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Revision as of 10:33, 25 April 2007
Class Focus, Spring 2007
- Organization Meeting and Rules of Engagement
- Biochemistry and Structure of Replicating Machines at the Protein-DNA Interface
- Molecular Mechanisms of Genomic Information Expansion
- A Revealing Structure of the Exon Junction Complex
Week 1: Introduction and Scheduling
Presentation Zen
- Slide Zen
- Delivery Zen
- Feel free to add links that help you
Evaluation Forms
Evaluation Form for Student Presentations
Week 2: Rewrite the textbooks on DNA Replication
Papers
- 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 |
- 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
- 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 |
- Bell SD. Molecular biology: prime-time progress. Nature. 2006 Feb 2;439(7076):542-3. DOI:10.1038/439542a |
- 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.
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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.
- 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 |
- 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 |
- 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 |
- 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 |
BND Cellulose Protocol [1]
Using Caffeine to Elute Replication Intermediates with Single Stranded Regions [2]
Lecture Slides
Lecture Slides Media:04122007_DNA_Replication.pdf
Discussion: Replication, Week2
Week 3:Go, Ichi, Nii, and San;New Components of DNA Replication
Papers
- 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
- 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 |
- 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 |
- 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 |
- 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 |
- 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 |
- 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 |
Lecture slides
Media:CMGcomplex-intro-17apr07clp.ppt
Week 4:non-coding RNAs
Papers
- 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 |
- 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
- 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 |
- 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 |
- 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 |
Nature podcast on Pollard paper
Week 7:Chromatin Structure
Papers
- 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
- Richmond TJ. Genomics: predictable packaging. Nature. 2006 Aug 17;442(7104):750-2. DOI:10.1038/442750a |
Week 8: Structure function of DNA Helicases
Papers
- 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 |
- 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 |
Bonus Materials
- 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 |
Week 9: A gripping story about the RNA exon junction complex
Papers
- 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
- 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 |
Final Presentations
Week 10
Chris - Papers
Outline of Talk and Discussion
- Introduction and background
- "Classic Paper" and "Cutting Edge Paper" (TBD) and how they relate to one another
- Summary and key points to begin discussion
- OPEN discussion (intended to be an informal discussion on the interface between Mathematics and biology (specifically biochemistry)).
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" [[3]]
Chayne - Papers
- 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 |
Bonus Materials
Week 11
Mahta - Papers
- 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 |
Bonus Materials
Jeremy - Papers
- Robertson MP and Scott WG. The structural basis of ribozyme-catalyzed RNA assembly. Science. 2007 Mar 16;315(5818):1549-53. DOI:10.1126/science.1136231 |
Bonus Materials
Larry - Papers
- 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 |
Bonus Materials
- 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
Proposed Paper(s) for Jon --Contact Jon for inquiries
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.
- 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 |
Bonus Materials
- 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 |
- 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 |
- Suck D. Common fold, common function, common origin?. Nat Struct Biol. 1997 Mar;4(3):161-5. DOI:10.1038/nsb0397-161 |
- Eggleston A. Hush, hush: the origin of telomeric silence. Nat Cell Biol. 2000 Feb;2(2):E27. DOI:10.1038/35000097 |
Other Suggestions, Depending on Student Interests (note podcast link below)
- 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 |
- 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 |
- 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 |
- Botchan M. Cell biology: a switch for S phase. Nature. 2007 Jan 18;445(7125):272-4. DOI:10.1038/445272a |
- 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 |
- 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