A global profile of replicative polymerase usage

Nature Structural and Molecular Biology

Volumn 22, Issue 3, 2015, Pages 192-198

  Daigaku, Yasukazu ^a   Keszthelyi, Andrea ^a   Müller, Carolin A ^b   Miyabe, Izumi ^a   Brooks, Tony ^c   Retkute, Renata ^d   Hubank, Mike ^c   Nieduszynski, Conrad A ^b   Carr, Antony M ^a  

^a UNIVERSITY OF SUSSEX   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c UNIVERSITY COLLEGE LONDON   (United Kingdom)

^d UNIVERSITY OF NOTTINGHAM   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA POLYMERASE; DOUBLE STRANDED DNA; FUNGAL DNA; FUNGAL ENZYME; RIBONUCLEASE; RIBONUCLEOTIDE; SINGLE STRANDED DNA; DNA; DNA DIRECTED DNA POLYMERASE ALPHA; DNA DIRECTED DNA POLYMERASE BETA; DNA DIRECTED DNA POLYMERASE GAMMA;

ARTICLE; CELL SYNCHRONIZATION; DNA REPLICATION; DNA REPLICATION ORIGIN; DNA REPLICATION TIMING; DNA SEQUENCE; DNA SYNTHESIS; DNA TEMPLATE; EXCISION REPAIR; FLUORESCENCE ACTIVATED CELL SORTING; FUNGAL GENE; GENE FREQUENCY; GENE MAPPING; IN VITRO STUDY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REPLICON; SCHIZOSACCHAROMYCES POMBE; SEQUENCE ANALYSIS; SOUTHERN BLOTTING; BIOLOGICAL MODEL; CHEMISTRY; GENETICS; PHYSIOLOGY; SCHIZOSACCHAROMYCES;

EUKARYOTA; SCHIZOSACCHAROMYCES POMBE;

DNA; DNA POLYMERASE I; DNA POLYMERASE II; DNA POLYMERASE III; DNA REPLICATION; MODELS, GENETIC; REPLICATION ORIGIN; SCHIZOSACCHAROMYCES;

EID: 84924198688     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb.2962     Document Type: Article

References (42)

1. Bartkova, J., et al. DNA damage response as a candidate anti-cancer barrier in early human tumorigenesis. Nature 434, 864-870 (2005
2. Gorgoulis, V.G., et al. Activation of the DNA damage checkpoint and genomic instability in human precancerous lesions. Nature 434, 907-913 (2005
3. Rhind, N. & Gilbert, D.M. DNA replication timing. Cold Spring Harb. Perspect. Biol. 5, a010132 (2013
4. Stillman, B. Origin recognition and the chromosome cycle. FEBS Lett. 579, 877-884 (2005
5. Hawkins, M., et al. High-resolution replication profiles define the stochastic nature of genome replication initiation and termination. Cell Reports 5, 1132-1141 (2013
6. Ryba, T., et al. Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types. Genome Res. 20, 761-770 (2010
7. ODonnell, M., Langston, L. & Stillman, B. Principles and concepts of DNA replication in bacteria, archaea, and eukarya. Cold Spring Harb. Perspect. Biol. 5, a010108 (2013
8. Moyer, S.E., Lewis, P.W. & Botchan, M.R. Isolation of the Cdc45/Mcm2-7/GINS (CMG) complex, a candidate for the eukaryotic DNA replication fork helicase. Proc. Natl. Acad. Sci. USA 103, 10236-10241 (2006
9. Gambus, A., et al. A key role for Ctf4 in coupling the MCM2-7 helicase to DNA polymerase alpha within the eukaryotic replisome. EMBO J. 28, 2992-3004 (2009
10. Simon, A.C., et al. A Ctf4 trimer couples the CMG helicase to DNA polymerase α in the eukaryotic replisome. Nature 510, 293-297 (2014
11. Sengupta, S., van Deursen, F., de Piccoli, G. & Labib, K. Dpb2 integrates the leading-strand DNA polymerase into the eukaryotic replisome. Curr. Biol. 23, 543-552 (2013
12. Handa, T., Kanke, M., Takahashi, T.S., Nakagawa, T. & Masukata, H. DNA polymerization-independent functions of DNA polymerase epsilon in assembly and progression of the replisome in fission yeast. Mol. Biol. Cell 23, 3240-3253 (2012
13. Muramatsu, S., Hirai, K., Tak, Y.S., Kamimura, Y. & Araki, H. CDK-dependent complex formation between replication proteins Dpb11, Sld2, Pol Ε, and GINS in budding yeast. Genes Dev. 24, 602-612 (2010
14. Pursell, Z.F., Isoz, I., Lundstrom, E.B., Johansson, E. & Kunkel, T.A. Yeast DNA polymerase epsilon participates in leading-strand DNA replication. Science 317, 127-130 (2007
15. Nick McElhinny, S.A., Gordenin, D.A., Stith, C.M., Burgers, P.M. & Kunkel, T.A. Division of labor at the eukaryotic replication fork. Mol. Cell 30, 137-144 (2008
16. Miyabe, I., Kunkel, T.A. & Carr, A.M. The major roles of DNA polymerases epsilon and delta at the eukaryotic replication fork are evolutionarily conserved. PLoS Genet. 7, e1002407 (2011
17. Nick McElhinny, S.A., et al. Abundant ribonucleotide incorporation into DNA by yeast replicative polymerases. Proc. Natl. Acad. Sci. USA 107, 4949-4954 (2010
18. Sparks, J.L., et al. RNase H2-initiated ribonucleotide excision repair. Mol. Cell 47, 980-986 (2012
19. Kim, N., et alMutagenic processing of ribonucleotides in DNA by yeast topoisomerase I. Science 332, 1561-1564 (2011
20. Williams, J.S., et al. Topoisomerase 1-mediated removal of ribonucleotides from nascent leading-strand DNA. Mol. Cell 49, 1010-1015 (2013
21. Sekiguchi, J. & Shuman, S. Site-specific ribonuclease activity of eukaryotic DNA topoisomerase I. Mol. Cell 1, 89-97 (1997
22. Watt, D.L., Johansson, E., Burgers, P.M. & Kunkel, T.A. Replication of ribonucleotide-containing DNA templates by yeast replicative polymerases. DNA Repair (Amst.) 10, 897-902 (2011
23. Williams, J.S. & Kunkel, T.A. Ribonucleotides in DNA: origins, repair and consequences. DNA Repair (Amst.) 19, 27-37 (2014
24. Lujan, S.A., Williams, J.S., Clausen, A.R., Clark, A.B. & Kunkel, T.A. Ribonucleotides are signals for mismatch repair of leading-strand replication errors. Mol. Cell 50, 437-443 (2013
25. Xu, J., et al. Genome-wide identification and characterization of replication origins by deep sequencing. Genome Biol. 13, R27 (2012
26. Shiozaki, K., Shiozaki, M. & Russell, P. Heat stress activates fission yeast Spc1/StyI MAPK by a MEKK-independent mechanism. Mol. Biol. Cell 9, 1339-1349 (1998
27. Müller, C.A., et al. The dynamics of genome replication using deep sequencing. Nucleic Acids Res. 42, e3 (2014
28. Retkute, R., Nieduszynski, C.A. & de Moura, A. Mathematical modeling of genome replication. Phys. Rev. E 86, 031916 (2012
29. Clausen, A.R., et al. Tracking replication enzymology in vivo by genome-wide mapping of ribonucleotide incorporation. Nat. Struct. Mol. Biol. doi: 10.1038/nsmb.2957 (26 January 2015
30. Koh, K.D., Balachander, S., Hesselberth, J.R. & Storici, F. Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA. Nat. Methods doi: 10.1038/nmeth.3259 (26 January 2015
31. Reijns, M.A.M., et al. Lagging strand replication shapes the mutational landscape of the genome. Nature doi: 10.1038/nature14183 (26 January 2015
32. Siow, C.C., Nieduszynska, S.R., Muller, C.A. & Nieduszynski, C.A. OriDB, the DNA replication origin database updated and extended. Nucleic Acids Res. 40, D682-D686 (2012
33. Fachinetti, D., et al. Replication termination at eukaryotic chromosomes is mediated by Top2 and occurs at genomic loci containing pausing elements. Mol. Cell 39, 595-605 (2010
34. Lang, G.I. & Murray, A.W. Mutation rates across budding yeast chromosome VI are correlated with replication timing. Genome Biol. Evol. 3, 799-811 (2011
35. Ulrich, H.D. & Takahashi, T. Readers of PCNA modifications. Chromosoma 122, 259-274 (2013
36. Dua, R., Levy, D.L. & Campbell, J.L. Analysis of the essential functions of the C-Terminal protein/protein interaction domain of Saccharomyces cerevisiae pol epsilon and its unexpected ability to support growth in the absence of the DNA polymerase domain. J. Biol. Chem. 274, 22283-22288 (1999
37. Feng, W. & DUrso, G. Schizosaccharomyces pombe cells lacking the amino-Terminal catalytic domains of DNA polymerase epsilon are viable but require the DNA damage checkpoint control. Mol. Cell. Biol. 21, 4495-4504 (2001
38. Georgescu, R.E., et al. Mechanism of asymmetric polymerase assembly at the eukaryotic replication fork. Nat. Struct. Mol. Biol. 21, 664-670 (2014
39. Moreno, S., Klar, A. & Nurse, P. Molecular genetic analysis of fission yeast Schizosaccharomyces pombe. Methods Enzymol. 194, 795-823 (1991
40. Watson, A.T., Garcia, V., Bone, N., Carr, A.M. & Armstrong, J. Gene tagging and gene replacement using recombinase-mediated cassette exchange in Schizosaccharomyces pombe. Gene 407, 63-74 (2008
41. Lipkin, D., Talbert, P.T. & Cohn, M. The mechanism of the alkaline hydrolysis of ribonucleic acids. J. Am. Chem. Soc. 76, 2871-2872 (1954
42. Zhang, Z., Theurkauf, W.E., Weng, Z. & Zamore, P.D. Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection. Silence 3, 9 (2012