MCB290 – Spring 2006 – DNA Replication, DNA Repair and Checkpoint Control
M. Botchan & D. Rio
This 290 will deal with DNA repair pathways, DNA replication and connections between the two.
We will also discuss more general aspects of each topic and how these machineries respond to
DNA damage checkpoint controls and signaling. Hopefully, we can also use this information as
well as our understanding of certain aspects of cell cycle to raise issues of drug design,
treatments and potential therapeutic strategies for cancer.
Meeting Room/Time: Thursdays 10AM to Noon, 80 Koshland Hall
Except Feb. 9 – 10:30AM to 12:30PM, 247 LSA
Format:
The presenter should prepare a 20-30 min. presentation of in-depth and
comprehensive background material on the topic to be presented/discussed. There will be a
review article handed out before the meeting, so everyone should have a general idea about
the topic area. Following the background/overview, the presenter will lead a group discussion
of one or two research papers on the topic at hand going in detail through the experiments and
figures and critically evaluating the data and conclusions reached.
Topics:
Week Date
Title
Presenter
1
Primosomes and replication
re-start in E. coli
Andy Antczak
Jan 26
Research Article:
Xu, L. and K. J. Marians (2003). "PriA mediates DNA replication pathway choice at
recombination intermediates." Mol Cell 11(3): 817-26.
Reviews:
Marians, K. J. (2004). "Mechanisms of replication fork restart in Escherichia coli." Philos
Trans R Soc Lond B Biol Sci 359(1441): 71-7.
Cox, M. M., M. F. Goodman, et al. (2000). "The importance of repairing stalled
replication forks." Nature 404(6773): 37-41.
Lovett, S. T. (2003). "Connecting replication and recombination." Mol Cell 11(3): 554-6.
2
Feb 2
Research Article:
DNA polymerase eta and repair
Ken Cadwell
McLlwraith, M. J., A. Vaisman, et al. (2005). "Human DNA polymerase eta promotes
DNA synthesis from strand invasion intermediates of homologous recombination." Mol
Cell 20(5): 783-92.
Reviews:
Plosky, B. S. and R. Woodgate (2004). "Switching from high-fidelity replicases to lowfidelity lesion-bypass polymerases." Curr Opin Genet Dev 14(2): 113-9.
Branzei, D. and M. Foiani (2005). "The DNA damage response during DNA replication."
Curr Opin Cell Biol 17(6): 568-75.
3
Feb 9
S-phase checkpoints - cell biology
Research Articles:
Katou, Y., Y. Kanoh, et al. (2003). "S-phase checkpoint proteins Tof1 and Mrc1 form a
stable replication-pausing complex." Nature 424(6952): 1078-83.
Feijoo, C., C. Hall-Jackson, et al. (2001). "Activation of mammalian Chk1 during DNA
replication arrest: a role for Chk1 in the intra-S phase checkpoint monitoring
replication origin firing." J Cell Biol 154(5): 913-23.
Shechter, D., V. Costanzo, et al. (2004). "ATR and ATM regulate the timing of DNA
replication origin firing." Nat Cell Biol 6(7): 648-55.
Fisher, D. and M. Mechali (2004). "Sleeping policemen for DNA replication?" Nat Cell
Biol 6(7): 576-7.
Reviews:
Bartek, J., C. Lukas, et al. (2004). "Checking on DNA damage in S phase." Nat Rev Mol
Cell Biol 5(10): 792-804.
Zhang, Y. W., T. Hunter, et al. (2006). "Turning the Replication Checkpoint On and Off."
Cell Cycle 5(2).
Niida, H. and M. Nakanishi (2005). "DNA damage checkpoints in mammals."
Mutagenesis. [Epub ahead of print]
Additional Background:
Zhang, Y. W., D. M. Otterness, et al. (2005). "Genotoxic stress targets human Chk1 for
degradation by the ubiquitin-proteasome pathway." Mol Cell 19(5): 607-18.
4
Feb 16
S-phase checkpoints - cancer therapy
Kasuen Wong
Research Articles:
Bartkova, J., Z. Horejsi, et al. (2005). "DNA damage response as a candidate anticancer barrier in early human tumorigenesis." Nature 434(7035): 864-70.
Gorgoulis, V. G., L. V. Vassiliou, et al. (2005). "Activation of the DNA damage
checkpoint and genomic instability in human precancerous lesions." Nature 434(7035):
907-13.
Reviews:
Venkitaraman, A. R. (2005). "Medicine: aborting the birth of cancer." Nature 434(7035):
829-30.
Motoyama, N. and K. Naka (2004). "DNA damage tumor suppressor genes and
genomic instability." Curr Opin Genet Dev 14(1): 11-6.
Zhou, B. B. and J. Bartek (2004). "Targeting the checkpoint kinases: chemosensitization
versus chemoprotection." Nat Rev Cancer 4(3): 216-25.
Kastan, M. B. and J. Bartek (2004). "Cell-cycle checkpoints and cancer." Nature
432(7015): 316-23.
5
Feb 23
RecQ helicases – at replication forks
Mike Botchan
Research Articles:
Sangrithi, M. N., J. A. Bernal, et al. (2005). "Initiation of DNA replication requires the
RECQL4 protein mutated in Rothmund-Thomson syndrome." Cell 121(6): 887-98.
Cobb, J. A., T. Schleker, et al. (2005). "Replisome instability, fork collapse, and gross
chromosomal rearrangements arise synergistically from Mec1 kinase and RecQ
helicase mutations." Genes Dev 19(24): 3055-69.
Reviews:
Hickson, I. D. (2003). "RecQ helicases: caretakers of the genome." Nat Rev Cancer
3(3): 169-78.
Cheok, C. F., C. Z. Bachrati, et al. (2005). "Roles of the Bloom's syndrome helicase in
the maintenance of genome stability." Biochem Soc Trans 33(Pt 6): 1456-9.
Foiani, M. (2003). "Molecular biology: Disruptive influence." Nature 423(6937): 234-5.
Pellicioli, A. and M. Foiani (2005). "Recombination at collapsed replication forks: the
payoff for survival." Mol Cell 18(6): 614-5.
Additional Background:
Karow, J. K., A. Constantinou, et al. (2000). "The Bloom's syndrome gene product
promotes branch migration of holliday junctions." Proc Natl Acad Sci U S A 97(12):
6504-8.
6
Mar 2
Research Articles:
DNA damage response / recognition
- visualizing DNArepair factors in cells;
alternate RFC?
Alexandra Folias
Ellison, V. and B. Stillman (2003). "Biochemical characterization of DNA damage
checkpoint complexes: clamp loader and clamp complexes with specificity for 5'
recessed DNA." PLoS Biol 1(2): E33.
Lisby, M., J. H. Barlow, et al. (2004). "Choreography of the DNA damage response:
spatiotemporal relationships among checkpoint and repair proteins." Cell 118(6): 699713.
Aten, J. A., J. Stap, et al. (2004). "Dynamics of DNA double-strand breaks revealed by
clustering of damaged chromosome domains." Science 303(5654): 92-5.
Reviews:
Lukas, J. and J. Bartek (2004). "Watching the DNA repair ensemble dance." Cell 118(6):
666-8.
Lisby, M. and R. Rothstein (2004). "DNA damage checkpoint and repair centers." Curr
Opin Cell Biol 16(3): 328-34.
Parrilla-Castellar, E. R., S. J. Arlander, et al. (2004). "Dial 9-1-1 for DNA damage: the
Rad9-Hus1-Rad1 (9-1-1) clamp complex." DNA Repair (Amst) 3(8-9): 1009-14.
McGowan, C. H. and P. Russell (2004). "The DNA damage response: sensing and
signaling." Curr Opin Cell Biol 16(6): 629-33.
7
Mar 9
ATM – biochemistry / telomeres
and TRF2 / Drosophila genetics
Aaron Boudreau
Research Articles:
Bakkenist, C. J. and M. B. Kastan (2003). "DNA damage activates ATM through
intermolecular autophosphorylation and dimer dissociation." Nature 421(6922): 499506.
Lee, J. H. and T. T. Paull (2004). "Direct activation of the ATM protein kinase by the
Mre11/Rad50/Nbs1 complex." Science 304(5667): 93-6.
Lee, J. H. and T. T. Paull (2005). "ATM activation by DNA double-strand breaks through
the Mre11-Rad50-Nbs1 complex." Science 308(5721): 551-4.
Reviews:
Yang, J., Y. Yu, et al. (2003). "ATM, ATR and DNA-PK: initiators of the cellular
genotoxic stress responses." Carcinogenesis 24(10): 1571-80.
Traven, A. and J. Heierhorst (2005). "SQ/TQ cluster domains: concentrated ATM/ATR
kinase phosphorylation site regions in DNA-damage-response proteins." Bioessays
27(4): 397-407.
Bartek, J. and J. Lukas (2003). "DNA repair: Damage alert." Nature 421(6922): 486-8.
d'Adda di Fagagna, F., S. H. Teo, et al. (2004). "Functional links between telomeres and
proteins of the DNA-damage response." Genes Dev 18(15): 1781-99.
Additional Background:
Wong, K. K., R. S. Maser, et al. (2003). "Telomere dysfunction and Atm deficiency
compromises organ homeostasis and accelerates ageing." Nature 421(6923): 643-8.
Kitagawa, R., C. J. Bakkenist, et al. (2004). "Phosphorylation of SMC1 is a critical
downstream event in the ATM-NBS1-BRCA1 pathway." Genes Dev 18(12): 1423-38.
Karlseder, J., K. Hoke, et al. (2004). "The telomeric protein TRF2 binds the ATM kinase
and can inhibit the ATM-dependent DNA damage response." PLoS Biol 2(8): E240.
Tarsounas, M., P. Munoz, et al. (2004). "Telomere maintenance requires the RAD51D
recombination/repair protein." Cell 117(3): 337-47.
Verdun, R. E., L. Crabbe, et al. (2005). "Functional human telomeres are recognized as
DNA damage in G2 of the cell cycle." Mol Cell 20(4): 551-61.
8
Mar 16
ATR / ATRIP and RPA –
damage recognition
Roy Pai
Research Article:
Zou, L. and S. J. Elledge (2003). "Sensing DNA damage through ATRIP recognition of
RPA-ssDNA complexes." Science 300(5625): 1542-8.
Zou, L., D. Liu, et al. (2003). "Replication protein A-mediated recruitment and activation
of Rad17 complexes." Proc Natl Acad Sci U S A 100(24): 13827-32.
Reviews:
Shechter, D., V. Costanzo, et al. (2004). "Regulation of DNA replication by ATR:
signaling in response to DNA intermediates." DNA Repair (Amst) 3(8-9): 901-8.
Carr, A. M. (2003). "Molecular biology. Beginning at the end." Science 300(5625): 15123.
9
Mar 23
BRCA1 & BRCA2
Yui Sanchatjate
Research Articles:
Galkin, V. E., F. Esashi, et al. (2005). "BRCA2 BRC motifs bind RAD51-DNA filaments."
Proc Natl Acad Sci U S A 102(24): 8537-42.
Farmer, H., N. McCabe, et al. (2005). "Targeting the DNA repair defect in BRCA mutant
cells as a therapeutic strategy." Nature 434(7035): 917-21.
Reviews:
Venkitaraman, A. R. (2004). "Tracing the network connecting BRCA and Fanconi
anaemia proteins." Nat Rev Cancer 4(4): 266-76.
Yoshida, K. and Y. Miki (2004). "Role of BRCA1 and BRCA2 as regulators of DNA
repair, transcription, and cell cycle in response to DNA damage." Cancer Sci 95(11):
866-71.
D'Andrea, A. D. and M. Grompe (2003). "The Fanconi anaemia/BRCA pathway." Nat
Rev Cancer 3(1): 23-34.
Ting, N. S. and W. H. Lee (2004). "The DNA double-strand break response pathway:
becoming more BRCAish than ever." DNA Repair (Amst) 3(8-9): 935-44.
Shivji, M. K. and A. R. Venkitaraman (2004). "DNA recombination, chromosomal stability
and carcinogenesis: insights into the role of BRCA2." DNA Repair (Amst) 3(8-9): 83543.
Additional Background:
Moynahan, M. E., A. J. Pierce, et al. (2001). "BRCA2 is required for homology-directed
repair of chromosomal breaks." Mol Cell 7(2): 263-72.
Powell, S. N., H. Willers, et al. (2002). "BRCA2 keeps Rad51 in line. High-fidelity
homologous recombination prevents breast and ovarian cancer?" Mol Cell 10(6):
1262-3.
Davies, A. A., J. Y. Masson, et al. (2001). "Role of BRCA2 in control of the RAD51
recombination and DNA repair protein." Mol Cell 7(2): 273-82.
Paull, T. T., D. Cortez, et al. (2001). "Direct DNA binding by Brca1." Proc Natl Acad Sci
U S A 98(11): 6086-91.
10
Mar 30
Homologous recombinational (HR)
repair – rad51C and mus81 – HJ
and branch migration - biochemistry
Xie Tang
Research Articles:
Boddy, M. N., P. H. Gaillard, et al. (2001). "Mus81-Eme1 are essential components of a
Holliday junction resolvase." Cell 107(4): 537-48.
Chen, X. B., R. Melchionna, et al. (2001). "Human Mus81-associated endonuclease
cleaves Holliday junctions in vitro." Mol Cell 8(5): 1117-27.
Liu, Y., J. Y. Masson, et al. (2004). "RAD51C is required for Holliday junction processing
in mammalian cells." Science 303(5655): 243-6.
Reviews:
Wyman, C., D. Ristic, et al. (2004). "Homologous recombination-mediated double-strand
break repair." DNA Repair (Amst) 3(8-9): 827-33.
Wyman, C., D. Ristic, et al. (2004). "Homologous recombination-mediated double-strand
break repair." DNA Repair (Amst) 3(8-9): 827-33.
O'Driscoll, M. and P. A. Jeggo (2006). "The role of double-strand break repair - insights
from human genetics." Nat Rev Genet 7(1): 45-54.
Additional Background:
Gaillard, P. H., E. Noguchi, et al. (2003). "The endogenous Mus81-Eme1 complex
resolves Holliday junctions by a nick and counternick mechanism." Mol Cell 12(3):
747-59.
Ciccia, A., A. Constantinou, et al. (2003). "Identification and characterization of the
human mus81-eme1 endonuclease." J Biol Chem 278(27): 25172-8.
Constantinou, A., X. B. Chen, et al. (2002). "Holliday junction resolution in human cells:
two junction endonucleases with distinct substrate specificities." Embo J 21(20): 557785.
Constantinou, A., A. A. Davies, et al. (2001). "Branch migration and Holliday junction
resolution catalyzed by activities from mammalian cells." Cell 104(2): 259-68.
Masson, J. Y., M. C. Tarsounas, et al. (2001). "Identification and purification of two
distinct complexes containing the five RAD51 paralogs." Genes Dev 15(24): 3296-307.
McPherson, J. P., B. Lemmers, et al. (2004). "Involvement of mammalian Mus81 in
genome integrity and tumor suppression." Science 304(5678): 1822-6.
11
Apr 6
Homologous recombinational (HR) repair Don Rio
– mre11/rad50/nbs1 (MRN) - biochemistry
Research Articles:
Paull, T. T. and M. Gellert (1998). "The 3' to 5' exonuclease activity of Mre 11 facilitates
repair of DNA double-strand breaks." Mol Cell 1(7): 969-79.
Paull, T. T. and M. Gellert (1999). "Nbs1 potentiates ATP-driven DNA unwinding and
endonuclease cleavage by the Mre11/Rad50 complex." Genes Dev 13(10): 1276-88.
Reviews:
Kobayashi, J., A. Antoccia, et al. (2004). "NBS1 and its functional role in the DNA
damage response." DNA Repair (Amst) 3(8-9): 855-61.
D'Amours, D. and S. P. Jackson (2002). "The Mre11 complex: at the crossroads of dna
repair and checkpoint signalling." Nat Rev Mol Cell Biol 3(5): 317-27.
Paull, T. T. (2001). "New glimpses of an old machine." Cell 107(5): 563-5.
12
Apr 9
Research Articles:
Homologous recombinational repair
– mre11/rad50/nbs1 (MRN) - structure
Alex Sabogal
Moreno-Herrero, F., M. de Jager, et al. (2005). "Mesoscale conformational changes in
the DNA-repair complex Rad50/Mre11/Nbs1 upon binding DNA." Nature 437(7057):
440-3.
de Jager, M., J. van Noort, et al. (2001). "Human Rad50/Mre11 is a flexible complex that
can tether DNA ends." Mol Cell 8(5): 1129-35.
Hopfner, K. P., A. Karcher, et al. (2001). "Structural biochemistry and interaction
architecture of the DNA double-strand break repair Mre11 nuclease and Rad50ATPase." Cell 105(4): 473-85.
Hopfner, K. P., A. Karcher, et al. (2001). "Structural biochemistry and interaction
architecture of the DNA double-strand break repair Mre11 nuclease and Rad50ATPase." Cell 105(4): 473-85.
Reviews:
Williams, R. S. and J. A. Tainer (2005). "A nanomachine for making ends meet: MRN is
a flexing scaffold for the repair of DNA double-strand breaks." Mol Cell 19(6): 724-6.
Shin, D. S., C. Chahwan, et al. (2004). "Structure and function of the double-strand
break repair machinery." DNA Repair (Amst) 3(8-9): 863-73.
Hopfner, K. P., C. D. Putnam, et al. (2002). "DNA double-strand break repair from head
to tail." Curr Opin Struct Biol 12(1): 115-22.
Hopfner, K. P. and J. A. Tainer (2003). "Rad50/SMC proteins and ABC transporters:
unifying concepts from high-resolution structures." Curr Opin Struct Biol 13(2): 249-55.
13
Apr 16
Non-homologous end joining (NHEJ)
- biochemistry & reconstitution
Bilge Ozaydin
Research Articles:
Ma, Y., H. Lu, et al. (2004). "A biochemically defined system for mammalian
nonhomologous DNA end joining." Mol Cell 16(5): 701-13.
Budman, J. and G. Chu (2005). "Processing of DNA for nonhomologous end-joining by
cell-free extract." Embo J 24(4): 849-60.
Baumann, P. and S. C. West (1998). "DNA end-joining catalyzed by human cell-free
extracts." Proc Natl Acad Sci U S A 95(24): 14066-70.
Reviews:
Downs, J. A. and S. P. Jackson (2004). "A means to a DNA end: the many roles of Ku."
Nat Rev Mol Cell Biol 5(5): 367-78.
Lieber, M. R., Y. Ma, et al. (2003). "Mechanism and regulation of human nonhomologous DNA end-joining." Nat Rev Mol Cell Biol 4(9): 712-20.
Paull, T. T. (2005). "Saving the ends for last: the role of pol mu in DNA end joining." Mol
Cell 19(3): 294-6.
Additional Background:
Hanakahi, L. A. and S. C. West (2002). "Specific interaction of IP6 with human Ku70/80,
the DNA-binding subunit of DNA-PK." Embo J 21(8): 2038-44.
Chappell, C., L. A. Hanakahi, et al. (2002). "Involvement of human polynucleotide kinase
in double-strand break repair by non-homologous end joining." Embo J 21(11): 282732.
Hanakahi, L. A., M. Bartlet-Jones, et al. (2000). "Binding of inositol phosphate to DNAPK and stimulation of double-strand break repair." Cell 102(6): 721-9.
14
Apr 23
Non-homologous end joining (NHEJ)
- mouse genetics
Brian Sullivan
Research Articles:
Gao, Y., Y. Sun, et al. (1998). "A critical role for DNA end-joining proteins in both
lymphogenesis and neurogenesis." Cell 95(7): 891-902.
Frank, K. M., J. M. Sekiguchi, et al. (1998). "Late embryonic lethality and impaired V(D)J
recombination in mice lacking DNA ligase IV." Nature 396(6707): 173-7.
Reviews:
Ferguson, D. O. and F. W. Alt (2001). "DNA double strand break repair and
chromosomal translocation: lessons from animal models." Oncogene 20(40): 5572-9.
Rooney, S., J. Chaudhuri, et al. (2004). "The role of the non-homologous end-joining
pathway in lymphocyte development." Immunol Rev 200: 115-31.
Additional Background:
Sekiguchi, J., D. O. Ferguson, et al. (2001). "Genetic interactions between ATM and the
nonhomologous end-joining factors in genomic stability and development." Proc Natl
Acad Sci U S A 98(6): 3243-8.
Rooney, S., J. Sekiguchi, et al. (2002). "Leaky Scid phenotype associated with defective
V(D)J coding end processing in Artemis-deficient mice." Mol Cell 10(6): 1379-90.
Gu, Y., J. Sekiguchi, et al. (2000). "Defective embryonic neurogenesis in Ku-deficient
but not DNA-dependent protein kinase catalytic subunit-deficient mice." Proc Natl
Acad Sci U S A 97(6): 2668-73.
Frank, K. M., N. E. Sharpless, et al. (2000). "DNA ligase IV deficiency in mice leads to
defective neurogenesis and embryonic lethality via the p53 pathway." Mol Cell 5(6):
993-1002.
Karanjawala, Z. E., N. Adachi, et al. (2002). "The embryonic lethality in DNA ligase IVdeficient mice is rescued by deletion of Ku: implications for unifying the heterogeneous
phenotypes of NHEJ mutants." DNA Repair (Amst) 1(12): 1017-26.
Couedel, C., K. D. Mills, et al. (2004). "Collaboration of homologous recombination and
nonhomologous end-joining factors for the survival and integrity of mice and cells."
Genes Dev 18(11): 1293-304.
Mills, K. D., D. O. Ferguson, et al. (2004). "Rad54 and DNA Ligase IV cooperate to
maintain mammalian chromatid stability." Genes Dev 18(11): 1283-92.
15
Apr 30
Non-homologous end joining (NHEJ)
- retrovirus connection
Yuko Nakajima
Research Article:
Lau, A., K. M. Swinbank, et al. (2005). "Suppression of HIV-1 infection by a small
molecule inhibitor of the ATM kinase." Nat Cell Biol 7(5): 493-500.
Reviews:
Skalka, A. M. and R. A. Katz (2005). "Retroviral DNA integration and the DNA damage
response." Cell Death Differ 12 Suppl 1: 971-8.
Daniel, R. and R. J. Pomerantz (2005). "ATM: HIV-1's Achilles heel?" Nat Cell Biol 7(5):
452-3.
Additional Background:
Daniel, R., J. G. Greger, et al. (2004). "Evidence that stable retroviral transduction and
cell survival following DNA integration depend on components of the nonhomologous
end joining repair pathway." J Virol 78(16): 8573-81.
Dehart, J. L., J. L. Andersen, et al. (2005). "The ataxia telangiectasia-mutated and
Rad3-related protein is dispensable for retroviral integration." J Virol 79(3): 1389-96.
Li, L., J. M. Olvera, et al. (2001). "Role of the non-homologous DNA end joining pathway
in the early steps of retroviral infection." Embo J 20(12): 3272-81.
Daniel, R., R. A. Katz, et al. (1999). "A role for DNA-PK in retroviral DNA integration."
Science 284(5414): 644-7.
Daniel, R., G. Kao, et al. (2003). "Evidence that the retroviral DNA integration process
triggers an ATR-dependent DNA damage response." Proc Natl Acad Sci U S A
100(8): 4778-83.
Daniel, R., G. Kao, et al. (2003). "Evidence that the retroviral DNA integration process
triggers an ATR-dependent DNA damage response." Proc Natl Acad Sci U S A
100(8): 4778-83.
Lau, A., R. Kanaar, et al. (2004). "Suppression of retroviral infection by the RAD52 DNA
repair protein." Embo J 23(16): 3421-9.