function of MCM proteins at a distance from replication forks. EMBO Rep. 2003 Jan;4(1):26-30. DOI:10.1038/sj.embor.embor706 |
16. Edwards MC, Tutter AV, Cvetic C, Gilbert CH, Prokhorova TA, and Walter JC. MCM2-7 complexes bind chromatin in a distributed pattern surrounding the origin recognition complex in Xenopus egg extracts. J Biol Chem. 2002 Sep 6;277(36):33049-57. DOI:10.1074/jbc.M204438200 |
16. Krude T, Musahl C, Laskey RA, and Knippers R. Human replication proteins hCdc21, hCdc46 and P1Mcm3 bind chromatin uniformly before S-phase and are displaced locally during DNA replication. J Cell Sci. 1996 Feb;109 ( Pt 2):309-18. DOI:10.1242/jcs.109.2.309 |
17. Kamada K, Kubota Y, Arata T, Shindo Y, and Hanaoka F. Structure of the human GINS complex and its assembly and functional interface in replication initiation. Nat Struct Mol Biol. 2007 May;14(5):388-96. DOI:10.1038/nsmb1231 |
18. Aparicio T, Ibarra A, and Méndez J. Cdc45-MCM-GINS, a new power player for DNA replication. Cell Div. 2006 Aug 24;1:18. DOI:10.1186/1747-1028-1-18 |

Lecture slides

Chayne's Intro slides (ppt)

Larry's slides on Moyer (ppt)

Week 4:non-coding RNAs

Papers

19. Chaumeil J, Le Baccon P, Wutz A, and Heard E. A novel role for Xist RNA in the formation of a repressive nuclear compartment into which genes are recruited when silenced. Genes Dev. 2006 Aug 15;20(16):2223-37. DOI:10.1101/gad.380906 |
20. Pollard KS, Salama SR, Lambert N, Lambot MA, Coppens S, Pedersen JS, Katzman S, King B, Onodera C, Siepel A, Kern AD, Dehay C, Igel H, Ares M Jr, Vanderhaeghen P, and Haussler D. An RNA gene expressed during cortical development evolved rapidly in humans. Nature. 2006 Sep 14;443(7108):167-72. DOI:10.1038/nature05113 |

Bonus Materials

21. Ponting CP and Lunter G. Evolutionary biology: human brain gene wins genome race. Nature. 2006 Sep 14;443(7108):149-50. DOI:10.1038/nature05154 |
22. Zaratiegui M, Irvine DV, and Martienssen RA. Noncoding RNAs and gene silencing. Cell. 2007 Feb 23;128(4):763-76. DOI:10.1016/j.cell.2007.02.016 |
23. Keohane AM, O'neill LP, Belyaev ND, Lavender JS, and Turner BM. X-Inactivation and histone H4 acetylation in embryonic stem cells. Dev Biol. 1996 Dec 15;180(2):618-30. DOI:10.1006/dbio.1996.0333 |
24. Heard E and Disteche CM. Dosage compensation in mammals: fine-tuning the expression of the X chromosome. Genes Dev. 2006 Jul 15;20(14):1848-67. DOI:10.1101/gad.1422906 |
25. O'Neill MJ. The influence of non-coding RNAs on allele-specific gene expression in mammals. Hum Mol Genet. 2005 Apr 15;14 Spec No 1:R113-20. DOI:10.1093/hmg/ddi108 |
26. Avner P and Heard E. X-chromosome inactivation: counting, choice and initiation. Nat Rev Genet. 2001 Jan;2(1):59-67. DOI:10.1038/35047580 |
27. Seward DJ, Cubberley G, Kim S, Schonewald M, Zhang L, Tripet B, and Bentley DL. Demethylation of trimethylated histone H3 Lys4 in vivo by JARID1 JmjC proteins. Nat Struct Mol Biol. 2007 Mar;14(3):240-2. DOI:10.1038/nsmb1200 |
28. Diaz-Perez SV, Ferguson DO, Wang C, Csankovszki G, Wang C, Tsai SC, Dutta D, Perez V, Kim S, Eller CD, Salstrom J, Ouyang Y, Teitell MA, Kaltenboeck B, Chess A, Huang S, and Marahrens Y. A deletion at the mouse Xist gene exposes trans-effects that alter the heterochromatin of the inactive X chromosome and the replication time and DNA stability of both X chromosomes. Genetics. 2006 Nov;174(3):1115-33. DOI:10.1534/genetics.105.051375 |
29. Chow JC, Yen Z, Ziesche SM, and Brown CJ. Silencing of the mammalian X chromosome. Annu Rev Genomics Hum Genet. 2005;6:69-92. DOI:10.1146/annurev.genom.6.080604.162350 |

Nature podcast on Pollard paper

Summary ppt of Chaumeil, et al

X Inactivation Intro Slides

Week 5: Consolidating weeks 2, 3 and 4 (Wed May 2 10AM)

Review of Methods/papers, answering questions from non-coding RNA and DNA Replication papers

Week 6: Student Research Forum

SRF 2007

Week 7: Nucleosome positioning and Chromatin Structure

Papers

30. Segal E, Fondufe-Mittendorf Y, Chen L, Thåström A, Field Y, Moore IK, Wang JP, and Widom J. A genomic code for nucleosome positioning. Nature. 2006 Aug 17;442(7104):772-8. DOI:10.1038/nature04979 |

Bonus Materials

31. Richmond TJ. Genomics: predictable packaging. Nature. 2006 Aug 17;442(7104):750-2. DOI:10.1038/442750a |
32. Kiyama R and Trifonov EN. What positions nucleosomes?--A model. FEBS Lett. 2002 Jul 17;523(1-3):7-11. DOI:10.1016/s0014-5793(02)02937-x |

• link to Eran Segal's Lab page where you can test your favorite sequence for predicted nucleosome occupancy

Lecture Slides

Nucleosome Coding Introduction

Nucleosome Coding Paper

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Nucleosome Coding- student Q&A

Week 8: Structure function of DNA Helicases

Papers

33. Enemark EJ and Joshua-Tor L. Mechanism of DNA translocation in a replicative hexameric helicase. Nature. 2006 Jul 20;442(7100):270-5. DOI:10.1038/nature04943 |

Bonus Materials

34. Eichman BF and Fanning E. The power of pumping together; deconstructing the engine of a DNA replication machine. Cell. 2004 Oct 1;119(1):3-4. DOI:10.1016/j.cell.2004.09.023 |
35. Gai D, Zhao R, Li D, Finkielstein CV, and Chen XS. Mechanisms of conformational change for a replicative hexameric helicase of SV40 large tumor antigen. Cell. 2004 Oct 1;119(1):47-60. DOI:10.1016/j.cell.2004.09.017 |
36. Hanson PI and Whiteheart SW. AAA+ proteins: have engine, will work. Nat Rev Mol Cell Biol. 2005 Jul;6(7):519-29. DOI:10.1038/nrm1684 |

37. :PCNA, the Maestro of the Replication Fork [[1]]

    A recent addition to Cell that looks at a critical component of the replication fork.

    --~~~~

38. Cozzarelli NR, Cost GJ, Nöllmann M, Viard T, and Stray JE. Giant proteins that move DNA: bullies of the genomic playground. Nat Rev Mol Cell Biol. 2006 Aug;7(8):580-8. DOI:10.1038/nrm1982 |

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BMCB625:Helicases

Helicase_DNA_Replication.ppt

Week 9: A gripping story about the RNA exon junction complex

Papers

39. Bono F, Ebert J, Lorentzen E, and Conti E. The crystal structure of the exon junction complex reveals how it maintains a stable grip on mRNA. Cell. 2006 Aug 25;126(4):713-25. DOI:10.1016/j.cell.2006.08.006 |

Bonus Materials

• Link to Schedule Page and Questions/Comments[[3]]

40. Tange TØ, Nott A, and Moore MJ. The ever-increasing complexities of the exon junction complex. Curr Opin Cell Biol. 2004 Jun;16(3):279-84. DOI:10.1016/j.ceb.2004.03.012 |
41. Andersen CB, Ballut L, Johansen JS, Chamieh H, Nielsen KH, Oliveira CL, Pedersen JS, Séraphin B, Le Hir H, and Andersen GR. Structure of the exon junction core complex with a trapped DEAD-box ATPase bound to RNA. Science. 2006 Sep 29;313(5795):1968-72. DOI:10.1126/science.1131981 |
42. Stroupe ME, Tange TØ, Thomas DR, Moore MJ, and Grigorieff N. The three-dimensional arcitecture of the EJC core. J Mol Biol. 2006 Jul 21;360(4):743-9. DOI:10.1016/j.jmb.2006.05.049 |
43. Shibuya T, Tange TØ, Sonenberg N, and Moore MJ. eIF4AIII binds spliced mRNA in the exon junction complex and is essential for nonsense-mediated decay. Nat Struct Mol Biol. 2004 Apr;11(4):346-51. DOI:10.1038/nsmb750 |
44. Ballut L, Marchadier B, Baguet A, Tomasetto C, Séraphin B, and Le Hir H. The exon junction core complex is locked onto RNA by inhibition of eIF4AIII ATPase activity. Nat Struct Mol Biol. 2005 Oct;12(10):861-9. DOI:10.1038/nsmb990 |
45. Shi H and Xu RM. Crystal structure of the Drosophila Mago nashi-Y14 complex. Genes Dev. 2003 Apr 15;17(8):971-6. DOI:10.1101/gad.260403 |
46. Cordin O, Banroques J, Tanner NK, and Linder P. The DEAD-box protein family of RNA helicases. Gene. 2006 Feb 15;367:17-37. DOI:10.1016/j.gene.2005.10.019 |

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Presentations:

• Introduction:File:053107 EJC.ppt
• Paper: File:EJC Presentation May2007.ppt (Note: 33MB File)

Link to Schedule page: BMCB625:Exon Jxn Complex

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Week 10: Individual Presentations

Chris - Papers

Outline of Talk and Discussion

1. Introduction: Perspectives between disciplines and establishing common languages
2. "Classic Paper" (as reference): Luria and Delbruck Fluctuation Test, trends via statistical arguements
3. "Main Paper" : Lactose Utilization as a model for Bistability
4. Discussion

PAPERS:

• MAIN PAPER: "Multistability in the lactose utilization network of Escherichia coli"

EM Ozbudak, et al, Nature 427, 737-740 (19 February 2004) [[4]]

• CLASSIC: "Mutations of Bacteria from Virus Sensitivity to Virus Resistance"

S. E. Luria and M. Delbrück, Genetics. 1943 November; 28(6): 491–511 [[5]]

• See Below: "Biologists Fixing Radios"

Chris - Bonus Materials

A good primer on how biologists and engineers look at a problem in different ways; while many comments do not address the complexity of biochemistry and genetics, it does provide an interesting perspective on what we consider "important." Also, of importance, in my opinion, is developing a common language by which numerous disciplines can communicate. I'll touch more on this particular topic during my talk. Y. Lazebnik, "Can a Biologist Fix a Radio? or, What I Learned while Studying Apoptosis" [[6]]

Chayne - Papers

47. Nöllmann M, Stone MD, Bryant Z, Gore J, Crisona NJ, Hong SC, Mitelheiser S, Maxwell A, Bustamante C, and Cozzarelli NR. Multiple modes of Escherichia coli DNA gyrase activity revealed by force and torque. Nat Struct Mol Biol. 2007 Apr;14(4):264-71. DOI:10.1038/nsmb1213 |

Chayne - Bonus Materials

• A good "News & Views" on the DNA Gyrase Article [[7]]

48. Maxwell A, Costenaro L, Mitelheiser S, and Bates AD. Coupling ATP hydrolysis to DNA strand passage in type IIA DNA topoisomerases. Biochem Soc Trans. 2005 Dec;33(Pt 6):1460-4. DOI:10.1042/BST0331460 |
48. Schoeffler AJ and Berger JM. Recent advances in understanding structure-function relationships in the type II topoisomerase mechanism. Biochem Soc Trans. 2005 Dec;33(Pt 6):1465-70. DOI:10.1042/BST0331465 |
49. Corbett KD and Berger JM. Structure, molecular mechanisms, and evolutionary relationships in DNA topoisomerases. Annu Rev Biophys Biomol Struct. 2004;33:95-118. DOI:10.1146/annurev.biophys.33.110502.140357 |
50. Gellert M, Mizuuchi K, O'Dea MH, and Nash HA. DNA gyrase: an enzyme that introduces superhelical turns into DNA. Proc Natl Acad Sci U S A. 1976 Nov;73(11):3872-6. DOI:10.1073/pnas.73.11.3872 |

Week 11: Individual Presentations

Mahta - Papers

51. Christov CP, Gardiner TJ, Szüts D, and Krude T. Functional requirement of noncoding Y RNAs for human chromosomal DNA replication. Mol Cell Biol. 2006 Sep;26(18):6993-7004. DOI:10.1128/MCB.01060-06 |

Mahta -Bonus Materials

52. Chen X and Wolin SL. The Ro 60 kDa autoantigen: insights into cellular function and role in autoimmunity. J Mol Med (Berl). 2004 Apr;82(4):232-9. DOI:10.1007/s00109-004-0529-0 |
53. Green CD, Long KS, Shi H, and Wolin SL. Binding of the 60-kDa Ro autoantigen to Y RNAs: evidence for recognition in the major groove of a conserved helix. RNA. 1998 Jul;4(7):750-65. DOI:10.1017/s1355838298971667 |
54. Pruijn GJ, Wingens PA, Peters SL, Thijssen JP, and van Venrooij WJ. Ro RNP associated Y RNAs are highly conserved among mammals. Biochim Biophys Acta. 1993 Dec 14;1216(3):395-401. DOI:10.1016/0167-4781(93)90006-y |
55. Stein AJ, Fuchs G, Fu C, Wolin SL, and Reinisch KM. Structural insights into RNA quality control: the Ro autoantigen binds misfolded RNAs via its central cavity. Cell. 2005 May 20;121(4):529-539. DOI:10.1016/j.cell.2005.03.009 |
56. Fuchs G, Stein AJ, Fu C, Reinisch KM, and Wolin SL. Structural and biochemical basis for misfolded RNA recognition by the Ro autoantigen. Nat Struct Mol Biol. 2006 Nov;13(11):1002-9. DOI:10.1038/nsmb1156 |
57. van Gelder CW, Thijssen JP, Klaassen EC, Sturchler C, Krol A, van Venrooij WJ, and Pruijn GJ. Common structural features of the Ro RNP associated hY1 and hY5 RNAs. Nucleic Acids Res. 1994 Jul 11;22(13):2498-506. DOI:10.1093/nar/22.13.2498 |
58. Hendrick JP, Wolin SL, Rinke J, Lerner MR, and Steitz JA. Ro small cytoplasmic ribonucleoproteins are a subclass of La ribonucleoproteins: further characterization of the Ro and La small ribonucleoproteins from uninfected mammalian cells. Mol Cell Biol. 1981 Dec;1(12):1138-49. DOI:10.1128/mcb.1.12.1138-1149.1981 |

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BMCB625:Noncoding Y RNA

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Jeremy - Papers

59. Zalfa F, Giorgi M, Primerano B, Moro A, Di Penta A, Reis S, Oostra B, and Bagni C. The fragile X syndrome protein FMRP associates with BC1 RNA and regulates the translation of specific mRNAs at synapses. Cell. 2003 Feb 7;112(3):317-27. DOI:10.1016/s0092-8674(03)00079-5 |

Jeremy-Bonus Materials

59. Zalfa F, Achsel T, and Bagni C. mRNPs, polysomes or granules: FMRP in neuronal protein synthesis. Curr Opin Neurobiol. 2006 Jun;16(3):265-9. DOI:10.1016/j.conb.2006.05.010 |

Larry - Papers

60. Ogi T and Lehmann AR. The Y-family DNA polymerase kappa (pol kappa) functions in mammalian nucleotide-excision repair. Nat Cell Biol. 2006 Jun;8(6):640-2. DOI:10.1038/ncb1417 |

Larry-Bonus Materials

News and Views

61. Lehmann AR. New functions for Y family polymerases. Mol Cell. 2006 Nov 17;24(4):493-5. DOI:10.1016/j.molcel.2006.10.021 |

Jon - Papers

62. Gao H, Cervantes RB, Mandell EK, Otero JH, and Lundblad V. RPA-like proteins mediate yeast telomere function. Nat Struct Mol Biol. 2007 Mar;14(3):208-14. DOI:10.1038/nsmb1205 |

Evidence that two smaller subunits of RPA bind weakly and preferentially to telomeric DNA. These telomere capping proteins have functional similarities (OB fold) with ssDNA binding proteins and may be involved in the recruitment of telomere maintenance proteins.

Jon - Bonus Materials

62. Haring SJ and Wold MS. A common means to an end. Nat Struct Mol Biol. 2007 Mar;14(3):176-7. DOI:10.1038/nsmb0307-176 |
63. Miller KM, Rog O, and Cooper JP. Semi-conservative DNA replication through telomeres requires Taz1. Nature. 2006 Apr 6;440(7085):824-8. DOI:10.1038/nature04638 |
64. Suck D. Common fold, common function, common origin?. Nat Struct Biol. 1997 Mar;4(3):161-5. DOI:10.1038/nsb0397-161 |
65. Eggleston A. Hush, hush: the origin of telomeric silence. Nat Cell Biol. 2000 Feb;2(2):E27. DOI:10.1038/35000097 |

So many papers, so little time: Papers we would have liked to cover (note podcast link below)

66. Olaussen KA, Dunant A, Fouret P, Brambilla E, André F, Haddad V, Taranchon E, Filipits M, Pirker R, Popper HH, Stahel R, Sabatier L, Pignon JP, Tursz T, Le Chevalier T, Soria JC, and IALT Bio Investigators. DNA repair by ERCC1 in non-small-cell lung cancer and cisplatin-based adjuvant chemotherapy. N Engl J Med. 2006 Sep 7;355(10):983-91. DOI:10.1056/NEJMoa060570 |
67. Kumagai A, Lee J, Yoo HY, and Dunphy WG. TopBP1 activates the ATR-ATRIP complex. Cell. 2006 Mar 10;124(5):943-55. DOI:10.1016/j.cell.2005.12.041 |
68. Zegerman P and Diffley JF. Phosphorylation of Sld2 and Sld3 by cyclin-dependent kinases promotes DNA replication in budding yeast. Nature. 2007 Jan 18;445(7125):281-5. DOI:10.1038/nature05432 |
69. Botchan M. Cell biology: a switch for S phase. Nature. 2007 Jan 18;445(7125):272-4. DOI:10.1038/445272a |
70. Kitamura E, Blow JJ, and Tanaka TU. Live-cell imaging reveals replication of individual replicons in eukaryotic replication factories. Cell. 2006 Jun 30;125(7):1297-308. DOI:10.1016/j.cell.2006.04.041 |
71. Meister P, Taddei A, and Gasser SM. In and out of the replication factory. Cell. 2006 Jun 30;125(7):1233-5. DOI:10.1016/j.cell.2006.06.014 |

Overlapping coverage but Podcast is interesting

72. Zhou T, Xu L, Dey B, Hessell AJ, Van Ryk D, Xiang SH, Yang X, Zhang MY, Zwick MB, Arthos J, Burton DR, Dimitrov DS, Sodroski J, Wyatt R, Nabel GJ, and Kwong PD. Structural definition of a conserved neutralization epitope on HIV-1 gp120. Nature. 2007 Feb 15;445(7129):732-7. DOI:10.1038/nature05580 |

Nature podcast on Zhou paper