Nuclear Structure and Function Research Group

Resources for CHAPTER 5: REPAIR
Updated on 4 July, 2014

The need for repair of damage
    Common damaging agents and lesions
        Box 5-1. Consequences of deamination of C and 5-MeC
Some experimental approaches
        Box 5-2. Repair defects and human disease
Types of repair
    Direct repair
    Base-excision repair
    Nucleotide-excision repair
    Mismatch repair
    Other repair mechanisms
    Accuracy in gap filling
        Box 5-3. Damage response systems in bacteria
Sites of repair
    Transcription and repair
Some consequences of inefficient repair

The need for repair of damage
Figure: 5-1.
Reference:
Lindahl, T. and Wood, R.D. (1999). Quality control by DNA repair. Science 286, 1897-1905. [PubMed]
Additional reference:
Foti, J.J., and Walker, G.C. (2010). SnapShot: DNA polymerases II mammals. Cell 141, 370. [PubMed]
Hoeijmakers, J.H. (2009). DNA damage, aging, and cancer. N. Engl. J. Med. 361, 1475-1485. [PubMed]
Takata, K., and Wood, R.D. (2009). Bypass specialists operate together. EMBO J. 28, 313-314. [PubMed]
Yao, N.Y., and O'Donnell, M. (2009). Replisome structure and conformational dynamics underlie fork progression past obstacles. Curr. Opin. Cell Biol. 21, 336-343. [PubMed]
Web link:
http://cancernet.nci.nih.gov/cancertopics/prevention-genetics-causes/causes Risk factors in cancer.

Common damaging agents and lesions
Figure: 5-2, 5-3.
Reference:
Lindahl, T. (1993). Instability and decay of the primary structure of DNA. Nature 362, 709-715. [PubMed]
Additional reference:
Foti, J.J., and Walker, G.C. (2010). SnapShot: DNA polymerases II mammals. Cell 141, 370. [PubMed]
Hoeijmakers, J.H. (2009). DNA damage, aging, and cancer. N. Engl. J. Med. 361, 1475-1485. [PubMed]

Box 5-1. Consequences of deamination of C and 5-^MeC
Reference:
Lindahl, T. (1993). Instability and decay of the primary structure of DNA. Nature 362, 709-715. [PubMed]
Additional reference:
Walsh, C.P., and Xu, G.L. (2006). Cytosine methylation and DNA repair. Curr. Top. Microbiol. Immunol. 301, 283-315. [PubMed]

Some experimental approaches
Figure: 5-4, 5-5.

Box 5-2. Repair defects and human disease
Reference:
Sancar, A. (1995). DNA repair in humans. Annu Rev. Genetics 29, 69-105. [PubMed]
Additional reference:
Cleaver, J.E., Lam, E.T., and Revet, I. (2009). Disorders of nucleotide excision repair: the genetic and molecular basis of heterogeneity. Nat. Rev. Genet. 10, 756-768. [PubMed]
Hoeijmakers, J.H. (2009). DNA damage, aging, and cancer. N. Engl. J. Med. 361, 1475-1485. [PubMed]
O'Driscoll, M. (2012). Diseases associated with defective responses to DNA damage. Cold Spring Harb. Perspect. Biol. 4, doi: 10.1101/cshperspect.a012773. [PubMed]
Pommier, Y., Sun, Y., Huang, S.N., Nitiss, J.L. (2016). Roles of eukaryotic topoisomerases in transcription, replication and genomic stability. Nat. Rev. Mol. Cell Biol. 17, 703-721. [PubMed]
Web link:
http://www.xps.org/ XP site.
http://www.atcp.org/ AT site.

Types of repair
Figure: 5-6.
Reference:
Sancar, A. (1995). DNA repair in humans. Annu Rev. Genetics 29, 69-105. [PubMed]
Wood, R.D. (1996). DNA repair in eukaryotes. Annu Rev. Biochem. 65, 135-167. [PubMed]
Additional reference:
Foti, J.J., and Walker, G.C. (2010). SnapShot: DNA polymerases II mammals. Cell 141, 370. [PubMed]
Hoeijmakers, J.H. (2009). DNA damage, aging, and cancer. N. Engl. J. Med. 361, 1475-1485. [PubMed]
Loeb, L.A., and Monnat R.J. (2008). DNA polymerases and human disease. Nat. Rev. Genet. 9, 594-604. [PubMed]
Peterson, C.L. (2004).  Cellular machineries for chromosomal DNA repair.  Genes Dev. 15, 602-616.  [PubMed]

Direct repair
Reference:
Sancar, A. (1995). DNA repair in humans. Annu Rev. Genetics 29, 69-105. [PubMed]
Additional reference:
Dalhus, B., Laerdahl, J.K., Backe, P.H., and Bjørås, M. (2009). DNA base repair--recognition and initiation of catalysis. FEMS Microbiol. Revs. 33, 1044-1078. [PubMed]

Base-excision repair
Reference:
Lindahl, T. and Wood, R.D. (1999). Quality control by DNA repair. Science 286, 1897-1905. [PubMed]
Additional reference:
David, S.S., O'Shea, V.L., and Kundu, S. (2007). Base-excision repair of oxidative DNA damage. Nature 447, 941-950. [PubMed]
Maynard, S., Schurman, S.H., Harboe, C., de Souza-Pinto, N.C., and Bohr, V.A. (2009). Base excision repair of oxidative DNA damage and association with cancer and aging. Carcinogenesis 30, 2-10. [PubMed]
Web link:
http://chem-faculty.ucsd.edu/kraut/bpol.html Movies of polymerase β.

Nucleotide-excision repair
Figure: 5-7.
Reference:
Huang, J.-C., Svoboda, D.L., Reardon, J.T. and Sancar, A. (1992). Human nucleotide excision nuclease removes thymine dimers from DNA by incising the 22nd phosphodiester bond 5' and the 6th phosphodiester bond 3' to the photodimer. Proc. Natl. Acad. Sci. USA 89, 3664-3668. [PubMed] [Full text]
Sancar, A. (1995). DNA repair in humans. Annu Rev. Genetics 29, 69-105. [PubMed]
de Laat, W.L., Jaspers, N.G.J. and Hoeijmakers, J.H.J. (1999). Molecular mechanisms of nucleotide excision repair. Genes Dev. 13, 768-785. [Full text]
Additional reference:
Guo, C., Tang, T.S., and Friedberg, E.C. (2010). SnapShot: nucleotide excision repair. Cell 140, 754-754. [PubMed]
Houtsmuller, A.B., Rademakers, S., Nigg, A.L., Hoogstraten, D., Hoeijmakers, J.H. and Vermeulen, W. (1999). Action of DNA repair endonuclease ERCC1/XPF in living cells. Science 284, 958-961. [PubMed]
Marteijn, J.A., Lans, H., Vermeulen, W., and Hoeijmakers, J.H. (2014). Understanding nucleotide excision repair and its roles in cancer and ageing. Nat. Rev. Mol. Cell Biol. 15, 465-481. [PubMed]
Mitra, S. (2011). Does evening sun increase the risk of skin cancer? Proc. Natl. Acad. Sci. USA 108, 18857-18858. [PubMed]

Mismatch repair
Reference:
Buermeyer, A.B., Deschenes, S.M., Baker, S.M. and Liskay, R.M. (1999). Mammalian DNA mismatch repair. Annu. Rev. Genet. 33, 533-564. [PubMed]
Additional reference:
Dalhus, B., Laerdahl, J.K., Backe, P.H., and Bjørås, M. (2009). DNA base repair--recognition and initiation of catalysis. FEMS Microbiol. Revs. 33, 1044-1078. [PubMed]
Larrea, A.A., Lujan, S.A., and Kunkel, T.A. (2010). SnapShot: DNA mismatch repair. Cell 141, 730. [PubMed]
Lynch, H.T., Lynch, P.M., Lanspa, S.J., Snyder, C.L., Lynch, J.F., and Boland, C.R. (2009). Review of the Lynch syndrome: history, molecular genetics, screening, differential diagnosis, and medicolegal ramifications. Clin. Genet. 76, 1-18. [PubMed]

Other repair mechanisms
Figure: 5-8.
Reference:
Lindahl, T. and Wood, R.D. (1999). Quality control by DNA repair. Science 286, 1897-1905. [PubMed]
Additional reference:
Deans, A.J., and West, S.C. (2011). DNA interstrand crosslink repair and cancer. Nat. Rev. Cancer 11, 467-480. [PubMed]
Hartlerode, A.J., and Scully, R. (2009). Mechanisms of double-strand break repair in somatic mammalian cells. Biochem. J 423, 157-168. [PubMed]
Lieber, M.R., and Wilson, T.E. (2010). SnapShot: Nonhomologous DNA end joining (NHEJ). Cell 142, 496-496. [PubMed]
Mazón, G., Mimitou, E.P., and Symington, L.S. (2010). SnapShot: Homologous recombination in DNA double-strand break repair. Cell 142, 648. [PubMed]
Prakash, S., Johnson, R.E., and Prakash, L. (2005). Eukaryotic translesion synthesis DNA polymerases: specificity of structure and function. Annu. Rev. Biochem. 74, 317-353. [PubMed]
Storici, F., Bebenek, K., Kunkel, T.A., Gordenin, D.A., and Resnick, M.A. (2007). RNA-templated DNA repair. Nature 447, 338-341. [PubMed]
Venkitaraman, A.R. (2009). Linking the cellular functions of BRCA genes to cancer pathogenesis and treatment. Annu. Rev. Pathol. 4, 461-487. [PubMed]

Accuracy in gap filling
Reference:
Lindahl, T. and Wood, R.D. (1999). Quality control by DNA repair. Science 286, 1897-1905. [PubMed]
Additional reference:
Foti, J.J., and Walker, G.C. (2010). SnapShot: DNA polymerases II mammals. Cell 141, 370. [PubMed]
Berdis, A.J. (2009). Mechanisms of DNA polymerases. Chem. Rev. 109, 2862-2879. [PubMed]
Loeb, L.A., and Monnat R.J. (2008). DNA polymerases and human disease. Nat. Rev. Genet. 9, 594-604. [PubMed]

Box 5-3. Damage response systems in bacteria
Reference:
Walker, G.C. (1985). Inducible DNA repair systems. Annu. Rev. Biochem. 54, 425-457.
Kowalczykowski, S.C., Dixon, D.A., Eggleston, A.K., Lauder, S.D. and Rehrauer, W.M. (1994). Biochemistry of homologous recombination in Escherichia coli. Microbiol. Rev. 58, 401-465. [PubMed]
Additional reference:
Fry, R.C., Begley, T.J., and Samson, L.D. (2005). Genome-wide responses to DNA-damaging agents. Annu. Rev. Microbiol. 59, 357-77. [PubMed]
Goosen, N., and Moolenaar, G.F. (2008). Repair of UV damage in bacteria. DNA Repair (Amst) 7, 353-379. [PubMed]

Sites of repair
Figure: 5-9.
Reference:
Jackson, D.A., Balajee, A.S., Mullenders, L. and Cook, P.R. (1994). Sites in human nuclei where DNA damaged by ultra-violet light is repaired: visualization and localization relative to the nucleoskeleton. J. Cell Sci. 107, 1745-1752. [PubMed] [Full text]
Additional reference:
Misteli, T., and Soutoglou, E. (2009). The emerging role of nuclear architecture in DNA repair and genome maintenance. Nat. Rev. Mol. Cell Biol. 10, 243-254. [PubMed]

Transcription and repair
Figure: 5-10.
Reference:
van Gool, A.J., van der Horst, G.T., Citterio, E. and Hoeijmakers, J.H. (1997). Cockayne syndrome: defective repair of transcription? EMBO J. 16, 4155-4162. [PubMed] [Full text]
Additional reference:
Compe, E., and Egly, J.M. (2012). TFIIH: when transcription met DNA repair. Nat. Rev. Mol. Cell Biol. 13, 343-354. [PubMed]
Fong, Y.W., Cattoglio, C., and Tjian, R. (2013). The intertwined roles of transcription and repair proteins. Mol. Cell 52, 291-302. [PubMed]
Moses, R.E., and O'Malley, B.W. (2012). DNA transcription and repair: a confluence. J. Biol. Chem. 287, 23266-23270. [PubMed]

Some consequences of inefficient repair
Table: 5-1.
Reference:
Modrich, P. (1994). Mismatch repair, genetic stability, and cancer. Science 266, 1959-1960.
Naegeli, H. (1994). Roadblocks and detours during DNA replication: mechanisms of mutagenesis in mammalian cells. BioEssays 16, 557-564. [PubMed]
Wang, J.Y. (1998). Cellular responses to DNA damage. Curr. Opin. Cell Biology 10, 240-247. [PubMed]
Additional reference:
Caldecott, K.W. (2008). Single-strand break repair and genetic disease. Nat. Rev. Genet. 9, 619-631. [PubMed]
Cleaver, J.E., Lam, E.T., and Revet, I. (2009). Disorders of nucleotide excision repair: the genetic and molecular basis of heterogeneity. Nat. Rev. Genet. 10, 756-768. [PubMed]
Hoeijmakers, J.H. (2009). DNA damage, aging, and cancer. N. Engl. J. Med. 361, 1475-1485. [PubMed]
Zegerman, P., and Diffley, J.F. (2009). DNA replication as a target of the DNA damage checkpoint. DNA Repair (Amst) 8, 1077-1088. [PubMed]
Web link: 
http://www.nature.com/nrc/posters/dnadamage/dna_poster.pdf The DNA damage response in tumorigenesis
and cancer treatment.

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